ChemWiki - User contributions [en]

Rep:Mod:maxk2

2009-11-13T18:23:13Z

Mk507: /* The IRC */

=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 <sup>1</sup> upon optimization..

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

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<sup>-1</sup> corresponding to the Cope Rearrangement.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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.

[[Image:Chair opt final.jpg|thumb|The final chair structure optimised from the IRC]]

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

Rep:Mod:maxk2

2009-11-13T18:19:04Z

Mk507: /* The IRC */

=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 <sup>1</sup> upon optimization..

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

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<sup>-1</sup> corresponding to the Cope Rearrangement.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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.

[[Image:Chair opt final.jpg|thumb|The final chair structure optimised from the IRC]]

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

Rep:Mod:maxk2

2009-11-13T18:18:22Z

Mk507: /* The IRC */

=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 <sup>1</sup> upon optimization..

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

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<sup>-1</sup> corresponding to the Cope Rearrangement.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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.

[[Image:Chair opt final.jpg|thumb|The final chair structure optimised from the IRC]]

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

Rep:Mod:maxk2

2009-11-13T18:18:03Z

Mk507: /* The IRC */

=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 <sup>1</sup> upon optimization..

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

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<sup>-1</sup> corresponding to the Cope Rearrangement.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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.

[[
Image:Chair opt final.jpg|thumb|The final chair structure optimised from the IRC]]

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

Rep:Mod:maxk2

2009-11-13T18:17:35Z

Mk507: /* Module 3 */

=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 <sup>1</sup> upon optimization..

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

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<sup>-1</sup> corresponding to the Cope Rearrangement.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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.

[[Image:Cope rearrangment vibration chair.jpg|thumb|The final chair structure optimised from the IRC]]

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

Rep:Mod:maxk2

2009-11-13T18:16:40Z

Mk507: /* The IRC */

=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 <sup>1</sup> upon optimization..

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

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<sup>-1</sup> corresponding to the Cope Rearrangement.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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.

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

File:Chair opt final.jpg

2009-11-13T18:16:32Z

Mk507: The final chair structure found from the IRC

The final chair structure found from the IRC

Rep:Mod:maxk2

2009-11-13T18:11:54Z

Mk507: /* The IRC */

=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 <sup>1</sup> upon optimization..

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

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<sup>-1</sup> corresponding to the Cope Rearrangement.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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

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

Rep:Mod:maxk2

2009-11-13T17:57:07Z

Mk507: /* Optimizing boat + Chair */

=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 <sup>1</sup> upon optimization..

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

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<sup>-1</sup> corresponding to the Cope Rearrangement.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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

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

Rep:Mod:maxk2

2009-11-13T17:56:03Z

Mk507: /* Optimizing boat + Chair */

=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 <sup>1</sup> upon optimization..

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

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<sup>-1</sup> corresponding to the Cope Rearrangement.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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.

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

Rep:Mod:maxk2

2009-11-13T17:51:43Z

Mk507: /* Optimizing boat + Chair */

Rep:Mod:maxk2

2009-11-13T17:45:27Z

Mk507: /* Optimizing boat + Chair */

Rep:Mod:maxk2

2009-11-13T17:40:09Z

Mk507: /* Module 3 */

Rep:Mod:maxk2

2009-11-13T17:33:35Z

Mk507: /* Module 3 */

Rep:Mod:maxk2

2009-11-13T17:27:14Z

Mk507: /* Module 3 */

Rep:Mod:maxk2

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Mk507: /* Module 3 */

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Mk507: /* Optimizing boat + Chair */

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Mk507: /* Optimizing boat + Chair */

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Mk507: /* Optimizing boat + Chair */

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Mk507: /* Computational Labs */

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2009-11-13T16:58:01Z

Mk507: /* Optimizing boat + Chair */

=Computational Labs=

==Module 3==

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

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 -231.688. 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, -231.69254, this also backed up the theory.

When this structure was optimized with a higher B3LYP basis set it was found that the bond lengths in the molecule got closer to literature values <sup>1</sup>.

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

When the frequency was calculated of the anti 2 molecule, it was found to have no imaginary frequencies and the thermodynamic data was as follows

Sum of electronic and zero-point Energies= -234.469203

Sum of electronic and thermal Energies= -234.461857

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500777

===Optimizing boat + Chair===

The transition state structure was first caclulated without the fixed coordinates and as expected one imaginary frequency was observed at -818.0cm<sup>-1</sup>.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

When the frozen coordinate method is used and the bonds that are breaking/forming are fixed at 2.2, 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

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

Rep:Mod:maxk2

2009-11-13T16:50:25Z

Mk507: /* Optimizing boat + Chair */

=Computational Labs=

==Module 3==

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

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 -231.688. 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, -231.69254, this also backed up the theory.

When this structure was optimized with a higher B3LYP basis set it was found that the bond lengths in the molecule got closer to literature values <sup>1</sup>.

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

When the frequency was calculated of the anti 2 molecule, it was found to have no imaginary frequencies and the thermodynamic data was as follows

Sum of electronic and zero-point Energies= -234.469203

Sum of electronic and thermal Energies= -234.461857

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500777

===Optimizing boat + Chair===

The transition state structure was first caclulated without the fixed coordinates and as expected one imaginary frequency was observed at -818.0cm<sup>-1</sup>.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

When the frozen coordinate method is used and the bonds that are breaking/forming are fixed at 2.2, 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.

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

Rep:Mod:maxk2

2009-11-13T16:43:35Z

Mk507: /* Optimizing boat + Chair */

=Computational Labs=

==Module 3==

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

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 -231.688. 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, -231.69254, this also backed up the theory.

When this structure was optimized with a higher B3LYP basis set it was found that the bond lengths in the molecule got closer to literature values <sup>1</sup>.

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

When the frequency was calculated of the anti 2 molecule, it was found to have no imaginary frequencies and the thermodynamic data was as follows

Sum of electronic and zero-point Energies= -234.469203

Sum of electronic and thermal Energies= -234.461857

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500777

===Optimizing boat + Chair===

The transition state structure was first caclulated without the fixed coordinates and as expected one imaginary frequency was observed at -818.0cm<sup>-1</sup>.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

When the frozen coordinate method is used and the bonds that are breaking/forming are fixed at 2.2, 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 2.2A.

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

Rep:Mod:maxk2

2009-11-13T16:37:44Z

Mk507: /* Module 3 */

=Computational Labs=

==Module 3==

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

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 -231.688. 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, -231.69254, this also backed up the theory.

When this structure was optimized with a higher B3LYP basis set it was found that the bond lengths in the molecule got closer to literature values <sup>1</sup>.

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

When the frequency was calculated of the anti 2 molecule, it was found to have no imaginary frequencies and the thermodynamic data was as follows

Sum of electronic and zero-point Energies= -234.469203

Sum of electronic and thermal Energies= -234.461857

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500777

===Optimizing boat + Chair===

The transition state structure was first caclulated without the fixed coordinates and as expected one imaginary frequency was observed at -818.0cm<sup>-1</sup>.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

When the frozen coordinate method is used and the bonds that are breaking/forming are fixed at 2.2, 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

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

Rep:Mod:maxk2

2009-11-13T16:33:40Z

Mk507: /* Optimizing boat + Chair */

=Computational Labs=

==Module 3==

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

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 -231.688. 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, -231.69254, this also backed up the theory.

When this structure was optimized with a higher B3LYP basis set it was found that the bond lengths in the molecule got closer to literature values <sup>1</sup>.

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

When the frequency was calculated of the anti 2 molecule, it was found to have no imaginary frequencies and the thermodynamic data was as follows

Sum of electronic and zero-point Energies= -234.469203

Sum of electronic and thermal Energies= -234.461857

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500777

===Optimizing boat + Chair===

The transition state structure was first caclulated without the fixed coordinates and as expected one imaginary frequency was observed at -818.0cm<sup>-1</sup>.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

When the frozen coordinate method is used and the bonds that are breaking/forming are fixed at 2.2,

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

Rep:Mod:maxk2

2009-11-13T16:24:32Z

Mk507: /* Computational Labs */

=Computational Labs=

==Module 3==

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

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 -231.688. 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, -231.69254, this also backed up the theory.

When this structure was optimized with a higher B3LYP basis set it was found that the bond lengths in the molecule got closer to literature values <sup>1</sup>.

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

When the frequency was calculated of the anti 2 molecule, it was found to have no imaginary frequencies and the thermodynamic data was as follows

Sum of electronic and zero-point Energies= -234.469203

Sum of electronic and thermal Energies= -234.461857

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500777

===Optimizing boat + Chair===

The transition state structure was first caclulated without the fixed coordinates and as expected one imaginary frequency was observed at -818.0cm<sup>-1</sup>.
[[Image:Cope rearrangment vibration chair.jpg|thumb|The illustration of the imaginary vibration corresponding to the cope rearrangment]]

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

File:Cope rearrangment vibration chair.jpg

2009-11-13T16:23:11Z

Mk507: The illistration of the imaginary vibration corresponding to the cope rearrangment

The illistration of the imaginary vibration corresponding to the cope rearrangment

Rep:Mod:maxk2

2009-11-13T16:21:38Z

Mk507: /* Optimizing boat + Chair */

=Computational Labs=

==Module 3==

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

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 -231.688. 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, -231.69254, this also backed up the theory.

When this structure was optimized with a higher B3LYP basis set it was found that the bond lengths in the molecule got closer to literature values <sup>1</sup>.

[[Image:Cope-anti2-opt-dft.jpg|thumb|The optimized anti 2 molecule]]

When the frequency was calculated of the anti 2 molecule, it was found to have no imaginary frequencies and the thermodynamic data was as follows

Sum of electronic and zero-point Energies= -234.469203

Sum of electronic and thermal Energies= -234.461857

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500777

===Optimizing boat + Chair===

The transition state structure was first caclulated without the fixed coordinates and as expected one imaginary frequency was observed at -818.0cm<sup>-1</sup>.

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

Rep:Mod:maxk2

2009-11-13T16:05:40Z

Mk507: /* Module 3 */

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Mk507: /* Module 3 */

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Mk507: /* Module 3 */

File:Cope-anti2-opt-dft.jpg

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Mk507:

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Mk507: /* Module 3 */

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Mk507: /* Module 3 */

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Mk507: /* Module 3 */

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2009-11-13T09:59:31Z

Mk507: /* Module 3 */

=Computational Labs=

==Module 3==

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

The second gauche structure was gauche 1 with a D2

Rep:Mod:maxk2

2009-11-13T09:57:04Z

Mk507: /* Module 3 */

=Computational Labs=

==Module 3==

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

Rep:Mod:maxk2

2009-11-13T09:42:03Z

Mk507: New page: =Computational Labs= ==Module 3==

=Computational Labs=

==Module 3==

Rep:Mod:maxk1

2009-11-05T23:22:29Z

Mk507: /* MiniProject */

= Module 1 =

== Part 1 ==

=== Cyclopentadiene ===

<u>Cyclopentadiene dimer 1
</u>

<jmol><jmolApplet><title>Maxkindred1.1.1</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>Maxkindred1.1.1.mol</uploadedFileContents>
</jmolApplet></jmol>

Torsion: 7.6718

Total Energy: 31.8834 kcal/mol

<u>Cyclopentadiene dimer 2
</u>

<jmol><jmolApplet><title>Maxkindred1.1.2</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>Maxkindred1.1.2.mol</uploadedFileContents>
</jmolApplet></jmol>

Torsion: 9.5157

Total Energy: 34.0071 kcal/mol

The relative torsion strain and total energies of thesee two molecules awould suggest that the first dimer is the more thermodynamically stable product. This would suggest that the dimer created in the synthesis, was created under kinetic conditions as is quite often the case with diels-alder reactions. The kinetic form is the one created due the stability of the transition state, as the kinetic t.s. is the less sterically hindered form.

<u>Cyclopentadiene dimer 3
</u>

<jmol><jmolApplet><title>Maxkindred1.1.3</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>Maxkindred1.1.3.mol</uploadedFileContents>
</jmolApplet></jmol>

Stretch: 1.2382

Bend: 18.9595

Torsion: 12.1018

Non-1,4 VDW: -1.4892

1,4 VDW: 5.7264

Total Energy: 35.6908 kcal/mol

<u>Cyclopentadiene dimer 4</u>

<jmol><jmolApplet><title>1.1.4</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>1.1.4.mol</uploadedFileContents>
</jmolApplet></jmol>

Stretch: 1.0896

Bend: 14.5179

Torsion: 12.5142

Non-1,4 VDW: -1.0490

1,4 VDW: 4.5010

Total Energy: 31.1718 kcal/mol

The overall energy of the 2 isomers suable product suggests that the dihydro derivative 4 is the more thermodynamically stable product as the double bond on the bridged 5 membered ring is more sterically hindered and therefore atttack here gives a more stable product. This is backed up by the other relative properties, the relative stretch, bend and VDW energies are significantly larger for the less stable derivative, dimer 3. The torsion values are very similar for both and the H-bonding is negligible as there are no electronegative atoms with lone pairs for any Hydrogen bonding to occur.

===Nucleophilic addition to a Pyridinum Ring===

If the MeMgI is inlcuded in the energy minimization for molecule 5 chem bio 3d produces an error file because the program does not understand bonding involving Mg atoms.

<u>Molecule 5</u>

<jmol><jmolApplet><title>Max1.1.5</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>Max1.1.5.mol</uploadedFileContents>
</jmolApplet></jmol>

Stretch: 2.2344

Bend: 14.1252

Stretch-Bend: 0.1325

Torsion: 5.0714

Non-1,4 VDW: -0.5186

1,4 VDW: 16.5496

Total Energy: 48.1377 kcal/mol

As can be seen from the rotating Jmol the carbonyl Oxygen is slightly above (8.5 degrees) the plane of the pyridinium ring and thefore when the incoming Organometallic reactant chelates to this carbonyl group it directs the methyl substituent onto the same face as the oxygen (the top face) at the 4 postion via the mechanism below.

[[Image:Maxkindred1.1.5.gif|thumb|The mechanism for the creation of molecule 6 from molecule 5]]

<jmol><jmolApplet><title>Max1.1.5wrong</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>Max1.1.5wrong.mol</uploadedFileContents>
</jmolApplet></jmol>

Stretch: 3.8490

Bend: 112.1884

Stretch-Bend: -0.2596

Torsion: 27.6170

Non-1,4 VDW: 0.9602

1,4 VDW: 29.8703

Charge/Dipole: -12.9192

Dipole/Dipole: -3.5802

Total Energy: 157.7258 kcal/mol

This is the only other place where the carbonyl will not revert to the position in the first example upon energy minimization but this conformation immediately sets off alarm bells due to the angles present on the bonds in the carbonyl group. This molecule can easily be drawn in 2d but upon minimization the energy and the bend values are extremely high so this molecule is unrealistic.

<u>Molecule 6</u>

Stretch: 2.2405

Bend: 16.2891

Stretch-Bend: 0.3305

Torsion: 5.6543

Non-1,4 VDW: -0.1921

1,4 VDW: 17.4977

Total Energy: 37.4646 kcal/mol

<u>
Molecule 7</u>

<jmol><jmolApplet><title>1.1.7</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>1.1.7.mol</uploadedFileContents>
</jmolApplet></jmol>

Stretch: 4.0850

Bend: 12.8146

Stretch-Bend: 0.4547

Torsion: 12.1794

Non-1,4 VDW: 4.7597

1,4 VDW: 29.1029

Total Energy: 72.1348 kcal/mol

In this molecule the carbonyl group is 25 degrees above the plain of the ring, directing the incoming reactant to the top face of the molecule (machanism)

===Taxol===

<u>Molecule 10</u>

<jmol><jmolApplet><title>Max1.1.10</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>Max1.1.10.mol</uploadedFileContents>
</jmolApplet></jmol>

Stretch: 2.4608

Bend: 10.8267

Stretch-Bend: 0.3010

Torsion: 17.3617

Non-1,4 VDW: -1.5920

1,4 VDW: 12.3564

Dipole/Dipole: 0.1438

Total Energy: 41.8583 kcal/mol

<u>Molecule 11</u>

<jmol><jmolApplet><title>Max1.1.11</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>Max1.1.11.mol</uploadedFileContents>
</jmolApplet></jmol>

Stretch: 2.5628

Bend: 10.7438

Stretch-Bend: 0.3335

Torsion: 19.7397

Non-1,4 VDW: -1.4427

1,4 VDW: 12.5436

Dipole/Dipole: -0.1785

Total Energy: 44.3022 kcal/mol

As can be seen from relative energies of these two molecules, molecule 10 is the more stable isomer, with the carbonyl group pointing up. This isomer has much less steric hinderance sorrounding the oxygen from the cyclohexane ring and the pentane ring.

[[Image:Comp labs mol 11.gif|thumb|The depiction of the H=bond in molecule 10]]The above does however mean that the carbonyl is further away from the double bond so may reduce the hinderance to attack from electrophiles, also when the carbonyl group is up there is the possibility of H-bonding across the molecule to the Hydrogen on the double bond making that double bond less reactive, see diagram. Due to these ovbservations the double bond on molecule 11 is thought would be more reactive.

The double-bond in large ringed structures like taxol can be "hyperstable" as the double bond has a bond angle of 120 degrees compared to 109 for a saturated carbon which allows the molecule to adopt a conformation for which if it were a single bond would have too high strain. <2>

Both these molecules above contained the cyclohexane ring in the chair formation, the twist-boat formation was also isolated for both, molecule 10 (twist-boat) had Total Energy: 54.1108 kcal/mol, molecule 11 (twist-boat) had Total Energy: 48.1586 kcal/mol. Neither boat form could be isolated.

[[Image:max1.1.10tb.jpg|thumb|left|The depiction of the twist-boat form of molecule 10]]

[[Image:max1.1.11tb.jpg|thumb|centre|The depiction of the twist-boat form of molecule 11]]

==Modelling Using Semi-empirical Molecular Orbital Theory.==

The molecule was found to have two flat rings and and the Cl above one double bond and its opposite hydrogen above the other. The homo of molecule 12 does diferentiate between the 2 double bonds, showing electron density on the Carbon-carbon double bond syn to he Cl molecule meaning that this bond would be more susceptible to any electrophilic attack on the molecule making that doube bond more nucleophilic.

The diene and the alkene derivative both only have one major C-Cl stretch, which occur at 770.89 and 775.15 cm<sup>-1</sup> and have an intensity of 25.1 and 19.9 respectively.
The major C=C stretch for the mono alkene derivative comes at 1758cm<sup>-1</sup> and for the diene at Normal 0 false false false EN-GB X-NONE X-NONE 1737.13, 1757.37cm<sup>-1</sup> with similar frequencies.

==References==
P. Camps, X. Pujol, S Vazquez, M. A. Pericas, C Puigjaner and L. Sola, Tetrahedron, 2001, 57, 8511

=Module 2=

the energy will have an error of ≈ 10 kJ/mol, so how much is this in atomic units (which are hartree)?
the dipole moment will be accurate to about 2 decimal places, ie 0.01 Deby.
frequencies in wavenumbers are by convention reported with no decimal places and for the purposes of this course you need to know that the accuracy is only to around 10cm-1 (the situtation is actually more complex, and is covered in my fourth year course "Computational Inorganic Chemistry")
intensities are rounded to the nearest whole integer and in fact the accuracy is much less that this, but this is convention
bond distances are accurate to ≈ 0.01 Å
bond angles are accurate to ≈ 0.1

===BH3===
The bond lengths for BH3 are all equal after optimisation at 1.19A and all the HBH angles being 120 degrees.
The NBO analysis shows each Hydrogen carrying -0.111 charge each and the Boron being +0.332 showing that the boron is electropositive as has been shown by its chemical (lewis acidic) properties.

===BCl3===

THe method used to optimise the BCl3 molecule was DFT and the basis set used was LANL2MB

Both calculations??

The reason we have to carry out a frequency analysis of the molecule is to make sure that the position of zero gradient found by the optimisation is in fact the minimum energy rather than the maximum energy. The analysis carries out a second derivative calculation to determine this.

The BCl3 bond length is 1.87A and the bond angle is 120 degrees.

Gaussview does not draw certain bonds in certain molecules as gaussview has been programmed to recognise bonds only up to a certain length, which is roughly around the size of a C-C bond, anything significantly longer than that e.g Metal – Phosphorus bonds , does not compute as a bond. This however does not represent a huge problem as the presence of a bond is for our purpose only and does not affect any calculations if it is there or not.

A bond is a region where there is a favourable overlap between 2 or more aligned orbitals (whether they be s, p or d) on adjacent molecules. The orbitals must be populated and the population of these orbital must lower the overall energy of the molecule for the bond to form.

The symmetry you expect to see in the ground state configuration is d3h, the same as the one you see from your Gaussian optimisation. This is interesting, as you would expect upon optimisation, the symmetry of the molecule to change to a trigonal pyramidal molecular geometry and tetrahedral electronic geometry with the B empty p orbital going up above the molecule. This form is lower in energy than the trigonal planar molecule.
Gaussian does not allow the molecule to adopt this formation as it doesn’t allow itself to break the symmetry of the molecule.

All these calculations are rather simple and can be conducted on the Chemistry Laptops and each take less than a minute.

Below is a MO diagram for BH3, containing the LCAO's made up of combined atomic orbitals, and the orbitals created by Gaussian. The orbitals created by Gaussian look slightly different to the LCAO's, the nodes are still in the same place but all positive overlap appears as one block of electron density.

[[Image:MkindredBH3 mo diagram.gif|thumb|The BH3 mo diagram]]

=Isomers of Mo(CO)4L2=

{| class="wikitable" border="1"
|+ Comparing literature bond lengths to gaussian results.
! Lit vs model !! Lit !! Model(Trans)/A !! Model(Cis)/A !

|-
| C=O || 1.18 || 1.19 || 1.19 ||
|-
| Mo-C || 2.08 || 2.1 || 2.1 ||
|-
|Mo-P || || 2.4 || 2.5 ||
|-
| P-Cl || 2.04 (non-metal bonded|| 2.4 || 2.4 ||
|}

The cis isomer is slightly higher in energy than the trans one (although its probably outside the accuracy of this method) due to the extra steric strain caused by the proximity of the larger PCl3 groups to each other. The E difference is .003 a.u .

Changing the size of the R groups on the PR groups will change the ratio of cis/trans isomer found as the reduction/increase of sterics in the cis form, e.g. changing R group to Ph would greatly increase the energy of the cis isomer as Ph is a much larger group than Cl.

There are no vibrations of a very low energy in the trans isomer, the cis isomer has 2 low energy vibrations at -2 and 12, when a vibration is this low in energy , this means there is a very low energy vibration for this vibration to occur. Therefore at room temperature this vibration will occur very rapidly.

Carbonyl stretches (cis) cm-1

Intensity

1808.87

1306.71

Unsymetric

1809.01

1297.17

Unsymetric (opposite to 1808.87)

1831.78

1.99

Symmettric

1881.57

0.06

Totally symmetric

This table shows that in reality there are only 2 viable unsymmetrical carbonyl stretches, but the fact the other two vibrations are present suggest that the molecule is not completely symmetrical because if it was these vibration would have an intensity of 0.

Carbonyl stretches (trans) cm-1

Intensity

1805.17

1161.96

1806.21

748.16

1815.05

621.53

1872.85

695.53

All these vibrations change the overall dipole moment of the molecule and therefore all have large intensities, these are the number of C=O shifts we would expect to see for each molecule, due to their different symmetries.

=MiniProject=

For my mini-project i have chosen to study the catalytic cycle of hydroformylation, in particular using the starting catalyst, HRh(Co)(PPh)3. However in order to speed up calculations Cl was used in place of the Ph groups.

The cycle would be studied in 3 different places marked 1, 2 and 3 on the picture below, representing the start of the cycle, where the substrate adds on and where the substrate is eliminated. The Mo’s for these three intermediates will be studied as will there charge distribution and CO vibrational frequencies to see how these change through the cycle.

The series will them be expanded to take in a series of metals from the same group as Rh and the charges, bond lengths and relative energies compared with that of the Rh complexes in order to try to ascertain why Rh is the best metal for this catalytic cycle.

<u>The MO for molecule 1</u>

The homo shows a bonding interaction between the Rh and the CO, a non-bonding interaction between the Rh and the H and a anti-bonding interaction between the Rh and the PCl3 groups.

The lumo shows similar carachteristics, from this it can be shown that upon substitution reactions, if an associative mechanism were used, if the Lumo was filled there would be a weakening of the PCl3 bonds and a strengthening of the CO bonds. If a dissociative mechanism were used the PCl3 has the weakest interaction at HOMO level so would be the most likely to leave. This explains why it is a PCl3 group that leaves when the alkene substitutes in rather than a CO group.

The homo-1 shows a bonding interaction between the metal and one P group and a small bonding interaction with both CO groups.

The homo-2 shows a strong bonding interaction with the CO groups and non-bonding interactions with the PCl3 groups.

The lumo +1 shows a bonding interaction between the metal and the Co and Pcl3 groups but a nonbonding interation between the metal and the H aswell as non-bonding interactions between the C and the O and the P and the Cl

The lumo +2 is non-bonding with respects to the metal and will therefore not be looked at in detail.

The IR spectras shows 2 CO stretch vibrations at

Rep:Mod:maxk1

2009-11-05T23:05:48Z

Mk507: /* Isomers of Mo(CO)4L2 */

Rep:Mod:maxk1

2009-11-05T23:02:07Z

Mk507: /* Isomers of Mo(CO)4L2 */

= Module 1 =

== Part 1 ==

=== Cyclopentadiene ===

<u>Cyclopentadiene dimer 1
</u>

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<uploadedFileContents>Maxkindred1.1.1.mol</uploadedFileContents>
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Torsion: 7.6718

Total Energy: 31.8834 kcal/mol

<u>Cyclopentadiene dimer 2
</u>

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Torsion: 9.5157

Total Energy: 34.0071 kcal/mol

The relative torsion strain and total energies of thesee two molecules awould suggest that the first dimer is the more thermodynamically stable product. This would suggest that the dimer created in the synthesis, was created under kinetic conditions as is quite often the case with diels-alder reactions. The kinetic form is the one created due the stability of the transition state, as the kinetic t.s. is the less sterically hindered form.

<u>Cyclopentadiene dimer 3
</u>

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Stretch: 1.2382

Bend: 18.9595

Torsion: 12.1018

Non-1,4 VDW: -1.4892

1,4 VDW: 5.7264

Total Energy: 35.6908 kcal/mol

<u>Cyclopentadiene dimer 4</u>

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Stretch: 1.0896

Bend: 14.5179

Torsion: 12.5142

Non-1,4 VDW: -1.0490

1,4 VDW: 4.5010

Total Energy: 31.1718 kcal/mol

The overall energy of the 2 isomers suable product suggests that the dihydro derivative 4 is the more thermodynamically stable product as the double bond on the bridged 5 membered ring is more sterically hindered and therefore atttack here gives a more stable product. This is backed up by the other relative properties, the relative stretch, bend and VDW energies are significantly larger for the less stable derivative, dimer 3. The torsion values are very similar for both and the H-bonding is negligible as there are no electronegative atoms with lone pairs for any Hydrogen bonding to occur.

===Nucleophilic addition to a Pyridinum Ring===

If the MeMgI is inlcuded in the energy minimization for molecule 5 chem bio 3d produces an error file because the program does not understand bonding involving Mg atoms.

<u>Molecule 5</u>

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Stretch: 2.2344

Bend: 14.1252

Stretch-Bend: 0.1325

Torsion: 5.0714

Non-1,4 VDW: -0.5186

1,4 VDW: 16.5496

Total Energy: 48.1377 kcal/mol

As can be seen from the rotating Jmol the carbonyl Oxygen is slightly above (8.5 degrees) the plane of the pyridinium ring and thefore when the incoming Organometallic reactant chelates to this carbonyl group it directs the methyl substituent onto the same face as the oxygen (the top face) at the 4 postion via the mechanism below.

[[Image:Maxkindred1.1.5.gif|thumb|The mechanism for the creation of molecule 6 from molecule 5]]

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<uploadedFileContents>Max1.1.5wrong.mol</uploadedFileContents>
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Stretch: 3.8490

Bend: 112.1884

Stretch-Bend: -0.2596

Torsion: 27.6170

Non-1,4 VDW: 0.9602

1,4 VDW: 29.8703

Charge/Dipole: -12.9192

Dipole/Dipole: -3.5802

Total Energy: 157.7258 kcal/mol

This is the only other place where the carbonyl will not revert to the position in the first example upon energy minimization but this conformation immediately sets off alarm bells due to the angles present on the bonds in the carbonyl group. This molecule can easily be drawn in 2d but upon minimization the energy and the bend values are extremely high so this molecule is unrealistic.

<u>Molecule 6</u>

Stretch: 2.2405

Bend: 16.2891

Stretch-Bend: 0.3305

Torsion: 5.6543

Non-1,4 VDW: -0.1921

1,4 VDW: 17.4977

Total Energy: 37.4646 kcal/mol

<u>
Molecule 7</u>

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<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>1.1.7.mol</uploadedFileContents>
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Stretch: 4.0850

Bend: 12.8146

Stretch-Bend: 0.4547

Torsion: 12.1794

Non-1,4 VDW: 4.7597

1,4 VDW: 29.1029

Total Energy: 72.1348 kcal/mol

In this molecule the carbonyl group is 25 degrees above the plain of the ring, directing the incoming reactant to the top face of the molecule (machanism)

===Taxol===

<u>Molecule 10</u>

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Stretch: 2.4608

Bend: 10.8267

Stretch-Bend: 0.3010

Torsion: 17.3617

Non-1,4 VDW: -1.5920

1,4 VDW: 12.3564

Dipole/Dipole: 0.1438

Total Energy: 41.8583 kcal/mol

<u>Molecule 11</u>

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Stretch: 2.5628

Bend: 10.7438

Stretch-Bend: 0.3335

Torsion: 19.7397

Non-1,4 VDW: -1.4427

1,4 VDW: 12.5436

Dipole/Dipole: -0.1785

Total Energy: 44.3022 kcal/mol

As can be seen from relative energies of these two molecules, molecule 10 is the more stable isomer, with the carbonyl group pointing up. This isomer has much less steric hinderance sorrounding the oxygen from the cyclohexane ring and the pentane ring.

[[Image:Comp labs mol 11.gif|thumb|The depiction of the H=bond in molecule 10]]The above does however mean that the carbonyl is further away from the double bond so may reduce the hinderance to attack from electrophiles, also when the carbonyl group is up there is the possibility of H-bonding across the molecule to the Hydrogen on the double bond making that double bond less reactive, see diagram. Due to these ovbservations the double bond on molecule 11 is thought would be more reactive.

The double-bond in large ringed structures like taxol can be "hyperstable" as the double bond has a bond angle of 120 degrees compared to 109 for a saturated carbon which allows the molecule to adopt a conformation for which if it were a single bond would have too high strain. <2>

Both these molecules above contained the cyclohexane ring in the chair formation, the twist-boat formation was also isolated for both, molecule 10 (twist-boat) had Total Energy: 54.1108 kcal/mol, molecule 11 (twist-boat) had Total Energy: 48.1586 kcal/mol. Neither boat form could be isolated.

[[Image:max1.1.10tb.jpg|thumb|left|The depiction of the twist-boat form of molecule 10]]

[[Image:max1.1.11tb.jpg|thumb|centre|The depiction of the twist-boat form of molecule 11]]

==Modelling Using Semi-empirical Molecular Orbital Theory.==

The molecule was found to have two flat rings and and the Cl above one double bond and its opposite hydrogen above the other. The homo of molecule 12 does diferentiate between the 2 double bonds, showing electron density on the Carbon-carbon double bond syn to he Cl molecule meaning that this bond would be more susceptible to any electrophilic attack on the molecule making that doube bond more nucleophilic.

The diene and the alkene derivative both only have one major C-Cl stretch, which occur at 770.89 and 775.15 cm<sup>-1</sup> and have an intensity of 25.1 and 19.9 respectively.
The major C=C stretch for the mono alkene derivative comes at 1758cm<sup>-1</sup> and for the diene at Normal 0 false false false EN-GB X-NONE X-NONE 1737.13, 1757.37cm<sup>-1</sup> with similar frequencies.

==References==
P. Camps, X. Pujol, S Vazquez, M. A. Pericas, C Puigjaner and L. Sola, Tetrahedron, 2001, 57, 8511

=Module 2=

the energy will have an error of ≈ 10 kJ/mol, so how much is this in atomic units (which are hartree)?
the dipole moment will be accurate to about 2 decimal places, ie 0.01 Deby.
frequencies in wavenumbers are by convention reported with no decimal places and for the purposes of this course you need to know that the accuracy is only to around 10cm-1 (the situtation is actually more complex, and is covered in my fourth year course "Computational Inorganic Chemistry")
intensities are rounded to the nearest whole integer and in fact the accuracy is much less that this, but this is convention
bond distances are accurate to ≈ 0.01 Å
bond angles are accurate to ≈ 0.1

===BH3===
The bond lengths for BH3 are all equal after optimisation at 1.19A and all the HBH angles being 120 degrees.
The NBO analysis shows each Hydrogen carrying -0.111 charge each and the Boron being +0.332 showing that the boron is electropositive as has been shown by its chemical (lewis acidic) properties.

===BCl3===

THe method used to optimise the BCl3 molecule was DFT and the basis set used was LANL2MB

Both calculations??

The reason we have to carry out a frequency analysis of the molecule is to make sure that the position of zero gradient found by the optimisation is in fact the minimum energy rather than the maximum energy. The analysis carries out a second derivative calculation to determine this.

The BCl3 bond length is 1.87A and the bond angle is 120 degrees.

Gaussview does not draw certain bonds in certain molecules as gaussview has been programmed to recognise bonds only up to a certain length, which is roughly around the size of a C-C bond, anything significantly longer than that e.g Metal – Phosphorus bonds , does not compute as a bond. This however does not represent a huge problem as the presence of a bond is for our purpose only and does not affect any calculations if it is there or not.

A bond is a region where there is a favourable overlap between 2 or more aligned orbitals (whether they be s, p or d) on adjacent molecules. The orbitals must be populated and the population of these orbital must lower the overall energy of the molecule for the bond to form.

The symmetry you expect to see in the ground state configuration is d3h, the same as the one you see from your Gaussian optimisation. This is interesting, as you would expect upon optimisation, the symmetry of the molecule to change to a trigonal pyramidal molecular geometry and tetrahedral electronic geometry with the B empty p orbital going up above the molecule. This form is lower in energy than the trigonal planar molecule.
Gaussian does not allow the molecule to adopt this formation as it doesn’t allow itself to break the symmetry of the molecule.

All these calculations are rather simple and can be conducted on the Chemistry Laptops and each take less than a minute.

Below is a MO diagram for BH3, containing the LCAO's made up of combined atomic orbitals, and the orbitals created by Gaussian. The orbitals created by Gaussian look slightly different to the LCAO's, the nodes are still in the same place but all positive overlap appears as one block of electron density.

[[Image:MkindredBH3 mo diagram.gif|thumb|The BH3 mo diagram]]

=Isomers of Mo(CO)4L2=

{| class="wikitable" border="1"
|+ Comparing literature bond lengths to gaussian results.
! Lit vs model !! Lit !! Model(Trans)/A !! Model(Cis)/A !

|-
| C=O || 1.18 || 1.19 || 1.19 ||
|-
| Mo-C || 2.08 || 2.1 || 2.1 ||
|-
|Mo-P || || 2.4 || 2.5 ||
|-
| P-Cl || || 2.4 || 2.4 ||
|}

The cis isomer is slightly higher in energy than the trans one (although its probably outside the accuracy of this method) due to the extra steric strain caused by the proximity of the larger PCl3 groups to each other. The E difference is .003 a.u .

Changing the size of the R groups on the PR groups will change the ratio of cis/trans isomer found as the reduction/increase of sterics in the cis form, e.g. changing R group to Ph would greatly increase the energy of the cis isomer as Ph is a much larger group than Cl.

There are no vibrations of a very low energy in the trans isomer, the cis isomer has 2 low energy vibrations at -2 and 12, when a vibration is this low in energy , this means there is a very low energy vibration for this vibration to occur. Therefore at room temperature this vibration will occur very rapidly.

Carbonyl stretches (cis) cm-1

Intensity

1808.87

1306.71

Unsymetric

1809.01

1297.17

Unsymetric (opposite to 1808.87)

1831.78

1.99

Symmettric

1881.57

0.06

Totally symmetric

This table shows that in reality there are only 2 viable unsymmetrical carbonyl stretches, but the fact the other two vibrations are present suggest that the molecule is not completely symmetrical because if it was these vibration would have an intensity of 0.

Carbonyl stretches (trans) cm-1

Intensity

1805.17

1161.96

1806.21

748.16

1815.05

621.53

1872.85

695.53

All these vibrations change the overall dipole moment of the molecule and therefore all have large intensities, these are the number of C=O shifts we would expect to see for each molecule, due to their different symmetries.

=MiniProject=

For my mini-project i have chosen to study the catalytic cycle of hydroformylation, in particular using the starting catalyst, HRh(Co)(PPh)3. However in order to speed up calculations Cl was used in place of the Ph groups.

The cycle would be studied in 3 different places marked 1, 2 and 3 on the picture below, representing the start of the cycle, where the substrate adds on and where the substrate is eliminated. The Mo’s for these three intermediates will be studied as will there charge distribution and CO vibrational frequencies to see how these change through the cycle.

The series will them be expanded to take in a series of metals from the same group as Rh and the charges, bond lengths and relative energies compared with that of the Rh complexes in order to try to ascertain why Rh is the best metal for this catalytic cycle.

<u>The MO for molecule 1</u>

The homo shows a bonding interaction between the Rh and the CO, a non-bonding interaction between the Rh and the H and a anti-bonding interaction between the Rh and the PCl3 groups.

The lumo shows similar carachteristics, from this it can be shown that upon substitution reactions, if an associative mechanism were used, if the Lumo was filled there would be a weakening of the PCl3 bonds and a strengthening of the CO bonds. If a dissociative mechanism were used the PCl3 has the weakest interaction at HOMO level so would be the most likely to leave. This explains why it is a PCl3 group that leaves when the alkene substitutes in rather than a CO group.

The homo-1 shows a bonding interaction between the metal and one P group and a small bonding interaction with both CO groups.

The homo-2 shows a strong bonding interaction with the CO groups and non-bonding interactions with the PCl3 groups.

The lumo +1 shows a bonding interaction between the metal and the Co and Pcl3 groups but a nonbonding interation between the metal and the H aswell as non-bonding interactions between the C and the O and the P and the Cl

The lumo +2 is non-bonding with respects to the metal and will therefore not be looked at in detail.

The IR spectras shows 2 CO stretch vibrations at

Rep:Mod:maxk1

2009-11-05T22:34:54Z

Mk507: /* Isomers of Mo(CO)4L2 */

= Module 1 =

== Part 1 ==

=== Cyclopentadiene ===

<u>Cyclopentadiene dimer 1
</u>

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<uploadedFileContents>Maxkindred1.1.1.mol</uploadedFileContents>
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Torsion: 7.6718

Total Energy: 31.8834 kcal/mol

<u>Cyclopentadiene dimer 2
</u>

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Torsion: 9.5157

Total Energy: 34.0071 kcal/mol

The relative torsion strain and total energies of thesee two molecules awould suggest that the first dimer is the more thermodynamically stable product. This would suggest that the dimer created in the synthesis, was created under kinetic conditions as is quite often the case with diels-alder reactions. The kinetic form is the one created due the stability of the transition state, as the kinetic t.s. is the less sterically hindered form.

<u>Cyclopentadiene dimer 3
</u>

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Stretch: 1.2382

Bend: 18.9595

Torsion: 12.1018

Non-1,4 VDW: -1.4892

1,4 VDW: 5.7264

Total Energy: 35.6908 kcal/mol

<u>Cyclopentadiene dimer 4</u>

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Stretch: 1.0896

Bend: 14.5179

Torsion: 12.5142

Non-1,4 VDW: -1.0490

1,4 VDW: 4.5010

Total Energy: 31.1718 kcal/mol

The overall energy of the 2 isomers suable product suggests that the dihydro derivative 4 is the more thermodynamically stable product as the double bond on the bridged 5 membered ring is more sterically hindered and therefore atttack here gives a more stable product. This is backed up by the other relative properties, the relative stretch, bend and VDW energies are significantly larger for the less stable derivative, dimer 3. The torsion values are very similar for both and the H-bonding is negligible as there are no electronegative atoms with lone pairs for any Hydrogen bonding to occur.

===Nucleophilic addition to a Pyridinum Ring===

If the MeMgI is inlcuded in the energy minimization for molecule 5 chem bio 3d produces an error file because the program does not understand bonding involving Mg atoms.

<u>Molecule 5</u>

<jmol><jmolApplet><title>Max1.1.5</title><color>white</color>
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<uploadedFileContents>Max1.1.5.mol</uploadedFileContents>
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Stretch: 2.2344

Bend: 14.1252

Stretch-Bend: 0.1325

Torsion: 5.0714

Non-1,4 VDW: -0.5186

1,4 VDW: 16.5496

Total Energy: 48.1377 kcal/mol

As can be seen from the rotating Jmol the carbonyl Oxygen is slightly above (8.5 degrees) the plane of the pyridinium ring and thefore when the incoming Organometallic reactant chelates to this carbonyl group it directs the methyl substituent onto the same face as the oxygen (the top face) at the 4 postion via the mechanism below.

[[Image:Maxkindred1.1.5.gif|thumb|The mechanism for the creation of molecule 6 from molecule 5]]

<jmol><jmolApplet><title>Max1.1.5wrong</title><color>white</color>
<size>150</size><script>zoom 100; cpk -20;</script>
<uploadedFileContents>Max1.1.5wrong.mol</uploadedFileContents>
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Stretch: 3.8490

Bend: 112.1884

Stretch-Bend: -0.2596

Torsion: 27.6170

Non-1,4 VDW: 0.9602

1,4 VDW: 29.8703

Charge/Dipole: -12.9192

Dipole/Dipole: -3.5802

Total Energy: 157.7258 kcal/mol

This is the only other place where the carbonyl will not revert to the position in the first example upon energy minimization but this conformation immediately sets off alarm bells due to the angles present on the bonds in the carbonyl group. This molecule can easily be drawn in 2d but upon minimization the energy and the bend values are extremely high so this molecule is unrealistic.

<u>Molecule 6</u>

Stretch: 2.2405

Bend: 16.2891

Stretch-Bend: 0.3305

Torsion: 5.6543

Non-1,4 VDW: -0.1921

1,4 VDW: 17.4977

Total Energy: 37.4646 kcal/mol

<u>
Molecule 7</u>

<jmol><jmolApplet><title>1.1.7</title><color>white</color>
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Stretch: 4.0850

Bend: 12.8146

Stretch-Bend: 0.4547

Torsion: 12.1794

Non-1,4 VDW: 4.7597

1,4 VDW: 29.1029

Total Energy: 72.1348 kcal/mol

In this molecule the carbonyl group is 25 degrees above the plain of the ring, directing the incoming reactant to the top face of the molecule (machanism)

===Taxol===

<u>Molecule 10</u>

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Stretch: 2.4608

Bend: 10.8267

Stretch-Bend: 0.3010

Torsion: 17.3617

Non-1,4 VDW: -1.5920

1,4 VDW: 12.3564

Dipole/Dipole: 0.1438

Total Energy: 41.8583 kcal/mol

<u>Molecule 11</u>

<jmol><jmolApplet><title>Max1.1.11</title><color>white</color>
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Stretch: 2.5628

Bend: 10.7438

Stretch-Bend: 0.3335

Torsion: 19.7397

Non-1,4 VDW: -1.4427

1,4 VDW: 12.5436

Dipole/Dipole: -0.1785

Total Energy: 44.3022 kcal/mol

As can be seen from relative energies of these two molecules, molecule 10 is the more stable isomer, with the carbonyl group pointing up. This isomer has much less steric hinderance sorrounding the oxygen from the cyclohexane ring and the pentane ring.

[[Image:Comp labs mol 11.gif|thumb|The depiction of the H=bond in molecule 10]]The above does however mean that the carbonyl is further away from the double bond so may reduce the hinderance to attack from electrophiles, also when the carbonyl group is up there is the possibility of H-bonding across the molecule to the Hydrogen on the double bond making that double bond less reactive, see diagram. Due to these ovbservations the double bond on molecule 11 is thought would be more reactive.

The double-bond in large ringed structures like taxol can be "hyperstable" as the double bond has a bond angle of 120 degrees compared to 109 for a saturated carbon which allows the molecule to adopt a conformation for which if it were a single bond would have too high strain. <2>

Both these molecules above contained the cyclohexane ring in the chair formation, the twist-boat formation was also isolated for both, molecule 10 (twist-boat) had Total Energy: 54.1108 kcal/mol, molecule 11 (twist-boat) had Total Energy: 48.1586 kcal/mol. Neither boat form could be isolated.

[[Image:max1.1.10tb.jpg|thumb|left|The depiction of the twist-boat form of molecule 10]]

[[Image:max1.1.11tb.jpg|thumb|centre|The depiction of the twist-boat form of molecule 11]]

==Modelling Using Semi-empirical Molecular Orbital Theory.==

The molecule was found to have two flat rings and and the Cl above one double bond and its opposite hydrogen above the other. The homo of molecule 12 does diferentiate between the 2 double bonds, showing electron density on the Carbon-carbon double bond syn to he Cl molecule meaning that this bond would be more susceptible to any electrophilic attack on the molecule making that doube bond more nucleophilic.

The diene and the alkene derivative both only have one major C-Cl stretch, which occur at 770.89 and 775.15 cm<sup>-1</sup> and have an intensity of 25.1 and 19.9 respectively.
The major C=C stretch for the mono alkene derivative comes at 1758cm<sup>-1</sup> and for the diene at Normal 0 false false false EN-GB X-NONE X-NONE 1737.13, 1757.37cm<sup>-1</sup> with similar frequencies.

==References==
P. Camps, X. Pujol, S Vazquez, M. A. Pericas, C Puigjaner and L. Sola, Tetrahedron, 2001, 57, 8511

=Module 2=

the energy will have an error of ≈ 10 kJ/mol, so how much is this in atomic units (which are hartree)?
the dipole moment will be accurate to about 2 decimal places, ie 0.01 Deby.
frequencies in wavenumbers are by convention reported with no decimal places and for the purposes of this course you need to know that the accuracy is only to around 10cm-1 (the situtation is actually more complex, and is covered in my fourth year course "Computational Inorganic Chemistry")
intensities are rounded to the nearest whole integer and in fact the accuracy is much less that this, but this is convention
bond distances are accurate to ≈ 0.01 Å
bond angles are accurate to ≈ 0.1

===BH3===
The bond lengths for BH3 are all equal after optimisation at 1.19A and all the HBH angles being 120 degrees.
The NBO analysis shows each Hydrogen carrying -0.111 charge each and the Boron being +0.332 showing that the boron is electropositive as has been shown by its chemical (lewis acidic) properties.

===BCl3===

THe method used to optimise the BCl3 molecule was DFT and the basis set used was LANL2MB

Both calculations??

The reason we have to carry out a frequency analysis of the molecule is to make sure that the position of zero gradient found by the optimisation is in fact the minimum energy rather than the maximum energy. The analysis carries out a second derivative calculation to determine this.

The BCl3 bond length is 1.87A and the bond angle is 120 degrees.

Gaussview does not draw certain bonds in certain molecules as gaussview has been programmed to recognise bonds only up to a certain length, which is roughly around the size of a C-C bond, anything significantly longer than that e.g Metal – Phosphorus bonds , does not compute as a bond. This however does not represent a huge problem as the presence of a bond is for our purpose only and does not affect any calculations if it is there or not.

A bond is a region where there is a favourable overlap between 2 or more aligned orbitals (whether they be s, p or d) on adjacent molecules. The orbitals must be populated and the population of these orbital must lower the overall energy of the molecule for the bond to form.

The symmetry you expect to see in the ground state configuration is d3h, the same as the one you see from your Gaussian optimisation. This is interesting, as you would expect upon optimisation, the symmetry of the molecule to change to a trigonal pyramidal molecular geometry and tetrahedral electronic geometry with the B empty p orbital going up above the molecule. This form is lower in energy than the trigonal planar molecule.
Gaussian does not allow the molecule to adopt this formation as it doesn’t allow itself to break the symmetry of the molecule.

All these calculations are rather simple and can be conducted on the Chemistry Laptops and each take less than a minute.

Below is a MO diagram for BH3, containing the LCAO's made up of combined atomic orbitals, and the orbitals created by Gaussian. The orbitals created by Gaussian look slightly different to the LCAO's, the nodes are still in the same place but all positive overlap appears as one block of electron density.

[[Image:MkindredBH3 mo diagram.gif|thumb|The BH3 mo diagram]]

=Isomers of Mo(CO)4L2=

{| class="wikitable" border="1"
|+ Comparing literature bond lengths to gaussian results.
! Lit vs model !! Lit !! Model(Trans)/A !! Model(Cis)/A !

|-
| C=O || 1.18 || 1.19 || 1.19 ||
|-
| Mo-C || || 2.1 || 2.1 ||
|-
|Mo-P || || 2.4 || 2.5 ||
|-
| P-Cl || || 2.4 || 2.4 ||
|}

The cis isomer is slightly higher in energy than the trans one (although its probably outside the accuracy of this method) due to the extra steric strain caused by the proximity of the larger PCl3 groups to each other. The E difference is .003 a.u .

Changing the size of the R groups on the PR groups will change the ratio of cis/trans isomer found as the reduction/increase of sterics in the cis form, e.g. changing R group to Ph would greatly increase the energy of the cis isomer as Ph is a much larger group than Cl.

There are no vibrations of a very low energy in the trans isomer, the cis isomer has 2 low energy vibrations at -2 and 12, when a vibration is this low in energy , this means there is a very low energy vibration for this vibration to occur. Therefore at room temperature this vibration will occur very rapidly.

Carbonyl stretches (cis) cm-1

Intensity

1808.87

1306.71

Unsymetric

1809.01

1297.17

Unsymetric (opposite to 1808.87)

1831.78

1.99

Symmettric

1881.57

0.06

Totally symmetric

This table shows that in reality there are only 2 viable unsymmetrical carbonyl stretches, but the fact the other two vibrations are present suggest that the molecule is not completely symmetrical because if it was these vibration would have an intensity of 0.

Carbonyl stretches (trans) cm-1

Intensity

1805.17

1161.96

1806.21

748.16

1815.05

621.53

1872.85

695.53

All these vibrations change the overall dipole moment of the molecule and therefore all have large intensities, these are the number of C=O shifts we would expect to see for each molecule, due to their different symmetries.

=MiniProject=

For my mini-project i have chosen to study the catalytic cycle of hydroformylation, in particular using the starting catalyst, HRh(Co)(PPh)3. However in order to speed up calculations Cl was used in place of the Ph groups.

The cycle would be studied in 3 different places marked 1, 2 and 3 on the picture below, representing the start of the cycle, where the substrate adds on and where the substrate is eliminated. The Mo’s for these three intermediates will be studied as will there charge distribution and CO vibrational frequencies to see how these change through the cycle.

The series will them be expanded to take in a series of metals from the same group as Rh and the charges, bond lengths and relative energies compared with that of the Rh complexes in order to try to ascertain why Rh is the best metal for this catalytic cycle.

<u>The MO for molecule 1</u>

The homo shows a bonding interaction between the Rh and the CO, a non-bonding interaction between the Rh and the H and a anti-bonding interaction between the Rh and the PCl3 groups.

The lumo shows similar carachteristics, from this it can be shown that upon substitution reactions, if an associative mechanism were used, if the Lumo was filled there would be a weakening of the PCl3 bonds and a strengthening of the CO bonds. If a dissociative mechanism were used the PCl3 has the weakest interaction at HOMO level so would be the most likely to leave. This explains why it is a PCl3 group that leaves when the alkene substitutes in rather than a CO group.

The homo-1 shows a bonding interaction between the metal and one P group and a small bonding interaction with both CO groups.

The homo-2 shows a strong bonding interaction with the CO groups and non-bonding interactions with the PCl3 groups.

The lumo +1 shows a bonding interaction between the metal and the Co and Pcl3 groups but a nonbonding interation between the metal and the H aswell as non-bonding interactions between the C and the O and the P and the Cl

The lumo +2 is non-bonding with respects to the metal and will therefore not be looked at in detail.

The IR spectras shows 2 CO stretch vibrations at