Computational Labs

Unless otherwise stated the hartree-fock method is used for all caclulations.

Module 3

The first anti structure optimised was the anti 4 structure with C1 symmettry and an energy of -231.693 a.u.

You would expect the anti structure to have a lower energy than the gauche structure due to lower steric interactions.

The second gauche structure was gauche 1 with a c2 symmettry with an energy of -231.688a.u. This backs up the above theory, and when my prediction for the lowest Energy structure, the anti 2 structure was lower in energy, matching the energy in appendix 1, -231.69254a.u., this also backed up the theory. This molecule was found to have a Ci symmetry.

When this structure was optimized again using a DFT method with a higher B3LYP basis set, after certain problems with the input file, Gaussview inserting certain unwanted additional keywords to the input file, it was found that the bond lengths in the molecule got closer to literature values ¹ upon optimization..

When the frequency was calculated again using the B3LYP method of the anti 2 molecule, it was found to have no imaginary frequencies signifiying a minima had been reached and the thermodynamic data was as follows

Sum of electronic and zero-point Energies= -234.469203a.u.

Sum of electronic and thermal Energies= -234.461857a.u.

Sum of electronic and thermal Enthalpies= -234.460913a.u.

Sum of electronic and thermal Free Energies= -234.500777a.u.

Optimizing boat + Chair

The transition state structure for the chair conformation was first caclulated without the fixed coordinates. Using the optimize to a TS (berny) job type calculating force constants once and produced a reasonable transition state with as expected one imaginary frequency vibration, observed at -818.0cm^-1 corresponding to the Cope Rearrangement.

Then the bonds that are breaking/forming are fixed at 2.2 in the fixed coordinate method, the molecule was reoptimized and then the frozen bonds were released and optimized seperately and these bonds relaxed to find the same minima as before, at a bond length of 2.02A.

When the boat was optimized using the QST2 method, which allows you to find the transition state between the product and the reactant of the reaction, the first attempt failed due to the method not being able to rotate the molecule around the central bonds to give a better TS. However once the central bonds were manually rotated the Gaussian Calculation failed to run due to coordinate problems and the problem was unable to be resolved.

The IRC

Using the optimized chair molecule the Intrinsic Reaction Coordinate can be calculated. This was calculated in the forward direction only using 60 points for the calculation. The IRC calculation calculation the force conastants once, only ran for 17 calculations. This means that it is difficult to tell wether the enrgy minima had been reached yet. However when the force constants were calculated at every step, the number of steps increased to 41 dropping to the same enrgy for the final step suggesting that the ppoint of 0 gradient on the IRC had been reached and that minimization of this structure would lead to the real confomer of the cope chair reaction

This molecule was then optimised to give the structure seen below, the gauche 2 structure with the same energy as appendix 1, suggesting that this is the structure that takes part in the chair confomer of the cope reaction.

The activation energies could not be calculated as the boat transition state could not be found.

References

http://www.springerlink.com/content/l4u57k08541h1040/fulltext.pdf