Third Year TS and Reactivity Lab

Transition States Exercises

In these exercises you will locate and characterise transition states of several Diels-Alder reactions. Before starting, you should complete the tutorial and decide which method suits you best.

Introduction

In this module you will locate and characterise transition structures for a variety of pericyclic reactions. The lab is split into two sections:

1) A tutorial section located here. It is not assessed, but it will introduce you to the methods and programs involved and it is highly recommended that you are familiar with all three methods before continuing.

2) An assessed exercise section below.

Don't rush the tutorial section. The exercises will become more straightforward once you have a good understanding of the techniques used in the tutorial section. In addition, the page includes solutions to common errors that are encountered along the way, and instructions for characterising transition state structures. Write up as you go along; constructing a wiki page might take longer than you expect! If you encounter any problems, talk to a demonstrator or a member of staff.

In the second year physical chemistry laboratory, you may have carried out dynamics calculations using model potential energy surfaces to explore transition states. In that computational experiment, the total energy could quickly be calculated for different geometries of a triatomic system using an analytical function of the atomic coordinates (for more information, see for example here and here).

In this experiment, you will be studying transition structures in larger molecules. There are no longer fitted formulae for the energy, and the molecular mechanics / force field methods that work well for structure determination cannot be used (in general) as they do not describe bonds being made and broken, and changes in bonding type / electron distribution. Instead, we use molecular orbital-based methods, numerically solving the Schrödinger equation, and locating transition structures based on the local shape of a potential energy surface. As well as showing what transition structures look like, reaction paths and barrier heights can also be calculated.

Suggested Time Frame

Try to complete the Tutorial by mid-Tuesday to give enough time for the exercise. By this time you should be comfortable with methods of optimising minima and transition states. The tutorial is not examined, but keep the files that you have created as they might come in useful later in the exercise.

All calculations should be completed by the end of Friday. The deadline for handing in is on the following Wednesday at noon to give you time to write up and format your report.

Mark Scheme

The break-down for the marks for this lab are as follows:

Introduction and conclusion	10%
Presentation	10%
Exercise 1	20%
Exercise 2	30%
Exercise 3	30%

Marks are awarded for presentation of data, including the use of tables, images and Jmol objects. If you're unsure what to put into your wiki report or how to structure it, ask a demonstrator.

Computational Methods

During this lab you will be using two electronic structure methods: the semi-empirical method PM6 and the Density Functional Theory (DFT) method B3LYP. Briefly, PM6 is a fitted method using experimental data to save resources and time during calculations. As a result, it is generally much faster than ab initio methods with reasonable results. B3LYP is a reasonably fast DFT methods that is capable of reproducing chemical data. In this lab, PM6 is used to generate initial geometries where possible, and this geometry is optimised with B3LYP.

A basis set is a set of functions that typically mimic atomic orbitals, which when combined linearly generate molecular orbitals. In a way, they are the building blocks of molecular orbitals. The higher the basis set, the more blocks are available to construct a molecular orbital, at the cost of computational effort.

Objectives

By the end of this lab:

• you will have explored advanced techniques in Gaussian, a computational chemistry program, and GaussView, the graphical user interface for Gaussian.
• you should be able to explain what a Transition State and a Potential Energy Surface are.
• you should be able to use chemical intuition to help you to locate stationary points on a Potential Energy Surface.
• you should be able to discuss the roles of sterics and secondary orbital interactions in determining the kinetic and thermodynamic products of a reaction.

Write up

Make sure your page name is unique (eg Mod:grj13TS), and every file that you upload has your username in it to prevent it being replaced (eg grj13_butadiene.png).

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?)

For each of your calculations, upload the log file and include a link in the wiki (this is not necessary if you have included a JMol for that calculation).

If you're expecting to use JMols later on, read the section on JMols first before submitting calculations

It is recommended to use ChemDraw to create MO diagrams and reaction coordinates.

Plagiarism

Submissions are checked for plagiarism. Do not copy text or images from other wiki pages. External images may be used if correctly cited, but it's always better to create your own.

Demonstrators

The demonstrators are Tristan (tam10), Nathan (nf710), and Francesca (fv611). If you're stuck and you can't proceed, you can send us an email and we'll try to help.

Hour Beginning	Monday	Tuesday	Wednesday	Thursday	Friday
10	Tristan	Francesca	-	Nathan	Tristan
11	-	-	-	-	-
12	-	-	-	-	-
13	-	-	-	-	-
14	Francesca	Nathan	-	Tristan	Francesca
15	-	-	-	-	-
16	Nathan	Tristan	-	Francesca	Nathan
17	-	-	-	-	-
18	-	-	-	-	-

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

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 (or Jmol objects) for each of the HOMO and LUMO of butadiene and ethene, 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.

Alternatively, you can extract these distances from an IRC log file using the script in this page to create an Excel file with the measurements for each geometry in the IRC and plot the results.

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

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 at the B3LYP/6-31G(d) level (Note that it is always fastest to optimise with PM6 first and then reoptimise with B3LYP). Confirm that you have a TS for each case using a frequency calculation.

Note: B3LYP calculations - especially those with calcfc and/or freq - take a long time to run. You can use this time to write up your wiki.

2) Run frequency calculations on cyclohexadiene, 1,3-dioxole, and the endo and exo products. Ensure you have no imaginary frequencies for these geometries.

Write up and Analysis

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) at room temperature (the corrected energies are labelled "Sum of electronic and thermal Free Energies", corresponding to the Gibbs free energy). Which are the kinetically and thermodynamically favourable products? More detail regarding thermochemistry in Gaussian is given here.

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.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

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

4) 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?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

Further Work

There are examples of several electrocyclic reactions on this page that you can try. These are a subset of pericyclic reactions like the ones above. For each case, find the IRC of the TS, which corresponds to the ground state or thermal reaction. Have a look at the HOMO and LUMO of the reactants, TS and products to justify why the reaction proceeds with either conrotation or disrotation.