Third Year TS and Reactivity Lab: Exercises
Contents
Exercise 1: Reaction of Butadiene with Ethylene
1) Optimise the reactants and TS at the PM6 level.
2) Confirm that you have the correct TS with a frequency calculation and IRC.
3) Optimise the products at the PM6 level.
Write up and Analysis
Confirm that you have the correct reactants, products, and TS.
Construct an MO diagram for the formation of the butadiene/ethene TS, including basic symmetry labels (symmetric/antisymmetric or s/a).
For each of the reactants and the TS, open the .chk (checkpoint) file. 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. Correlate these MOs with the ones in your MO diagram to show which orbitals interact. 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)?
Alternatively, you can extract these distances from an IRC log file using the script to create an Excel file with the measurements for each geometry in the IRC and plot the results.
Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole
1) Using any of the methods in the tutorial, locate 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?
