ChemWiki - User contributions [en]

Rep:Mod:YTL14

2017-03-10T11:54:16Z

Ytl14: /* Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO2 */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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|}

{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure 2: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre|Figure 3: Symmetry requirements]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure 4:Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure 4''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to literature (1.36 Å and 1.54 Å respectively). The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å. <ref name="Bond length" />

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script> frame 18; mo 14; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|200px]]
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
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| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure 5: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene.(HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

[[File:Ytl14 exercise2 MO.PNG|center|thumb|Figure 6: Inverse electron demand of Diels Alder|300px]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

[[File:Ytl14 exercise2 secondaryinteraction.tif|center|Figure 7: Secondary interaction between carbon and oxygen]]
Oxygen is marked red.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px|Figure 7: Energy profile of cheletropic and Diels Alder reactions]]

From '''Table 8''' and '''Figure 7''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|center|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
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<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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<script>frame 16</script>
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| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi-orbital above and below the plane. Xylylene is unstable compared to the product. Aromaticity is the driving force of the reaction.

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uniheidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
<ref name="Bond length">S. S. Batsanov, Inorg. Mater. Transl. from Neorg. Mater. Orig. Russ. Text, 2001, 37, 871–885.</ref>
</references>

Rep:Mod:YTL14

2017-03-10T11:52:10Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
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<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
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<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure 2: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre|Figure 3: Symmetry requirements]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure 4:Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure 4''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to literature (1.36 Å and 1.54 Å respectively). The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å. <ref name="Bond length" />

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<size>200</size>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<title>Symmetric</title>
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<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
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<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|200px]]
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure 5: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene.(HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

[[File:Ytl14 exercise2 MO.PNG|center|thumb|Figure 6: Inverse electron demand of Diels Alder|300px]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

[[File:Ytl14 exercise2 secondaryinteraction.tif|center|Figure 7: Secondary interaction between carbon and oxygen]]
Oxygen is marked red.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px|Figure 6: Energy profile of cheletropic and Diels Alder reactions]]

From '''Table 8''' and '''Figure 6''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|center|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uniheidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
<ref name="Bond length">S. S. Batsanov, Inorg. Mater. Transl. from Neorg. Mater. Orig. Russ. Text, 2001, 37, 871–885.</ref>
</references>

Rep:Mod:YTL14

2017-03-10T11:50:42Z

Ytl14: /* Exercise 1: Reaction of Butadiene with Ethylene */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Symmetric, 2 nodes</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
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<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
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<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure 2: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre|Figure 3: Symmetry requirements]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure 4:Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure 4''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to literature (1.36 Å and 1.54 Å respectively). The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å. <ref name="Bond length" />

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
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<script>frame 6</script>
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| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|200px]]
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|-
| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure 3: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene.(HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

[[File:Ytl14 exercise2 MO.PNG|center|thumb|300px|Figure 4: Inverse electron demand of Diels Alder]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

[[File:Ytl14 exercise2 secondaryinteraction.tif|center|Figure 5: Secondary interaction between carbon and oxygen]]
Oxygen is marked red.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px|Figure 6: Energy profile of cheletropic and Diels Alder reactions]]

From '''Table 8''' and '''Figure 6''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|center|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
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<script>frame 16</script>
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</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uniheidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
<ref name="Bond length">S. S. Batsanov, Inorg. Mater. Transl. from Neorg. Mater. Orig. Russ. Text, 2001, 37, 871–885.</ref>
</references>

Rep:Mod:YTL14

2017-03-10T11:47:00Z

Ytl14:

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<script>Symmetric, no node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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|}

{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure 2: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure 2:Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure 2''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to literature (1.36 Å and 1.54 Å respectively). The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å. <ref name="Bond length" />

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure 3: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene.(HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

[[File:Ytl14 exercise2 MO.PNG|center|thumb|300px|Figure 4: Inverse electron demand of Diels Alder]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

[[File:Ytl14 exercise2 secondaryinteraction.tif|center|Figure 5: Secondary interaction between carbon and oxygen]]
Oxygen is marked red.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px|Figure 6: Energy profile of cheletropic and Diels Alder reactions]]

From '''Table 8''' and '''Figure 6''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
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| '''Diels Alder (Exo)'''
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| '''Cheletropic'''
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| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uniheidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
<ref name="Bond length">S. S. Batsanov, Inorg. Mater. Transl. from Neorg. Mater. Orig. Russ. Text, 2001, 37, 871–885.</ref>
</references>

Rep:Mod:YTL14

2017-03-10T11:43:51Z

Ytl14: /* Reference */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
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| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure 2: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure 2:Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure 2''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to literature (1.36 Å and 1.54 Å respectively). The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å. <ref name="Bond length" />

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|200px]]
| <jmol><jmolApplet>
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<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
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<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
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<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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|}

[[File:Ytl14 exercise2 energy profile.PNG|center|Figure 3: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene.(HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

[[File:Ytl14 exercise2 MO.PNG|center|thumb|300px|Figure 4: Inverse electron demand of Diels Alder]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

[[File:Ytl14 exercise2 secondaryinteraction.tif|center|Figure 5: Secondary interaction between carbon and oxygen]]
Oxygen is marked red.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px]]

From '''Table 8''' and '''Figure 5''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|center|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
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<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uniheidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
<ref name="Bond length">S. S. Batsanov, Inorg. Mater. Transl. from Neorg. Mater. Orig. Russ. Text, 2001, 37, 871–885.</ref>
</references>

Rep:Mod:YTL14

2017-03-10T11:43:20Z

Ytl14:

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
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<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
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| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure 2: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure 2:Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure 2''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to literature (1.36 Å and 1.54 Å respectively). The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å. <ref name="Bond length" />

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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|-
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
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<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|200px]]
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<script>frame 6</script>
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|-
| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure 3: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene.(HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

[[File:Ytl14 exercise2 MO.PNG|center|thumb|300px|Figure 4: Inverse electron demand of Diels Alder]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

[[File:Ytl14 exercise2 secondaryinteraction.tif|center|Figure 5: Secondary interaction between carbon and oxygen]]
Oxygen is marked red.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px]]

From '''Table 8''' and '''Figure 5''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|center|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
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| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uniheidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
<ref name="introduction">S. S. Batsanov, Inorg. Mater. Transl. from Neorg. Mater. Orig. Russ. Text, 2001, 37, 871–885.</ref>
</references>

Rep:Mod:YTL14

2017-03-10T11:39:28Z

Ytl14:

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
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| <jmol><jmolApplet>
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<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure 2: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure 2:Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure 2''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
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<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<title>Symmetric</title>
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<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|200px]]
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<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure 3: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene.(HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

[[File:Ytl14 exercise2 MO.PNG|center|thumb|300px|Figure 4: Inverse electron demand of Diels Alder]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

[[File:Ytl14 exercise2 secondaryinteraction.tif|center|Figure 5: Secondary interaction between carbon and oxygen]]
Oxygen is marked red.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px]]

From '''Table 8''' and '''Figure 5''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|center|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T11:38:27Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Symmetric, 2 nodes</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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<title>1,3-Dioxole</title>
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<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
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<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|200px]]
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene.(HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

[[File:Ytl14 exercise2 MO.PNG|center|thumb|300px|Figure: Inverse electron demand of Diels Alder]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

[[File:Ytl14 exercise2 secondaryinteraction.tif|center|Figure: Secondary interaction between carbon and oxygen]]
Oxygen is marked red.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|center|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

File:Ytl14 exercise2 secondaryinteraction.tif

2017-03-10T11:35:56Z

Ytl14: Ytl14 uploaded a new version of File:Ytl14 exercise2 secondaryinteraction.tif

File:Ytl14 exercise2 secondaryinteraction.tif

2017-03-10T11:31:23Z

Ytl14:

Rep:Mod:YTL14

2017-03-10T11:26:38Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
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<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
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<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
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<size>200</size>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
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<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|200px]]
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|-
| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene.(HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

[[File:Ytl14 exercise2 MO.PNG|center|thumb|300px|Figure: Inverse electron demand of Diels Alder]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
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<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|center|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 68</script>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
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<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

File:Ytl14 exercise2 MO.PNG

2017-03-10T11:24:08Z

Ytl14:

Rep:Mod:YTL14

2017-03-10T10:45:41Z

Ytl14: /* Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO2 */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<script>Symmetric, no node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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|}

{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
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<color>white</color>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|400px]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|center|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
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| '''Cheletropic'''
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| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:44:47Z

Ytl14: /* Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO2 */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
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| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
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<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|200px]]
| <jmol><jmolApplet>
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<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG|thumb|250px]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
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<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 16</script>
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</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:42:32Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
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<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<script>Asymmetric, 1 node</script>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
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<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|200px]]
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
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| '''Cheletropic'''
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:41:55Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
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<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
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<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
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<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG|thumb|250px]]
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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| [[File:Ytl14 exercise2 exo TS chemdraw.JPG|thumb|250px]]
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<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 18</script>
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</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 68</script>
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|<jmol><jmolApplet>
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<script>frame 18</script>
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</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:40:24Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
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<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
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<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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<script>frame 17; vibration 2</script>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:Ytl14 exercise2 endo TS chemdraw.JPG]]
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<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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| [[File:Ytl14 exercise2 exo TS chemdraw.JPG]]
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| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
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<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:39:02Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Symmetric, 2 nodes</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:File:Ytl14 exercise2 endo TS chemdraw.JPG]]
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| [[File:File:Ytl14 exercise2 exo TS chemdraw.JPG]]
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[[File:Ytl14 exercise2 energy profile.PNG|center|Figure: Energy profile of the reactions]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:32:50Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
| [[File:File:Ytl14 exercise2 endo TS chemdraw.JPG]]
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
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| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:13:50Z

Ytl14: /* Exercise 1: Reaction of Butadiene with Ethylene */

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

[[File:Ytl14 sym plane.JPG|thumb|center|Figure 1: Plane of symmetry]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
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| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
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<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
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<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<title>LUMO, Symmetric</title>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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<title>LUMO, Symmetric</title>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
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<title>HOMO, Symmetric</title>
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<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
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<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:10:44Z

Ytl14:

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO. [[File:Ytl14 sym plane.JPG]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Symmetric, 2 nodes</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
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<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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|-
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
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<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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|chemdraw ts
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<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
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| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:08:33Z

Ytl14:

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO. [[File:Ytl14 sym plane.JPG]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Asymmetric, 1 node</script>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
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| <jmol><jmolApplet>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
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<color>white</color>
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<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
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| <jmol><jmolApplet>
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<color>white</color>
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<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
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<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<title>LUMO+1, Asymmetric</title>
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<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
<size>200</size>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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|}

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
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|<jmol><jmolApplet>
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| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===
<references>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T10:02:45Z

Ytl14:

====<u>Introduction</u> <ref name="introduction" />====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO. [[File:Ytl14 sym plane.JPG]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<color>white</color>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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<title>Asymmetric</title>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<title>HOMO, Symmetric</title>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>===

Rep:Mod:YTL14

2017-03-10T10:00:47Z

Ytl14: /* Introduction */

====<u>Introduction</u>====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO. [[File:Ytl14 sym plane.JPG]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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|}

{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
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<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
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<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
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<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
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<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

Rep:Mod:YTL14

2017-03-10T09:58:15Z

Ytl14: /* Exercise 1: Reaction of Butadiene with Ethylene */

Rep:Mod:YTL14

2017-03-10T09:53:52Z

Ytl14:

====<u>Introduction</u>====

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO. [[File:Ytl14 sym plane.JPG]]

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="margin-left: auto; margin-right: auto; border: none; background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<color>white</color>
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<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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|}

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
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<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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<title>Asymmetric</title>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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|chemdraw ts
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<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

Rep:Mod:YTL14

2017-03-10T09:51:49Z

Ytl14:

===<u>Introduction</u>===

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency). <ref name="introduction"/><references>

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO. [[File:Ytl14 sym plane.JPG]]

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="margin-left: auto; margin-right: auto; border: none; background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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<title>Symmetric</title>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
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|-
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T09:50:10Z

Ytl14:

===<u>Introduction</u>=== <ref name="introduction"/><references>

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO. [[File:Ytl14 sym plane.JPG]]

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="margin-left: auto; margin-right: auto; border: none; background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
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<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<size>200</size>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
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<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
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<script>frame 18</script>
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<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
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| '''Cheletropic'''
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| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T09:46:13Z

Ytl14:

====<u>Introduction</u><ref name="introduction" />
<references>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO. [[File:Ytl14 sym plane.JPG]]

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="margin-left: auto; margin-right: auto; border: none; background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
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<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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<title>Ethene</title>
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{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
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| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script> frame 18; mo 14; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T09:38:54Z

Ytl14:

====<u>Introduction</u><ref name="introduction" />
<references>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

^http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
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<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
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[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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|chemdraw ts
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<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
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<script>frame 18</script>
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| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
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| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
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| '''Cheletropic'''
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Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>===

===<u>Reference</u>
<ref name="introduction">http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf</ref>
</references>

Rep:Mod:YTL14

2017-03-10T09:37:33Z

Ytl14: /* Introduction */

====<u>Introduction</u><ref name="introduction" />
<references>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to either transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the force at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

^http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script> frame 18; mo 14; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
<color>white</color>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

File:Ytl14 sym plane.JPG

2017-03-10T04:23:24Z

Ytl14:

File:Ytl14 exercise2 exo TS chemdraw.JPG

2017-03-10T04:22:17Z

Ytl14:

File:Ytl14 exercise2 endo TS chemdraw.JPG

2017-03-10T04:21:33Z

Ytl14:

Rep:Mod:YTL14

2017-03-10T03:18:13Z

Ytl14: /* Introduction */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

A potential energy surface (PES) is used to analyse the molecular structure change in a chemical reaction. In a simple diatomic molecule, the 1D PES is a curve resulting from the combination of functions considering (1) the repulsion between the two atoms at very short internuclear distance (2) Coulombic attraction between the two ions and (3) energy at equilibrium is represented by a Harmonic oscillator. This provide a curve with energy at the y-axis and internuclear distance or the reaction coordinate at the x-axis. This estimation is good for simple diatomic molecule formation/dissociation.

However, as the molecule becomes larger more variables are involved. The degrees of freedom (3N-6 for non-linear structure, while 3N-5 for linear molecule; N is the number of atom) gives the dimensionality of the PES. In the determination of degrees of freedom, the translational and rotational energy of the molecule are opt out as the potential energy of a molecule does not change upon translation or rotation in space. PES is dependent on the relative position of the one atom to another (geometry).

A minima on PES is a point corresponds to transition states, reactants, products and intermediates. It can be classified as local minima or global minima. A saddle point on a PES is the maximum connecting two minima in the minimum energy pathway, i.e the transition state. As at this point going down either direction will result in a lower energy conformation/structure. The gradient and thus the forces at the transition state is zero. The same applies to the minima. These points at which the forces are zero also known as stationary point. A frequency calculation of the stationary point allows one to understand the nature of the structure at that particular point such as frequency, vibrational modes etc. The transition state is the first saddle point by definition and is indicated by the presence of one negative frequency (imaginary frequency).

^http://www.uni-heidelberg.de/institute/fak12/AC/hofmann/acf_theo/MinNoMin.pdf

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
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<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
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|}

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T20:51:19Z

Ytl14:

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table 4: Changes in bond length during the course of the reaction
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 5: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
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<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table 6: MOs of the transition state in endo and exo pathway
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
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<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
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<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
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<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table 7: Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table 8 Thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table 8''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table 9: Endo, exo and cheletropic reaction compared
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T20:47:08Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
<size>200</size>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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<title>LUMO, Symmetric</title>
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|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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|}

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

Diels-Alder reaction between cyclohexadiene and 1,3-Dioxole are inverse electron demand. The 1,3-dioxole is electron rich due to the delocalisation of oxygen lone pair into the pi-system of 1,3-dioxole. This creates a repulsion of the donated electron and HOMO electrons. This results in a rise in HOMO energy, which then has a comparable energy with the LUMO of the diene. The LUMO of 1,3-dioxole and HOMO of cyclohexadiene are closer in energy. Hence they interact more strongly than HOMO of 1,3-dioxole and LUMO of cyclohexadiene. (HOMO-diene and LUMO-dienophile interact stronger in normal oxygen demand Diels-Alder).

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

In Diels-Alder reaction, the endo pathway is normally the preferred pathway due to secondary interaction which is said to lower the energy of the transition state.

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T20:29:13Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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<title>Symmetric</title>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
<size>200</size>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

The HOMO of cyclohexadiene and LUMO of 1,3-dioxole are both asymmetric, hence they interact to form LUMO+1 and HOMO-1 orbitals in the transition states.
Meanwhile, the LUMO of cyclohexadiene and HOMO of 1,3-dioxole are both symmetric. The interaction of both results in HOMO and LUMO orbitals in the transition states.

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
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<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<title>LUMO, Symmetric</title>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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|}

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T20:25:42Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>Asymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>Symmetric</title>
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<script> frame 18; mo 14; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>Asymmetric</title>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
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<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T20:24:04Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
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<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
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<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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|chemdraw ts
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<script>frame 6</script>
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|-
| <jmol><jmolApplet>
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| <jmol><jmolApplet>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T20:21:50Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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|chemdraw ts
| <jmol><jmolApplet>
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<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
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<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
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<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO, Symmetric</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1, Asymmetric</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T20:18:07Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
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<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T20:06:47Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, Diels-Alder reaction of cyclohexadiene and 1,3-Dioxole were studied. The reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry study was performed using the IRC data obtained at PM6 level.

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster). Hence endo product is the major product.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
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|chemdraw ts
| <jmol><jmolApplet>
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<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
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<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T19:59:34Z

Ytl14: /* Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO2 */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
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<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
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<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
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<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, the reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry studies was performed using the IRC data obtained at PM6 level.

Diels Alder reaction of

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster).

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
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</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
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<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
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<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimization of the distorted structure. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were re-optimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
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|<jmol><jmolApplet>
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<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}

Diels-Alder and cheletropic products all contain an aromatic benzyl group. At the beginning of the reaction, the six-membered ring in xylylene has 2 C=C bonds. As the new bonds begin to form, all the six bonds are in conjugation (C-C bond is in between C-C single bond and C=C bond). The products formed are aromatic with pi=orbital above and below the plane.

===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T19:24:29Z

Ytl14: /* Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO2 */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
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<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<script>Asymmetric, 1 node</script>
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<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
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<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, the reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry studies was performed using the IRC data obtained at PM6 level.

Diels Alder reaction of

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster).

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
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<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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|-
| <jmol><jmolApplet>
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| <jmol><jmolApplet>
<color>white</color>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
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<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimisation. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were reoptimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

From '''Table''' and '''Figure''', it was found that cheletropic product was the thermodynamic and kinetic product.

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}
===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T19:22:32Z

Ytl14: /* Exercise 3 */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
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<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
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<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
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<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
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From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, the reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry studies was performed using the IRC data obtained at PM6 level.

Diels Alder reaction of

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster).

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
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| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 14; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3: Hetero-Diels-Alder and Cheletropic of o-xylylene and SO<sub>2</sub></u>====

The Hetero-Diels-Alder and Cheletropic reaction between o-xylylene and SO<sub>2</sub> were studied. The products of these reactions were firstly optimised, the newly formed bonds on the optimised product were broken and followed by optimisation. IRC calculation was performed on the transition states obtained. The reactants and products from the IRC were reoptimized. All calculations were done at PM6 level.

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}
===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T18:51:01Z

Ytl14: /* Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, the reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry studies was performed using the IRC data obtained at PM6 level.

Diels Alder reaction of

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster).

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.120615
| style="text-align: center" | 0.118665
| style="text-align: center" | 0.065793
| style="text-align: center" | 0.075809
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.172488
| style="text-align: center" | 0.173266
| style="text-align: center" | 0.137941
| style="text-align: center" | 0.138906
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.070675
| style="text-align: center" | 0.070929
| style="text-align: center" | 0.037802
| style="text-align: center" | 0.037976
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 136.1926
| style="text-align: center" | 143.3549
| style="text-align: center" | 189.4351
| style="text-align: center" | 165.6612
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -131.117
| style="text-align: center" | -125.3309
| style="text-align: center" | -99.33054
| style="text-align: center" | -73.4799
|}

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
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<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
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<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 14; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3</u>====

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}
===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T18:45:11Z

Ytl14: /* Exercise 3 */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, the reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry studies was performed using the IRC data obtained at PM6 level.

Diels Alder reaction of

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster).

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 14; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3</u>====

{| class="wikitable"
|+ Table : thermochemistry data
| rowspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}
===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T18:44:48Z

Ytl14: /* Exercise 3 */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, the reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry studies was performed using the IRC data obtained at PM6 level.

Diels Alder reaction of

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster).

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 14; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3</u>====

{| class="wikitable"
|+ Table : thermochemistry data
| roqspan="2" style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}
===<u>Conclusion</u>

Rep:Mod:YTL14

2017-03-09T18:43:54Z

Ytl14: /* Exercise 3 */

====<u>Introduction</u>====
In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)

====<u>Exercise 1: Reaction of Butadiene with Ethylene</u>====

Method 2 was used. The reactants, transition state and product are optimised at PM6 level.

Diels-Alder reaction is thermal cycloaddition between a conjugated, electron-rich diene and an electron-poor dienophile. The conjugated diene must adopt a s-cis conformation. In this exercise we will focus on the Frontier Molecular Orbital (FMO) theory developed by Kenichi Fukui in the 1950's. The interaction between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the reactants participate in bond formation. As electron density 'flows' (or charge transfer) from HOMO to LUMO.

{| class="wikitable"
|+ Table 1: HOMO and LUMO of butadiene and ethene
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Butadiene</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Asymmetric, 1 node</script>
<size>200</size>
<script>frame 16; mo 11; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, 2 nodes</script>
<size>200</size>
<script>frame 16; mo 12; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 diene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>Ethene</title>
<color>white</color>
<size>200</size>
<script> frame 14</script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<script>Symmetric, no node</script>
<size>200</size>
<script> frame 14; mo 6; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>Asymmetric, 1 node</script>
<script> frame 14; mo 7; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise1 ethene opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

.

{| class="wikitable" border="1"
|+ Table 2: MOs of transition state
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Species'''
| colspan="2" style="text-align: center; background: #ffcfdf; color: black;"|'''MO'''
|-
| rowspan="4" |<jmol><jmolApplet>
<title>Transition state</title>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| colspan="2" style="text-align: center;"| Interaction between HOMO of ethene and LUMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 17; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 18; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| colspan="2" style="text-align: center;" | Interaction between LUMO of ethene and HOMO of butadiene
|-
| <jmol><jmolApplet>
<title>HOMO-1, Bonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 16; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<title>LUMO+1, Antibonding</title>
<color>white</color>
<size>200</size>
<script>frame 16; mo 19; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

From the transition state MOs, it is clearly shown that the interacting MOs are as follow:

1. HOMO (butadiene) - LUMO (ethene) give HOMO-1 and LUMO+1. All four MOs are asymmetric.
2. LUMO (butadiene) - HOMO (ethene) give HOMO and LUMO. All four MOs are symmetric.

Hence it is confirmed that for an allowed interaction, the HOMO and LUMO have to be of the same symmetry. While for the case where the interacting MOs are of different symmetry the reaction is forbidden.

[[File:Ytl14 exercise1 MO diagram.PNG|thumb|centre|Figure: MO diagram of the reaction.]]

The two bonding MOs generate the two new C-C σ-bonds in 1-cyclohexene.

[[File:Ytl14 exercise1 symmetric requirement.PNG|500px|thumb|centre]]

{| class="wikitable"
|+ Table 3
|-
! style="background: #ffcfdf; color: black;" | '''Reactants'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''Vibrations at transition state'''
|-
| [[File:Ytl14 exercise1 TS label.PNG|thumb|centre|200px]] Carbon labelled in reactants
| [[File:Ytl14 exercise1 product label.PNG|thumb|centre|200px]] Carbon labelled in product
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 17; vibration 2</script>
<uploadedFileContents>Ytl14 exercise1 TS opt and freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Ytl14 exercise1 internuclear distance plot.PNG|thumb|centre|500px|Figure :Internuclear Distance plotted against the Reaction Coordinate for Dissociation of 1-cyclohexene]]

IRC showed the dissociation of 1-cyclohexene to butadiene and ethene. Referring to '''Figure''', reaction coordinates at -5.73, 0 and 11.49 correspond to product, transition state and reactants respectively.

Two sp3 C-C bonds are formed between C8 and C11, and C14 and C1.
New sp2 C=C bond is formed between C4 and C6.
The sp2 C=C and sp3 C-C bond lengths are of good comparison to '''literature''' (1.36 Å and 1.54 Å respectively).

'''REFERENCE''' The Van der Waals radius of a carbon atom is 1.70 Å. In the transition state, the distance between the carbons forming new bonds are 2.115 Å, which is in between two times the Van der Waals radius (3.40 Å) and 1.70 Å.

{| class="wikitable"
|+ Table
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond broken'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C11=C14
| style="text-align: center" | 1.327
| style="text-align: center" | C11--C14
| style="text-align: center" | 1.382
| style="text-align: center" | C11-C14
| style="text-align: center" | 1.541
|-
| style="text-align: center" | C1=C4
| style="text-align: center" | 1.335
| style="text-align: center" | C1--C4
| style="text-align: center" | 1.38
| style="text-align: center" | C1-C4
| style="text-align: center" | 1.501
|-
| style="text-align: center" | C6=C8
| style="text-align: center" | 1.335
| style="text-align: center" | C6--C8
| style="text-align: center" | 1.38
| style="text-align: center" | C6-C8
| style="text-align: center" | 1.501
|-
| colspan="6" style="text-align: center; background: #ffcfdf; color: black;" | '''Bond formed'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Bond length (Å)'''
|-
| style="text-align: center" | C4-C6
| style="text-align: center" | 1.468
| style="text-align: center" | C4--C6
| style="text-align: center" | 1.411
| style="text-align: center" | C4=C6
| style="text-align: center" | 1.338
|-
| style="text-align: center" | C8,C11
| style="text-align: center" | non-bonding
| style="text-align: center" | C8--C11
| style="text-align: center" | 2.115
| style="text-align: center" | C8-C11
| style="text-align: center" | 1.54
|-
| style="text-align: center" | C14,C1
| style="text-align: center" | non-bonding
| style="text-align: center" | C14--C1
| style="text-align: center" | 2.115
| style="text-align: center" | C14-C1
| style="text-align: center" | 1.54
|}

TS bond lengths resemble the reactants' bond length (compare to products'), hence according to Hammond's postulate this is an early transition state.
Formation of the two bonds is synchronous, i.e concerted, with the same bond lengths. No radical nor ionic intermediates was formed.

====<u>Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole</u>====

In this exercise, the reactants, transition states and products were optimised at PM6 level. The transition states were reoptimised at B3LYP-6d to confirm the structure obtained. Thermochemistry studies was performed using the IRC data obtained at PM6 level.

Diels Alder reaction of

[[File:Ytl14 exercise2 energy profile.PNG]]

The endo product is both the thermodynamic (more negative reaction energies (Er), indicative of a higher stability) and kinetic product (lower activation energy (Ea), hence the endo product forms faster).

{| class="wikitable"
|+ Table 1: HOMO and LUMO of Cyclohexadiene and 1,3-Dioxole
|-
! style="background: #ffcfdf; color: black;" | '''Species'''
! style="background: #ffcfdf; color: black;" | '''HOMO'''
! style="background: #ffcfdf; color: black;" | '''LUMO'''
|-
| <jmol><jmolApplet>
<title>Cyclohexadiene</title>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6; mo 16; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6; mo 17; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14_EXERCISE2_CYCLOHEXADIENE_OPT_AND_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<title>1,3-Dioxole</title>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG </uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 14; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script> frame 18; mo 15; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>YTL14 EXERCISE2 DIOXOLE OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable"
|+ Table :
|-
! colspan="2" style="background: #ffcfdf; color: black;" | '''Endo pathway'''
! colspan="2" style="background: #ffcfdf; color: black;" | '''Exo pathway'''
|-
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14 exercise2 TS1 irced product mo.LOG </uploadedFileContents>
</jmolApplet></jmol>
|chemdraw ts
| <jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 6</script>
<uploadedFileContents>Ytl14_exercise2_TS2_product_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO+1</title>
<size>200</size>
<script>frame 6; mo 32; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>LUMO</title>
<size>200</size>
<script>frame 6; mo 31; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|-
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14 exercise2 TS 1 pm6 freq opt mo endo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO</title>
<size>200</size>
<script>frame 6; mo 30; mo nodots nomesh fill translucent; mo titleformat ""</script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
| <jmol><jmolApplet>
<color>white</color>
<title>HOMO-1</title>
<size>200</size>
<script>frame 6; mo 29; mo nodots nomesh fill translucent; mo titleformat "" </script>
<uploadedFileContents>Ytl14_exercise2_TS2_pm6_exo_opt_freq_and_mo.LOG</uploadedFileContents>
</jmolApplet></jmol>
|}

====<u>Exercise 3</u>====

{| class="wikitable"
|+ Table : thermochemistry data
| style="text-align: center; background: #ffcfdf; color: black;" |
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''0 K'''
| colspan="3" style="text-align: center; background: #ffcfdf; color: black;" | '''298 K'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Energy'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Endo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Exo'''
| style="text-align: center; background: #ffcfdf; color: black;" | '''Cheletropic'''
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reactant (Hartree/particle)'''
| style="text-align: center" | 0.116934
| style="text-align: center" | 0.116955
| style="text-align: center" | 0.114807
| style="text-align: center" | 0.058769
| style="text-align: center" | 0.059656
| style="text-align: center" | 0.070991
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Transition state (Hartree/particle)'''
| style="text-align: center" | 0.126589
| style="text-align: center" | 0.128172
| style="text-align: center" | 0.13556
| style="text-align: center" | 0.090559
| style="text-align: center" | 0.092082
| style="text-align: center" | 0.099062
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Product (Hartree/particle)'''
| style="text-align: center" | 0.057503
| style="text-align: center" | 0.056644
| style="text-align: center" | 0.034556
| style="text-align: center" | 0.021704
| style="text-align: center" | 0.021455
| style="text-align: center" | 0.0000002
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Activation energy (kJ/mol)'''
| style="text-align: center" | 25.34395
| style="text-align: center" | 29.45023
| style="text-align: center" | 52.43245
| style="text-align: center" | 83.45939
| style="text-align: center" | 85.13446
| style="text-align: center" | 70.92138
|-
| style="text-align: center; background: #ffcfdf; color: black;" | '''Reaction energy (kJ/mol)'''
| style="text-align: center" | -156.0413
| style="text-align: center" | -158.3465
| style="text-align: center" | -70.92138
| style="text-align: center" | -97.31941
| style="text-align: center" | -100.2967
| style="text-align: center" | -179.3638
|}

[[File:Ytl14 exercise3 energy diagram.PNG]]

{| class="wikitable"
|+ Table :
|-
! style="background: #ffcfdf; color: black;" | '''Reaction'''
! style="background: #ffcfdf; color: black;" | '''Transition state'''
! style="background: #ffcfdf; color: black;" | '''Product'''
! style="background: #ffcfdf; color: black;" | '''IRC'''
|-
| '''Diels Alder (Endo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA endo TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 4</script>
<uploadedFileContents>Ytl14 exercise3 DA ENDO PRODUCT IRCED OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA endo TS IRC.gif|thumb|300px]]
|-
| '''Diels Alder (Exo)'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 68</script>
<uploadedFileContents>Ytl14 exercise3 exo DA SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 18</script>
<uploadedFileContents>Ytl14 exercise3 DA EXO IRCED PRODUCT OPT AND FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 DA exo sym break TS IRC.gif|thumb|300px]]
|-
| '''Cheletropic'''
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 10</script>
<uploadedFileContents>Ytl14 CHELETROPIC SYM BREAK TS.LOG</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 16</script>
<uploadedFileContents>Ytl14_exercise3_cheletropic_irces_product_opt_and_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>
| [[File:Ytl14 exercise3 cheletropic sym break TS IRC.gif|thumb|300px]]
|}
===<u>Conclusion</u>