Third Year TS and Reactivity Lab: Exercises

This is the assessed exercise section for the third year TS and reactivity lab. For information about the lab and assessment return to the main lab page. Make sure that you have completed the Tutorial section before attempting the exercises.

Exercise 1: Reaction of Butadiene with Ethylene

Calculations

1. Calculate the reactants, product, and TS at the PM6 level.

2. Run an IRC calculation to confirm that you have the correct TS.

3. Recalculate the reactants, products, and TS at the B3LYP/6-31G(d) level.

Write up and Analysis

• Confirm that you have the correct reactants, products, and TS. Explain how you can identify the nature of the stationary points on the PES. This only needs to be explained in detail for exercise 1, in the next two exercises your log files will be evidence that you know how to calculate and recognise the correct structures.
• Compare the results from the IRC calculation to the optimised butadiene. Are there any differences?

• Construct an MO diagram for the formation of the butadiene/ethene TS, including basic symmetry labels (symmetric/antisymmetric or s/a)
• View the MOs of the reactants and the TS in GaussView:

• Open the .chk (checkpoint) file of the structure.
• Under the Edit menu, choose MOs and visualise the MOs.

• Include images for each of the HOMO and LUMO of butadiene and ethylene, and the four MOs these produce for the TS on your MO diagram with the corresponding MOs in your MO diagram.
• What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')? Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction, and an antisymmetric-antisymmetric interaction.

• Include measurements of the 4 C-C bond lengths of the reactants and the 6 C-C bond lengths of the TS and products.
• How do the bond lengths change as the reaction progresses? What are typical sp³ and sp² C-C bond lengths? What is the Van der Waals radius of the C atom? How does this compare with the length of the partly formed C-C bonds in the TS? Is the formation of the two bonds synchronous or asynchronous (viewing the vibrational mode may help here too)?

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

1) Calculate both the endo and exo TSs using PM6. Confirm that you have a TS for each case using a frequency calculation.

2) Optimise and run frequency calculations for cyclohexadiene, 1,3-dioxole, and the endo and exo products at the PM6 level. Ensure you have the correct number of imaginary frequencies for these geometries.

Write up and Analysis

Confirm that you have the correct reactants, products, and TS.

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

In the .log files for each calculation, find a section named "Thermochemistry". Tabulate the energies and determine the reaction barriers and reaction energies (in kJ/mol, PM6) at room temperature (the corrected energies are labeled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? See more detail regarding thermochemistry in Gaussian.

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

Exercise 3: Diels-Alder vs Cheletropic

See the o-Xylylene-SO2 Cycloaddition section in the tutorial as a guide.

In the tutorial, you will have ended up with either the endo or the exo TS and adduct for the Diels-Alder reaction. In this exercise, include both TSs and both adducts for each of the cheletropic and Diels-Alder reactions.

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

Write up and Analysis

Confirm that you have the correct reactants, products, and TS.

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

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

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