ChemWiki - User contributions [en]

Rep:Mod:hnt14Y3

2018-03-14T11:22:25Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Introduction ==

In this project, a series of pericyclic reactions were explored. Diels-Alder cycloaddition, chelotropic and electrocyclic reactions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) of a transition state or product are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO. Both inverse and normal demand Diels-Alder cycloaddition were under investigation.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical PM6 method and Density Functional Theory (DFT) B3LYP method. This allowed the MOs (molecular orbitals) of each to be visualised and their relative energy levels to be determined. The MOs are built by linearly combining basis sets. Hence, this is a quantum mechanical approach to generating MOs. The PM6 optimisation is faster and thus offers an initial optimisation which can be more accurately optimised using the more complex B3LYP where necessary.

A potential energy surface (PES) shows how the potential energy of a system changes along numerous reaction coordinates. Along a particular coordinate, the transition state is a maximum, where the gradient is zero. Transition states occur at maxima because they are high in energy and unstable. However, the transition state is also a minimum in all other directions, thus making it a saddle point. The reactants and products along a reaction coordinate will be minima, also with a zero gradient. As the first derivative is zero in both cases, a second derivative (the curvature) is determined to distinguish between maxima and minima. The second derivative will have a negative value for a maximum and a positive value for a minimum. Thus, when trying to locate a transition state in GaussView by running a frequency calculation, a single negative frequency value will be an indication that a transition state has been found.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, an MO diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to visualise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussian, molecules and transition states for a large range of reactions can be optimised. Furthermore, MOs and reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T11:21:40Z

Hnt14: /* Introduction */

== Introduction ==

In this project, a series of pericyclic reactions were explored. Diels-Alder cycloaddition, chelotropic and electrocyclic reactions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) of a transition state or product are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO. Both inverse and normal demand Diels-Alder cycloaddition were under investigation.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical PM6 method and Density Functional Theory (DFT) B3LYP method. This allowed the MOs (molecular orbitals) of each to be visualised and their relative energy levels to be determined. The MOs are built by linearly combining basis sets. Hence, this is a quantum mechanical approach to generating MOs. The PM6 optimisation is faster and thus offers an initial optimisation which can be more accurately optimised using the more complex B3LYP where necessary.

A potential energy surface (PES) shows how the potential energy of a system changes along numerous reaction coordinates. Along a particular coordinate, the transition state is a maximum, where the gradient is zero. Transition states occur at maxima because they are high in energy and unstable. However, the transition state is also a minimum in all other directions, thus making it a saddle point. The reactants and products along a reaction coordinate will be minima, also with a zero gradient. As the first derivative is zero in both cases, a second derivative (the curvature) is determined to distinguish between maxima and minima. The second derivative will have a negative value for a maximum and a positive value for a minimum. Thus, when trying to locate a transition state in GaussView by running a frequency calculation, a single negative frequency value will be an indication that a transition state has been found.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to visualise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussian, molecules and transition states for a large range of reactions can be optimised. Furthermore, MOs and reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T11:18:55Z

Hnt14: /* Conclusion */

== Introduction ==

In this project, a series of pericyclic reactions were explored. Diels-Alder cycloaddition, chelotropic and electrocyclic reactions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO and LUMO of a transition state or product are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO. Both inverse and normal demand Diels-Alder cycloaddition were under investigation.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical PM6 method and Density Functional Theory (DFT) B3LYP method. This allowed the MOs of each to be visualised and their relative energy levels to be determined. The MOs are built by linearly combining basis sets. Hence, this is a quantum mechanical approach to generating MOs. The PM6 optimisation is faster and thus offers an initial optimisation which can be more accurately optimised using the more complex B3LYP where necessary.

A potential energy surface (PES) shows how the potential energy of a system changes along numerous reaction coordinates. Along a particular coordinate, the transition state is a maximum, where the gradient is zero. Transition states occur at maxima because they are high in energy and unstable. However, the transition state is also a minimum in all other directions, thus making it a saddle point. The reactants and products along a reaction coordinate will be minima, also with a zero gradient. As the first derivative is zero in both cases, a second derivative (the curvature) is determined to distinguish between maxima and minima. The second derivative will have a negative value for a maximum and a positive value for a minimum. Thus, when trying to locate a transition state in GaussView by running a frequency calculation, a single negative frequency value will be an indication that a transition state has been found.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to visualise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussian, molecules and transition states for a large range of reactions can be optimised. Furthermore, MOs and reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T11:14:04Z

Hnt14: /* Conclusion */

== Introduction ==

In this project, a series of pericyclic reactions were explored. Diels-Alder cycloaddition, chelotropic and electrocyclic reactions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO and LUMO of a transition state or product are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO. Both inverse and normal demand Diels-Alder cycloaddition were under investigation.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical PM6 method and Density Functional Theory (DFT) B3LYP method. This allowed the MOs of each to be visualised and their relative energy levels to be determined. The MOs are built by linearly combining basis sets. Hence, this is a quantum mechanical approach to generating MOs. The PM6 optimisation is faster and thus offers an initial optimisation which can be more accurately optimised using the more complex B3LYP where necessary.

A potential energy surface (PES) shows how the potential energy of a system changes along numerous reaction coordinates. Along a particular coordinate, the transition state is a maximum, where the gradient is zero. Transition states occur at maxima because they are high in energy and unstable. However, the transition state is also a minimum in all other directions, thus making it a saddle point. The reactants and products along a reaction coordinate will be minima, also with a zero gradient. As the first derivative is zero in both cases, a second derivative (the curvature) is determined to distinguish between maxima and minima. The second derivative will have a negative value for a maximum and a positive value for a minimum. Thus, when trying to locate a transition state in GaussView by running a frequency calculation, a single negative frequency value will be an indication that a transition state has been found.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, MOs and reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T11:13:08Z

Hnt14: /* Conclusion */

== Introduction ==

In this project, a series of pericyclic reactions were explored. Diels-Alder cycloaddition, chelotropic and electrocyclic reactions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO and LUMO of a transition state or product are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO. Both inverse and normal demand Diels-Alder cycloaddition were under investigation.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical PM6 method and Density Functional Theory (DFT) B3LYP method. This allowed the MOs of each to be visualised and their relative energy levels to be determined. The MOs are built by linearly combining basis sets. Hence, this is a quantum mechanical approach to generating MOs. The PM6 optimisation is faster and thus offers an initial optimisation which can be more accurately optimised using the more complex B3LYP where necessary.

A potential energy surface (PES) shows how the potential energy of a system changes along numerous reaction coordinates. Along a particular coordinate, the transition state is a maximum, where the gradient is zero. Transition states occur at maxima because they are high in energy and unstable. However, the transition state is also a minimum in all other directions, thus making it a saddle point. The reactants and products along a reaction coordinate will be minima, also with a zero gradient. As the first derivative is zero in both cases, a second derivative (the curvature) is determined to distinguish between maxima and minima. The second derivative will have a negative value for a maximum and a positive value for a minimum. Thus, when trying to locate a transition state in GaussView by running a frequency calculation, a single negative frequency value will be an indication that a transition state has been found.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T11:11:01Z

Hnt14: /* Introduction */

== Introduction ==

In this project, a series of pericyclic reactions were explored. Diels-Alder cycloaddition, chelotropic and electrocyclic reactions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO and LUMO of a transition state or product are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO. Both inverse and normal demand Diels-Alder cycloaddition were under investigation.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical PM6 method and Density Functional Theory (DFT) B3LYP method. This allowed the MOs of each to be visualised and their relative energy levels to be determined. The MOs are built by linearly combining basis sets. Hence, this is a quantum mechanical approach to generating MOs. The PM6 optimisation is faster and thus offers an initial optimisation which can be more accurately optimised using the more complex B3LYP where necessary.

A potential energy surface (PES) shows how the potential energy of a system changes along numerous reaction coordinates. Along a particular coordinate, the transition state is a maximum, where the gradient is zero. Transition states occur at maxima because they are high in energy and unstable. However, the transition state is also a minimum in all other directions, thus making it a saddle point. The reactants and products along a reaction coordinate will be minima, also with a zero gradient. As the first derivative is zero in both cases, a second derivative (the curvature) is determined to distinguish between maxima and minima. The second derivative will have a negative value for a maximum and a positive value for a minimum. Thus, when trying to locate a transition state in GaussView by running a frequency calculation, a single negative frequency value will be an indication that a transition state has been found.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T11:10:06Z

Hnt14: /* Introduction */

== Introduction ==

In this project, a series of pericyclic reactions were explored. Diels-Alder cycloaddition, chelotropic and electrocyclic reactions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO and LUMO of a transition state or product are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO. Both inverse and normal demand Diels-Alder cycloaddition were under investigation.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical PM6 method and Density Functional Theory (DFT) B3LYP method. This allowed the MOs of each to be visualised and their relative energy levels to be determined. The MOs are built by linearly combining basis sets. Hence, this is a quantum mechanical approach to generating MOs. The PM6 optimisation is faster and thus offers an initial optimisation which can be more accurately optimised using the more complex B3LYP where necessary.

A potential energy surface (PES) shows how the potential energy of a system changes along numerous reaction coordinates. Along a particular coordinate, the transition state is a maximum, where the gradient is zero. Transition states occur at maxima because they are high in energy and unstable. However, the transition state is also a minimum in all other directions, thus making it a saddle point. The reactants and products along a reaction coordinate will be minima, also with a zero gradient. As the first derivative is zero in both cases, a second derivative (the curvature) is determined to distinguish between maxima and minima. The second derivative will have a negative value for a maximum and a positive value for a minimum. Thus, when trying to locate a transition state in GaussView by running a frequency calculation, a negative frequency value will be an indication that a transition state has been found.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T11:07:24Z

Hnt14: /* Introduction */

== Introduction ==

In this project, a series of pericyclic reactions were explored. Diels-Alder cycloaddition, chelotropic and electrocyclic reactions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO and LUMO are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical PM6 method and Density Functional Theory (DFT) B3LYP method. This allowed the MOs of each to be visualised and their relative energy levels to be determined. The MOs are built by linearly combining basis sets. Hence, this is a quantum mechanical approach to generating MOs. The PM6 optimisation is faster and thus offers an initial optimisation which can be more accurately optimised using the more complex B3LYP where necessary.

A potential energy surface (PES) shows how the potential energy of a system changes along numerous reaction coordinates. Along a particular coordinate, the transition state is a maximum, where the gradient is zero. Transition states occur at maxima because they are high in energy and unstable. However, the transition state is also a minimum in all other directions, thus making it a saddle point. The reactants and products along a reaction coordinate will be minima, also with a zero gradient. As the first derivative is zero in both cases, a second derivative (the curvature) is determined to distinguish between maxima and minima. The second derivative will have a negative value for a maximum and a positive value for a minimum. Thus, when trying to locate a transition state in GaussView by running a frequency calculation, a negative frequency value will be an indication that a transition state has been found.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T10:31:25Z

Hnt14: /* Introduction */

== Introduction ==

In this project, a series of pericyclic reactions was explored. The outcome of a reaction is affected by which reactant orbitals interact to form the HOMO and LUMO of the transition state or product. Diels-Alder cycloaddition, chelotropic and electrocyclic reactions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO and LUMO are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical PM6 method and Density Functional Theory (DFT) B3LYP method. This allowed the MOs of each to be visualised and their relative energy levels to be determined. The MOs are built by linearly combining basis sets. Hence, this is a quantum mechanical approach to generating MOs. The PM6 optimisation is faster and thus offers an initial optimisation which can be more accurately optimised using B3LYP where necessary.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T09:59:14Z

Hnt14: /* Introduction */

== Introduction ==

In this project, a series of pericyclic reactions was explored. The outcome of a reaction is affected by what reactant orbitals interact to form the HOMO and LUMO of the transition state or product. Diels-Alder cycloaddition, chelotropic and electrocyclic additions were all studied. A Diels-Alder cycloaddition between a diene and a dienophile can be normal or inverse demand. A normal demand reaction occurs when the HOMO and LUMO are formed from the diene HOMO and the dienophile LUMO. Inverse demand occurs as a result of interaction between the diene LUMO and dienophile HOMO.

The reactants, products and transition states were built in GaussView and optimised using the semi-empirical method PM6 and Density Functional Theory (DFT) B3LYP. This allowed the MOs of each to be visualised and the relative energy levels in a reaction to be determined.

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T08:59:49Z

Hnt14: /* Question 3ː Diels-Alder vs Chelotropic */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring prefers to be aromatic to lower the molecule's energy. Formation of the products would result in the formation of a benzenoid ring. This 'aromatisation' makes these reactions favourable and results in overall stabilisation. This can be observed in the IRCs, where the bond lengths in the six-membered ring become equal throughout the reaction, indicating the ring is aromatic.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T08:50:19Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T08:48:07Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction betweenC<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for carbon-carbon single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T08:42:42Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that there is an interaction betweenC<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> in the transition state. In the product, bonds are formed at these sites that have a length of 1.54 Å, as expected for single bonds.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-14T08:34:16Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 3.4 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T23:31:34Z

Hnt14: /* Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T23:26:16Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T23:24:43Z

Hnt14: /* Conclusion */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of cyclical reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, molecules and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted which can then be used for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T23:20:02Z

Hnt14: /* Question 3ː Diels-Alder vs Chelotropic */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|400px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|400px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|400px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|400px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bond compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|400px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T23:00:34Z

Hnt14: /* Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|400px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|400px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T22:53:45Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|400px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|400px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T22:49:51Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Introduction ==

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path that occurs at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T22:39:43Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition between ethylene and butadiene. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the Carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T22:27:17Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

Figure 1 shows the reaction scheme for the cycloaddition between butadiene and ethylene. In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition between ethylene and butadiene. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>

<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the Carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T22:19:44Z

Hnt14: /* Question 3ː Diels-Alder vs Chelotropic */

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition between ethylene and butadiene. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>

<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the Carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T21:17:48Z

Hnt14: /* Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole */

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition between ethylene and butadiene. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>

<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the Carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|center|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|center|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|center|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T21:15:13Z

Hnt14: /* Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole */

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition between ethylene and butadiene. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>

<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the Carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

{| class="wikitable" border="1"
|+ Table 4-Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Exo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Exo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> ||<jmol>
<jmolApplet>
<title>Exo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 EXOTSB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Endo TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Endo TS LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>Endo TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 44; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 ENDOTSB3LYPH.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 22; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Cyclohexadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 18; mo 23; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 CYCLOHEXADIENEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|| <jmol>
<jmolApplet>
<title>1,3-Dioxole LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 12; mo 20; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 OPTMINDIOXOLEB3LYP.LOG </uploadedFileContents>
</jmolApplet>
</jmol>
|}

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|center|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|center|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|center|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T21:14:02Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition between ethylene and butadiene. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 1- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>TS HOMO -1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO</title>

<color>white</color>
<size>160</size>
<script>frame 20; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS LUMO +1</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| <jmol>
<jmolApplet>
<title>Ethylene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Ethylene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_OPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>Butadiene LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 36; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14_BUTADIENEOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the Carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|center|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|center|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|center|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T21:13:19Z

Hnt14: /* Future Work */

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition between ethylene and butadiene. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the Carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|center|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|center|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|center|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The bond formation is suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T21:12:26Z

Hnt14: /* Future Work */

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition between ethylene and butadiene. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the Carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|center|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|center|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|center|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The orbital interactions are suprafacial, as seen in Figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T21:11:44Z

Hnt14: /* Future Work */

== Question 1ː Reaction of Butadiene with Ethylene ==

[[File:SchemeImage.PNG|500px|thumb|right|none|Figure 1-Reaction Scheme for [4+2] cycloaddition between butadiene and ethylene]]
[[File:MODiagramImageUPDATED.PNG|500px|thumb|right|none|Figure 2-MO diagram for the transition state of the [4+2] cycloaddition between butadiene and ethylene]]

In Figure 2, a molecular orbital (MO) diagram is constructed based on the interacting orbitals in the transition state of the Diels-Alder cycloaddition between ethylene and butadiene. These were determined by observing the relevant orbitals of the transition state formed from the HOMO and LUMO of each of the reactants in GaussView. The orbitals drawn in the MO diagram in Figure 2 correlate with those extracted from GaussView, which are shown in Table 1. It can be concluded from the resulting MOs in the transition state that only orbitals of the same symmetry are allowed to interact. Thus, there is a symmetry requirement for two interacting orbitals. In the case of orbitals with different symmetry, the interaction is forbidden and the orbital overlap integral will be zero. For orbitals of the same symmetry, the interaction is allowed and the overlap integral is non-zero. The results are summarised in Table 2.

{| class="wikitable" border="1"
|+ Table 2-Allowed and Forbidden Interactions
! !! Allowed !! Forbidden !! Orbital Overlap Integral
|-
| Symmetric-Symmetric || X || || Non-zero
|-
| Asymmetric-Asymmetric || X || || Non-zero
|-
| Symmetric-Asymmetric || || X || Zero
|}

In the reaction, the distances between atoms vary depending on whether a bond is being made or broken. Where a bond is being broken, its length will increase in the transition state until the bond eventually breaks. In the case of a bond being made, the distance between the atoms decreases as the bond forms. Where a bond is going from a single bond to a double bond, the bond length shortens and vice versa. The typical bond length for a single sp<sup>3</sup>-sp<sup>3</sup> C-C bond is 1.54 Å <ref name="Bond lengths"/> and 1.34 Å <ref name="Bond lengths"/> for a double sp<sup>3</sup>-sp<sup>2</sup> bond. In the transition state, the two bonds being formed are between C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub>. Both have a length of 2.11 Å between the carbon atoms in the transition state. This is considerably less than twice the Van der Waals radius of the Carbon atom which is 1.7 Å. Hence, it can be concluded that a bond is being formed between each pair of carbon atoms in the transition state.
The overall change in bond lengths can be seen in Table 3.

{| class="wikitable" border="1"
|+ Table 3-Bond lengths (Å) in reactants, transition states and products
! !! Butadiene !! Ethylene !! Transition State !! Product !! Change in bond
|-
| C<sub>1</sub>-C<sub>2</sub> || 1.3335 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>2</sub>-C<sub>3</sub> || 1.4708 || - || 1.4111 || 1.3331 || Shorter
|-
| C<sub>3</sub>-C<sub>4</sub> || 1.3334 || - || 1.3798 || 1.4926 || Longer
|-
| C<sub>4</sub>-C<sub>5</sub> || - || - || 2.1146 || 1.5358 || -
|-
| C<sub>5</sub>-C<sub>6</sub> || - || 1.3273 || 1.3818 || 1.5376 || Longer
|-
| C<sub>1</sub>-C<sub>6</sub> || - || - || 2.1149 || 1.5358 || -
|}

The vibration shown below corresponds to the vibration along the reaction path at the transition state of the reaction. As the two new bonds at C<sub>4</sub>-C<sub>5</sub> and C<sub>1</sub>-C<sub>6</sub> form at the same time, the reaction is concerted and the formation of the two bonds is synchronous.

<jmol>
<jmolApplet>
<title> Figure 3-Vibration Mode at the Transition State</title>
<color>white</color>
<size>300</size>
<script>frame 21; vibration 1;rotate x -20; </script>
<uploadedFileContents>HNT14_TSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

Files for the optimised reactants at PM6 levelː [[Media:HNT14_OPTMINPM6.LOG|Ethylene Optimisation]], [[Media:HNT14_BUTADIENEOPTMINPM6.LOG|Butadiene Optimisation]]

Files for the optimised transition state and the IRC at PM6 level: [[Media:HNT14_TSPM6.LOG|TS Optimisation]],[[Media:HNT14 IRC.LOG|IRC]]

File for the optimised product at PM6 levelː [[Media:HNT14 PRODUCTOPTPM6.LOG|Product Optimisation]]

== Question 2ː Reaction of Cyclohexadiene and 1,3-Dioxole ==

[[File:ReactionSchemeImage2.PNG|500px|thumb|right|none|Figure 4-Reaction Scheme for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole]]

[[File:MODIAGRAMENDOEXO.PNG|500px|thumb|right|none|Figure 5-Exo and Endo MO Diagrams for [4+2] cycloaddition between cyclohexadiene and 1,3-dioxole Transition States]]

The MO's of both the exo and endo transition states can be seen in Figure 5. The relative energy levels were determined using the B3LYP optimisations of the reactants and transition states in GaussView. It was observed again from the MOs that only orbitals of the same symmetry interact. The orbitals in Table 4 correlate with the energy levels and MOs in figure 5.

This reaction is an inverse demand Diels-Alder reaction because the HOMOs and LUMOs of both the exo and endo transition states occur as a result of the interaction between the diene (cyclohexadiene) LUMO and the dienophile (1,3-dioxole) HOMO.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 166.30 || -65.15
|-
| Endo || 158.51 || -68.75
|}

The endo adduct has a lower reaction barrier (due to the endo ts being of lower energy) than the exo adduct, indicating the endo product will be the kinetically favourable product (faster formation). Furthermore, the endo adduct also has a lower reaction energy than the exo adduct, meaning the endo product is also the thermodynamically favourable product. The energies can be seen in Table 5.

The lower energy of the endo ts is due to the secondary orbital interactions arising from orbital overlap between the O p orbital and the diene pi system. TS Stabilisation is hence a result of conjugation. This can only be achieved in the endo conformation, where the orbitals are in the correct orientation for overlap, as opposed to the orbitals in the exo adduct. This is in accordance with the endo rule.

The energies in Table 5 were calculated using the free energies of the reactants, products and transition states of the endo and exo adducts, which can be found in the log files below extracted from GaussView.

Files for the optimised reactants at B3LYP levelː [[Media:HNT14 CYCLOHEXADIENEB3LYP.LOG |Cyclohexadiene Optimisation]], [[Media:HNT14 OPTMINDIOXOLEB3LYP.LOG |1,3-Dioxole Optimisation]]

Files for the optimised transition states at B3LYP levelː[[Media:HNT14 EXOTSB3LYP.LOG |Exo TS Optimisation]], [[Media:HNT14 ENDOTSB3LYPH.LOG |Endo TS Optimisation]]

Files for the IRCs of the optimised transition states at PM6 levelː [[Media:HNT14 IRCEXOTSPM6I.LOG |Exo IRC]], [[Media:HNT14 IRCENDOTSPM6I.LOG |Endo IRC]]

Files for the optimised products at B3LYP levelː [[Media:HNT14 PRODUCTEXOB3LYPXXY.LOG |Exo Product Optimisation]], [[Media:HNT14 PRODUCTENDOB3LYPXX.LOG |Endo Product Optimisation]]

== Question 3ː Diels-Alder vs Chelotropic ==

[[File:Q3imagereactionscheme4.PNG|500px|thumb|right|none|Figure 6-Reaction Scheme for Diels-Alder and chelotropic pathways for the reaction between Xylylene and SO<sub>2</sub>]]

The reaction scheme in Figure 6 shows both the Diels-Alder and chelotropic reaction pathways at one of the dienes in o-xylylene. The Diels-Alder reaction can result in both an endo and exo product.

[[File:Hnt14 ALTexoGIFXXX.gif|500px|thumb|center|none|Figure 7-Exo adduct IRC]]

[[File:Hnt14 altendoXXYGIF.gif|500px|thumb|center|none|Figure 8-Endo adduct IRC]]

[[File:Hnt14 chelotropicGIFXXX.gif|500px|thumb|center|none|Figure 9-Chelotropic adduct IRC]]

The IRCs of the exo, endo and chelotropic reactions can be seen in Figures 7, 8 and 9 respectively. These allow the reaction coordinates to be visualised. Xylylene is highly unstable because the ring is not aromatic and thus high in energy. Formation of the products would result in the formation of a benzene ring. This 'aromatisation' makes these reactions favourable and results in overal stabilisation.

{| class="wikitable" border="1"
|+ Table 5- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 87.19 || -98.23
|-
| Endo || 83.22 || -97.58
|-
| Chelotropic || 105.53 || -154.56
|}

In Table 5, the reaction barriers and energies are calculated for each of endo, exo and chelotropic adducts as before. As can be seen, the exo adduct has a lower reaction energy, making the exo product the more thermodynamically favourable product (compared to the endo product). This is because steric strain is minimised in the exo conformation. On the other hand,the endo adduct affords the lowest reaction barrier due to secondary orbital interactions, making the endo product the fastest forming (kinetically favourable) product. However, the exo and endo energies are only marginally different. In contrast, The chelotropic adduct has a much higher reaction barrier, meaning its formation is considerably slower than both the exo and endo products. The exo and endo adducts form stable six-membered ring transition states (resulting in faster formation), whereas the chelotropic transition state contains a 5-membered ring, making it sterically unfavourable due to ring strain. However, the chelotropic adduct also has the lowest reaction energy by far, making it the most thermodynamically favourable product. The driving force is the formation of the double S=O bonds compared with the much weaker single S-O bonds. This results in increased stabilisation and thus lower energy (thermodynamically stable) products. The relative reaction profiles for each of the two Diels-Alder reactions and the chelotropic reaction can be seen in figure 10.

[[File:ReactionprofileEX3.PNG|500px|thumb|right|none|Figure 10-Reaction profiles for endo, exo and chelotropic reactions]]

Files for the optimsed reactions at PM6 levelː [[Media:HNT14 XYLYLENEOPTMINPM6.LOG |Xylylene optimisation]], [[Media:HNT14 SO2OPTMINPM6.LOG |SO<sub>2</sub> optimisation]]

File for the optimised transition states at PM6 levelː [[Media:HNT14 EXODIELSALDERT1EXOTS2PM6.LOG |Exo TS optimisation]], [[Media:HNT14 DIELSALDERENDOTSPM6FINALPM6.LOG |Endo TS optimisation]], [[Media:HNT14 chelotropicTSPM6.LOG |Chelotropic TS optimisation]]

Files for IRCs at PM6 levelː [[Media:HNT14 IRCEXODIELSALDERPM6.LOG |Exo TS IRC]], [[Media:HNT14 IRCDIELSALDERENDOPM6.LOG |Endo TS IRC]], [[Media:HNT14 IRCCHELOTROPICPM6.LOG |Chelotropic TS IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 EXODIELSALDERPRODUCTPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTENDODIELSALDEROPTMINPM6.LOG |Exo product optimisation]], [[Media:HNT14 PRODUCTCHELOTROPICOPTMINPM6.LOG |Chelotropic product optimisation]]

=== Reaction at Cyclic Diene ===

Both the Diels-Alder and chelotropic reactions can occur at the cyclic diene as well. This will also result in exo, endo and chelotropic products. The reaction barriers and energies are reported in Table 6.

{| class="wikitable" border="1"
|+ Table 6- Reaction Barriers and Energies
! Adduct !! Reaction Barrier (kJ/mol) !! Reaction Energy (kJ/mol)
|-
| Exo || 121.27 || 22.15
|-
| Endo || 113.42 || 17.70
|-
| Chelotropic || 142.14 || 48.74
|}

As can be observed, the reaction barriers for all three adducts are very high, meaning reaction at the cyclic diene is kinetically unfavourable. Furthermore, the reaction energies of all three adducts are very high, probably due to the non-aromatic product formation. Hence reaction at this diene is also thermodynamically unfavourable.

Files for the optimised transition states at PM6 levelː[[Media:HNT14 ALTEXOTSPM6.LOG |Alternative exo TS optimisation]], [[Media:HNT14 ALTENDOTSPM6.LOG |Alternative endo TS optimisation]],
[[Media:HNT14 ALTTYPE2TSPM6.LOG |Alternative chelotropic TS optimisation]]

Files for the IRCs at PM6 levelː [[Media:HNT14 IRCALTEXOTSPM6HNZT.LOG |Alternative exo IRC]], [[Media:HNT14 IRCALTENDOTSPM6.LOG |Alternative endo IRC]], [[Media:HNT14 IRCALTTYPE2TSPM6.LOG |Alternative chelotropic IRC]]

Files for the optimised products at PM6 levelː [[Media:HNT14 PRODUCTALTEXOOPTMINPM6.LOG |Alternative exo product optimisation]], [[Media:HNT14 ALTENDOPRODUCTOPTMINPM6.LOG |Alternative endo product optimisation]], [[Media:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG |Alternative chelotropic product optimisation]]

== Future Work ==

[[File:Futureworkscheme.PNG|500px|thumb|right|none|Figure 11-Reaction Scheme for electrocylic reaction]]

[[File:Disrotationhnt14.PNG|500px|thumb|right|none|Figure 12-Electrocyclic reaction by disrotation]]

The scheme shown in Figure 11 represents an electrocyclic reaction occuring by disrotation. The orbital interactions are suprafacial, as seen in figure 12.
The LUMO of the reactant and the HOMO of the transition state that are visualised with Gaussview are consistent with those in figure 12, confirming that the reaction proceeds by disrotation. The visualised MOs are observed in Table 7.

{| class="wikitable" border="1"
|+ Table 7- Interacting Orbitals
|-
| <jmol>
<jmolApplet>
<title>Reactant LUMO</title>
<color>white</color>
<size>160</size>
<script>frame 20; mo 34; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTUREREACTANTOPTMINPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol> || <jmol>
<jmolApplet>
<title>TS HOMO</title>
<color>white</color>
<size>160</size>
<script>frame 94; mo 33; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>HNT14 FUTURETSPM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

File for optimised reactant at PM6 levelː [[Media:HNT14 FUTUREREACTANTOPTMINPM6.LOG |Reactant optimisation]]

File for optimised TS at PM6 levelː [[Media:HNT14 FUTURETSPM6.LOG |TS optimisation]]

File for IRC at PM6 levelː [[Media:HNT14 IRCFUTURETSPM6.LOG |IRC]]

File for optimised product at PM6 levelː [[Media:HNT14 FUTUREPRODUCTOPTMINPM6.LOG |Product optimisation]]

== Conclusion ==

Gaussview was used to optimise a series of pericyclic reactionsː Diels-Alder, chelotropic and electrocyclic reactions. With Gaussview, products, reactants and transition states for a large range of reactions can be optimised. Furthermore, reaction coordinates can be visualised and free energies extracted for finding reaction barriers and energies. In this project, this data was extracted for well known reactions. However, the same software and methods can be used for reactions of which the outcome is less well known. This means computational methods can be used to predict the outcome and likelihood of a reaction, giving quantitative results on how a reaction may proceed. Hence, invaluable information can be extracted using these techniques, highlighting the importance of computational chemistry.

== References ==

<references>
<ref name="Bond lengths">Zavitsas, A. (2003). The Relation between Bond Lengths and Dissociation Energies of Carbon−Carbon Bonds. The Journal of Physical Chemistry A, 107(6), pp.897-898. </ref>

Rep:Mod:hnt14Y3

2018-03-13T20:33:27Z

Hnt14: /* Future Work */

Rep:Mod:hnt14Y3

2018-03-13T20:23:38Z

Hnt14: /* Future Work */

File:HNT14 FUTUREREACTANTOPTMINPM6.LOG

2018-03-13T20:23:14Z

Hnt14:

File:HNT14 IRCFUTURETSPM6.LOG

2018-03-13T20:22:48Z

Hnt14:

File:HNT14 FUTURETSPM6.LOG

2018-03-13T20:22:15Z

Hnt14:

File:HNT14 FUTUREPRODUCTOPTMINPM6.LOG

2018-03-13T20:19:26Z

Hnt14:

Rep:Mod:hnt14Y3

2018-03-13T20:18:24Z

Hnt14: /* Future Work */

File:Disrotationhnt14.PNG

2018-03-13T20:16:59Z

Hnt14:

Rep:Mod:hnt14Y3

2018-03-13T20:13:51Z

Hnt14: /* Future Work */

Rep:Mod:hnt14Y3

2018-03-13T20:13:33Z

Hnt14: /* Future Work */

Rep:Mod:hnt14Y3

2018-03-13T20:12:48Z

Hnt14: /* Question 3ː Diels-Alder vs Chelotropic */

File:Futureworkscheme.PNG

2018-03-13T20:12:29Z

Hnt14:

Rep:Mod:hnt14Y3

2018-03-13T20:01:13Z

Hnt14: /* Question 3ː Diels-Alder vs Chelotropic */

Rep:Mod:hnt14Y3

2018-03-13T20:00:29Z

Hnt14: /* Question 1ː Reaction of Butadiene with Ethylene */

Rep:Mod:hnt14Y3

2018-03-13T19:58:30Z

Hnt14: /* Question 3ː Diels-Alder vs Chelotropic */

Rep:Mod:hnt14Y3

2018-03-13T19:52:44Z

Hnt14: /* Reaction at Cyclic Diene */

Rep:Mod:hnt14Y3

2018-03-13T19:52:16Z

Hnt14: /* Reaction at Cyclic Diene */

Rep:Mod:hnt14Y3

2018-03-13T19:52:05Z

Hnt14: /* Reaction at Cyclic Diene */

File:HNT14 PRODUCTALTTYPE2OPTMINPM6.LOG

2018-03-13T19:50:43Z

Hnt14: