ChemWiki - User contributions [en]

Rep:Mod:dmc4

2008-11-26T16:33:02Z

Jt706:

'''Physical Computational Chemistry'''
Module 3, Experiment 3
Cope rearrangement

# 1,5-hexadiene ‘anti’ structure:

[[Image:Hexa_anti.jpg]]

[[Image:Hexa_anti_a.jpg]]

I would expect the ‘gauche’ structure’s final energy to be higher than that of the ‘anti’ structure’s final energy because there is steric hindrance with regard to the bond angle between the 2 alkene bonds.

# 1,5-hexadiene ‘gauche’ structure:

[[Image:Hexa_gauche.jpg]]

[[Image:Hexa_gauche_a.jpg]]

{| class="prettytable"
| Structure
| Final Energy (Hartrees)

|-
| Anti
| -231.69260213

|-
| Gauche
| -231.69153035

|}

{| class="prettytable"
| Structure
| Point Group

|-
| Anti
| C2

|-
| Gauche
| C2

|}
Both molecules have a point group of C2. The results show that the anti has a more negative energy value, thus, the gauche conformation has a higher final energy value, which suggests that my prediction was correct. According to the appendix (1), I have optimised the molecules anti-1 and gauche-4.

# Lowest energy conformation of 1,5-hexadiene structure prediction:

[[Image:Hexa_low.jpg]]

# When compared to the structures in the appendix (1), my prediction looks similar to the anti-1 structure. The energies are similar but there are different point groups for each molecule, the predicted molecule has a C1 point group, whereas, the appendix molecule has a C2 point group.

[[Image:Hexa_comp.jpg]]

# Anti-2 conformation (Ci point group)

[[Image:Hexa_comp_2.jpg]]

{| class="prettytable"
| Structure
| Final Energy (Hartrees)

|-
| Anti-Ci (own)
| -231.69253530

|-
| Anti-Ci (appendix)
| -231.69254

|}
The molecule that I optimised is very similar to the one from the appendix. However, the point group is C1 as opposed to Ci. I tried rearranging the atoms in the molecule, but as you can see they look very similar, thus, I will continue to use the molecule shown in the picture as my Ci molecule.

# B3YLP/6-31G calculation:

[[Image:B3ylp.jpg]]

The geometry of the higher level calculation has not changed very much. However, there is a significant change in the final energy values as the new value is -231.6117040 Hartrees compared with the -231.69253530 Hartrees from the lower level calculation.

#

Sum of electronic and zero-point Energies= -234.469204

Sum of electronic and thermal Energies= -234.461858

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500776

Experimental energies

'''Summary of energies (in hartree) '''

{| class="prettytable"
|
| <center>'''HF/3-21G''' </center>
| <center>'''HF/3-21G''' </center>
| <center>'''HF/3-21G''' </center>
| <center>'''B3LYP/6-31G*''' </center>
| <center>'''B3LYP/6-31G*''' </center>
| <center>'''B3LYP/6-31G*''' </center>

|-
|
| <center>'''Electronic energy''' </center>
| <center>'''Sum of electronic and zero-point energies''' </center>
| <center>'''Sum of electronic and thermal energies''' </center>
| <center>'''Electronic energy''' </center>
| <center>'''Sum of electronic and zero-point energies''' </center>
| <center>'''Sum of electronic and thermal energies''' </center>

|-
|
|
| <center>'''at 0 K''' </center>
| <center>'''at 298.15 K''' </center>
|
| <center>'''at 0 K''' </center>
| <center>'''at 298.15 K''' </center>

|-
| '''Chair TS'''
| <center>-231.619322 </center>
| <center>-231.466705 </center>
| <center>-231.461346 </center>
| <center>-234.556983 </center>
| <center>-234.414919 </center>
| <center>-234.408998 </center>

|-
| '''Boat TS'''
| <center>-231.602802 </center>
| <center>-231.450929 </center>
| <center>-231.445300 </center>
| <center>-234.543093 </center>
| <center>-234.402340 </center>
| <center>-234.396006 </center>

|-
| '''Reactant anti2'''
| <center>-231.692535 </center>
| <center>-231.539539 </center>
| <center>-231.532566 </center>
| <center>-234.611710 </center>
| <center>-234.469203 </center>
| <center>-234.461856 </center>

'''Optimizing the "Chair" and "Boat" Transition Structures'''

[[Image:Chairboat.jpg]]

(a)-(d) On the left is the chair transition state that was optimised using the Berny optimisation. On the right is the chair transition state that was optimised using the frozen co-ordinate optimisation.

{| class="prettytable"
| Bond
| Chair TS (Berny) bond length (A)
| Chair TS (freeze) bond length (A)

|-
| Bond formation
| 2.02025
| 1.55082

|-
| Bond breaking
| 2.02027
| 4.39021

|}
As the table shows, the frozen co-ordinate optimisation has more realistic bond distances for the bond formation and bond breaking. The Berny optimisation has distances that are similar. This could suggest that the Berny optimisation would show the molecule before it entered the transition state and the frozen co-ordinate optimisation would show the molecule as it was about to leave the transition state.

(e) For some reason the boat calculation did not fail and the reason behind this I do not know. I had all the atoms numbered exactly the same as the wiki page (even the hydrogens) but the calculation did work. Whether this is relevant or not is not determinable.

[[Image:Worked.jpg]]

(f) I ran a minimum optimisation of the final point on the IRC.

Chair transition state: left = 3-21G level; right = 6-31G (d) level

[[Image:Opt1.jpg]]

[[Image:Opt2.jpg]]

This is the chair transition state optimised via the Berny optimisation technique.

As you can see from the energies, the 3-21G energy IRC optimisation has a very similar energy to the Berny optimisation (a difference of 0.00000001H). However, the 6-31G IRC optimisation shows quite a large energy difference to the Berny optimisation energy. This could suggest that the 6-31G IRC optimisation is closer to being the transition state of the molecule than the other optimisations. However, due to the inaccuracy of the optimisation choice, this might not be the minimum of the transition state and this just could be one of many minimums that are present in the reaction pathway.

# Boat transition state: left = 3-21G level; right = 6-31G (d) level

[[Image:Opt3.jpg]]

Chair transition state: left = 3-21G level; right = 6-31G (d) level

[[Image:Opt4.jpg]]

Both sets of transition states show that the 6-31G optimisation shows a more negative total energy value. Moreover, both the 3-21G optimisations and the 6-31G optimisations have energies that are close to each other.

{| class="prettytable"
| Transition state type
| Experimental activation energy (kcal/mol)
| 6-31G optimisation activation energy (kcal/mol)

|-
| Chair
| 33.5 ± 0.5
| 89.41804

|-
| Boat
| 44.7 ± 2.0
| 89.50550

|}
I used the zero point vibrational energy as the 6-31G optimisation activation energy. The table shows that the values between the experimental and computational activation energies are greatly different. This suggests that my computational transition states structures could have been incorrect.

Diels alder cycloaddition

Cis-butadiene HOMO:

[[Image:Cishomo.jpg]]

Symmetry with respect to plane = anti-symmetric.

Cis-butadiene LUMO:

[[Image:Cislumo.jpg]]

Symmetry with respect to plane = symmetric.

I attempted to create the transition state the same way that the boat transition state was created (the Q2TS calculation) but I got the structure below that could not show any MO’s, therefore, I had to create the transition state with the method used to create the chair transition state.

[[Image:Trans1.jpg]]

Transition state:

[[Image:Trans2.jpg]]

Transition state HOMO:

[[Image:Transhomo.jpg]]

Symmetry with respect to plane = symmetric.

Transition state LUMO:

[[Image:Translumo.jpg]]

Symmetry with respect to plane = anti-symmetric.

Geometry and bond lengths of partly formed C-C sigma bonds:

[[Image:Geo.jpg]]

Bond lengths of partly formed C-C sigma bonds: 4.14872A and 4.31774A.

The vibration that demonstrates the reaction pathway for the transition state is shown below:

[[Image:Vib.jpg]]

The bond formation seems to be asynchronus.

HOMO of transition structure:

[[Image:Homotrans.jpg]]

The HOMO at the transition state appears to be symmetric or “s”.

Exo maleic energy

[[Image:Exomale.jpg]]

Endo maleic energy

[[Image:Endomale.jpg]]

Exo maleic energy: -688.71418400H

Endo maleic energy: -688.64873554H

This shows that the exo configuration had more energy than the endo configuration, thus, less stable. This could be due to the strain from the two sections of the cyclic molecule that are close together, ie the parts that are pointing in the same direction.

The endo structure has the oxygen groups pointing in the opposite direction to the bridging carbons, whereas, the exo structure has both groups pointing the same way.

Ran out of time for the rest of the exercise.

Rep:Mod:dmc4

2008-11-26T16:29:39Z

Jt706:

'''Physical Computational Chemistry'''
Module 3, Experiment 3
Cope rearrangement

# 1,5-hexadiene ‘anti’ structure:

[[Image:Hexa_anti.jpg]]

[[Image:Hexa_anti_a.jpg]]

I would expect the ‘gauche’ structure’s final energy to be higher than that of the ‘anti’ structure’s final energy because there is steric hindrance with regard to the bond angle between the 2 alkene bonds.

# 1,5-hexadiene ‘gauche’ structure:

[[Image:Hexa_gauche.jpg]]

[[Image:Hexa_gauche_a.jpg]]

{| class="prettytable"
| Structure
| Final Energy (Hartrees)

|-
| Anti
| -231.69260213

|-
| Gauche
| -231.69153035

|}

{| class="prettytable"
| Structure
| Point Group

|-
| Anti
| C2

|-
| Gauche
| C2

|}
Both molecules have a point group of C2. The results show that the anti has a more negative energy value, thus, the gauche conformation has a higher final energy value, which suggests that my prediction was correct. According to the appendix (1), I have optimised the molecules anti-1 and gauche-4.

# Lowest energy conformation of 1,5-hexadiene structure prediction:

[[Image:Hexa_low.jpg]]

# When compared to the structures in the appendix (1), my prediction looks similar to the anti-1 structure. The energies are similar but there are different point groups for each molecule, the predicted molecule has a C1 point group, whereas, the appendix molecule has a C2 point group.

[[Image:Hexa_comp.jpg]]

# Anti-2 conformation (Ci point group)

[[Image:Hexa_comp_2.jpg]]

{| class="prettytable"
| Structure
| Final Energy (Hartrees)

|-
| Anti-Ci (own)
| -231.69253530

|-
| Anti-Ci (appendix)
| -231.69254

|}
The molecule that I optimised is very similar to the one from the appendix. However, the point group is C1 as opposed to Ci. I tried rearranging the atoms in the molecule, but as you can see they look very similar, thus, I will continue to use the molecule shown in the picture as my Ci molecule.

# B3YLP/6-31G calculation:

[[Image:B3ylp.jpg]]

The geometry of the higher level calculation has not changed very much. However, there is a significant change in the final energy values as the new value is -231.6117040 Hartrees compared with the -231.69253530 Hartrees from the lower level calculation.

#

Sum of electronic and zero-point Energies= -234.469204

Sum of electronic and thermal Energies= -234.461858

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500776

Experimental energies

'''Summary of energies (in hartree) '''

{| class="prettytable"
|
| <center>'''HF/3-21G''' </center>
| <center>'''HF/3-21G''' </center>
| <center>'''HF/3-21G''' </center>
| <center>'''B3LYP/6-31G*''' </center>
| <center>'''B3LYP/6-31G*''' </center>
| <center>'''B3LYP/6-31G*''' </center>

|-
|
| <center>'''Electronic energy''' </center>
| <center>'''Sum of electronic and zero-point energies''' </center>
| <center>'''Sum of electronic and thermal energies''' </center>
| <center>'''Electronic energy''' </center>
| <center>'''Sum of electronic and zero-point energies''' </center>
| <center>'''Sum of electronic and thermal energies''' </center>

|-
|
|
| <center>'''at 0 K''' </center>
| <center>'''at 298.15 K''' </center>
|
| <center>'''at 0 K''' </center>
| <center>'''at 298.15 K''' </center>

|-
| '''Chair TS'''
| <center>-231.619322 </center>
| <center>-231.466705 </center>
| <center>-231.461346 </center>
| <center>-234.556983 </center>
| <center>-234.414919 </center>
| <center>-234.408998 </center>

|-
| '''Boat TS'''
| <center>-231.602802 </center>
| <center>-231.450929 </center>
| <center>-231.445300 </center>
| <center>-234.543093 </center>
| <center>-234.402340 </center>
| <center>-234.396006 </center>

|-
| '''Reactant (''anti2'')'''
| <center>-231.692535 </center>
| <center>-231.539539 </center>
| <center>-231.532566 </center>
| <center>-234.611710 </center>
| <center>-234.469203 </center>
| <center>-234.461856 </center>

'''Optimizing the "Chair" and "Boat" Transition Structures'''

[[Image:Chairboat.jpg]]

(a)-(d) On the left is the chair transition state that was optimised using the Berny optimisation. On the right is the chair transition state that was optimised using the frozen co-ordinate optimisation.

{| class="prettytable"
| Bond
| Chair TS (Berny) bond length (A)
| Chair TS (freeze) bond length (A)

|-
| Bond formation
| 2.02025
| 1.55082

|-
| Bond breaking
| 2.02027
| 4.39021

|}
As the table shows, the frozen co-ordinate optimisation has more realistic bond distances for the bond formation and bond breaking. The Berny optimisation has distances that are similar. This could suggest that the Berny optimisation would show the molecule before it entered the transition state and the frozen co-ordinate optimisation would show the molecule as it was about to leave the transition state.

(e) For some reason the boat calculation did not fail and the reason behind this I do not know. I had all the atoms numbered exactly the same as the wiki page (even the hydrogens) but the calculation did work. Whether this is relevant or not is not determinable.

[[Image:Worked.jpg]]

(f) I ran a minimum optimisation of the final point on the IRC.

Chair transition state: left = 3-21G level; right = 6-31G (d) level

[[Image:Opt1.jpg]]

[[Image:Opt2.jpg]]

This is the chair transition state optimised via the Berny optimisation technique.

As you can see from the energies, the 3-21G energy IRC optimisation has a very similar energy to the Berny optimisation (a difference of 0.00000001H). However, the 6-31G IRC optimisation shows quite a large energy difference to the Berny optimisation energy. This could suggest that the 6-31G IRC optimisation is closer to being the transition state of the molecule than the other optimisations. However, due to the inaccuracy of the optimisation choice, this might not be the minimum of the transition state and this just could be one of many minimums that are present in the reaction pathway.

# Boat transition state: left = 3-21G level; right = 6-31G (d) level

[[Image:Opt3.jpg]]

Chair transition state: left = 3-21G level; right = 6-31G (d) level

[[Image:Opt4.jpg]]

Both sets of transition states show that the 6-31G optimisation shows a more negative total energy value. Moreover, both the 3-21G optimisations and the 6-31G optimisations have energies that are close to each other.

{| class="prettytable"
| Transition state type
| Experimental activation energy (kcal/mol)
| 6-31G optimisation activation energy (kcal/mol)

|-
| Chair
| 33.5 ± 0.5
| 89.41804

|-
| Boat
| 44.7 ± 2.0
| 89.50550

|}
I used the zero point vibrational energy as the 6-31G optimisation activation energy. The table shows that the values between the experimental and computational activation energies are greatly different. This suggests that my computational transition states structures could have been incorrect.

Diels alder cycloaddition

Cis-butadiene HOMO:

[[Image:Cishomo.jpg]]

Symmetry with respect to plane = anti-symmetric.

Cis-butadiene LUMO:

[[Image:Cislumo.jpg]]

Symmetry with respect to plane = symmetric.

I attempted to create the transition state the same way that the boat transition state was created (the Q2TS calculation) but I got the structure below that could not show any MO’s, therefore, I had to create the transition state with the method used to create the chair transition state.

[[Image:Trans1.jpg]]

Transition state:

[[Image:Trans2.jpg]]

Transition state HOMO:

[[Image:Transhomo.jpg]]

Symmetry with respect to plane = symmetric.

Transition state LUMO:

[[Image:Translumo.jpg]]

Symmetry with respect to plane = anti-symmetric.

Geometry and bond lengths of partly formed C-C sigma bonds:

[[Image:Geo.jpg]]

Bond lengths of partly formed C-C sigma bonds: 4.14872A and 4.31774A.

The vibration that demonstrates the reaction pathway for the transition state is shown below:

[[Image:Vib.jpg]]

The bond formation seems to be asynchronus.

HOMO of transition structure:

[[Image:Homotrans.jpg]]

The HOMO at the transition state appears to be symmetric or “s”.

Exo maleic energy

[[Image:Exomale.jpg]]

Endo maleic energy

[[Image:Endomale.jpg]]

Exo maleic energy: -688.71418400H

Endo maleic energy: -688.64873554H

This shows that the exo configuration had more energy than the endo configuration, thus, less stable. This could be due to the strain from the two sections of the cyclic molecule that are close together, ie the parts that are pointing in the same direction.

The endo structure has the oxygen groups pointing in the opposite direction to the bridging carbons, whereas, the exo structure has both groups pointing the same way.

Ran out of time for the rest of the exercise.

File:Endomale.jpg

2008-11-26T16:29:27Z

Jt706:

File:Exomale.jpg

2008-11-26T16:28:52Z

Jt706:

File:Homotrans.jpg

2008-11-26T16:28:05Z

Jt706:

File:Vib.jpg

2008-11-26T16:26:53Z

Jt706:

File:Geo.jpg

2008-11-26T16:25:59Z

Jt706:

File:Translumo.jpg

2008-11-26T16:24:27Z

Jt706:

File:Transhomo.jpg

2008-11-26T16:24:08Z

Jt706:

File:Trans2.jpg

2008-11-26T16:23:07Z

Jt706:

File:Trans1.jpg

2008-11-26T16:22:53Z

Jt706:

File:Cislumo.jpg

2008-11-26T16:21:41Z

Jt706:

File:Cishomo.jpg

2008-11-26T16:21:22Z

Jt706:

File:Opt4.jpg

2008-11-26T16:20:19Z

Jt706:

File:Opt3.jpg

2008-11-26T16:19:51Z

Jt706:

File:Opt2.jpg

2008-11-26T16:18:51Z

Jt706:

File:Opt1.jpg

2008-11-26T16:18:33Z

Jt706:

File:Worked.jpg

2008-11-26T16:16:36Z

Jt706:

File:Chairboat.jpg

2008-11-26T16:16:13Z

Jt706:

File:B3ylp.jpg

2008-11-26T16:14:58Z

Jt706:

File:Hexa comp 2.jpg

2008-11-26T16:13:35Z

Jt706:

File:Hexa comp.jpg

2008-11-26T16:13:12Z

Jt706:

File:Hexa low.jpg

2008-11-26T16:12:48Z

Jt706:

File:Hexa gauche a.jpg

2008-11-26T16:10:42Z

Jt706:

File:Hexa gauche.jpg

2008-11-26T16:10:25Z

Jt706:

File:Hexa anti a.jpg

2008-11-26T16:09:04Z

Jt706:

File:Hexa anti.jpg

2008-11-26T16:08:39Z

Jt706:

Rep:Mod:dmc4

2008-11-26T16:02:50Z

Jt706: New page: '''Physical Computational Chemistry'''= Module 3, Experiment 3 = Cope rearrangement # 1,5-hexadiene ‘anti’ structure: Image: Image: I would expect the ‘gauche’ structu...

'''Physical Computational Chemistry'''= Module 3, Experiment 3 =
Cope rearrangement

# 1,5-hexadiene ‘anti’ structure:

[[Image:]]

[[Image:]]

I would expect the ‘gauche’ structure’s final energy to be higher than that of the ‘anti’ structure’s final energy because there is steric hindrance with regard to the bond angle between the 2 alkene bonds.

# 1,5-hexadiene ‘gauche’ structure:

[[Image:]]

[[Image:]]

{| class="prettytable"
| Structure
| Final Energy (Hartrees)

|-
| Anti
| -231.69260213

|-
| Gauche
| -231.69153035

|}

{| class="prettytable"
| Structure
| Point Group

|-
| Anti
| C2

|-
| Gauche
| C2

|}
Both molecules have a point group of C2. The results show that the anti has a more negative energy value, thus, the gauche conformation has a higher final energy value, which suggests that my prediction was correct. According to the appendix (1), I have optimised the molecules anti-1 and gauche-4.

# Lowest energy conformation of 1,5-hexadiene structure prediction:

[[Image:]]

# When compared to the structures in the appendix (1), my prediction looks similar to the anti-1 structure. The energies are similar but there are different point groups for each molecule, the predicted molecule has a C1 point group, whereas, the appendix molecule has a C2 point group.

[[Image:]]

# Anti-2 conformation (Ci point group)

[[Image:]]

{| class="prettytable"
| Structure
| Final Energy (Hartrees)

|-
| Anti-Ci (own)
| -231.69253530

|-
| Anti-Ci (appendix)
| -231.69254

|}
The molecule that I optimised is very similar to the one from the appendix. However, the point group is C1 as opposed to Ci. I tried rearranging the atoms in the molecule, but as you can see they look very similar, thus, I will continue to use the molecule shown in the picture as my Ci molecule.

# B3YLP/6-31G calculation:

[[Image:]]

The geometry of the higher level calculation has not changed very much. However, there is a significant change in the final energy values as the new value is -231.6117040 Hartrees compared with the -231.69253530 Hartrees from the lower level calculation.

#

Sum of electronic and zero-point Energies= -234.469204

Sum of electronic and thermal Energies= -234.461858

Sum of electronic and thermal Enthalpies= -234.460913

Sum of electronic and thermal Free Energies= -234.500776

Experimental energies

'''Summary of energies (in hartree) '''

{| class="prettytable"
|
| <center>'''HF/3-21G''' </center>
| <center>'''HF/3-21G''' </center>
| <center>'''HF/3-21G''' </center>
| <center>'''B3LYP/6-31G*''' </center>
| <center>'''B3LYP/6-31G*''' </center>
| <center>'''B3LYP/6-31G*''' </center>

|-
|
| <center>'''Electronic energy''' </center>
| <center>'''Sum of electronic and zero-point energies''' </center>
| <center>'''Sum of electronic and thermal energies''' </center>
| <center>'''Electronic energy''' </center>
| <center>'''Sum of electronic and zero-point energies''' </center>
| <center>'''Sum of electronic and thermal energies''' </center>

|-
|
|
| <center>'''at 0 K''' </center>
| <center>'''at 298.15 K''' </center>
|
| <center>'''at 0 K''' </center>
| <center>'''at 298.15 K''' </center>

|-
| '''Chair TS'''
| <center>-231.619322 </center>
| <center>-231.466705 </center>
| <center>-231.461346 </center>
| <center>-234.556983 </center>
| <center>-234.414919 </center>
| <center>-234.408998 </center>

|-
| '''Boat TS'''
| <center>-231.602802 </center>
| <center>-231.450929 </center>
| <center>-231.445300 </center>
| <center>-234.543093 </center>
| <center>-234.402340 </center>
| <center>-234.396006 </center>

|-
| '''Reactant (''anti2'')'''
| <center>-231.692535 </center>
| <center>-231.539539 </center>
| <center>-231.532566 </center>
| <center>-234.611710 </center>
| <center>-234.469203 </center>
| <center>-234.461856 </center>

|}
Compare

'''Optimizing the "Chair" and "Boat" Transition Structures'''

[[Image:]]

(a)-(d) On the left is the chair transition state that was optimised using the Berny optimisation. On the right is the chair transition state that was optimised using the frozen co-ordinate optimisation.

{| class="prettytable"
| Bond
| Chair TS (Berny) bond length (A)
| Chair TS (freeze) bond length (A)

|-
| Bond formation
| 2.02025
| 1.55082

|-
| Bond breaking
| 2.02027
| 4.39021

|}
As the table shows, the frozen co-ordinate optimisation has more realistic bond distances for the bond formation and bond breaking. The Berny optimisation has distances that are similar. This could suggest that the Berny optimisation would show the molecule before it entered the transition state and the frozen co-ordinate optimisation would show the molecule as it was about to leave the transition state.

(e) For some reason the boat calculation did not fail and the reason behind this I do not know. I had all the atoms numbered exactly the same as the wiki page (even the hydrogens) but the calculation did work. Whether this is relevant or not is not determinable.

[[Image:]]

(f) I ran a minimum optimisation of the final point on the IRC.

Chair transition state: left = 3-21G level; right = 6-31G (d) level

[[Image:]]

[[Image:]]

This is the chair transition state optimised via the Berny optimisation technique.

As you can see from the energies, the 3-21G energy IRC optimisation has a very similar energy to the Berny optimisation (a difference of 0.00000001H). However, the 6-31G IRC optimisation shows quite a large energy difference to the Berny optimisation energy. This could suggest that the 6-31G IRC optimisation is closer to being the transition state of the molecule than the other optimisations. However, due to the inaccuracy of the optimisation choice, this might not be the minimum of the transition state and this just could be one of many minimums that are present in the reaction pathway.

# Boat transition state: left = 3-21G level; right = 6-31G (d) level

[[Image:]]

Chair transition state: left = 3-21G level; right = 6-31G (d) level

[[Image:]]

Both sets of transition states show that the 6-31G optimisation shows a more negative total energy value. Moreover, both the 3-21G optimisations and the 6-31G optimisations have energies that are close to each other.

{| class="prettytable"
| Transition state type
| Experimental activation energy (kcal/mol)
| 6-31G optimisation activation energy (kcal/mol)

|-
| Chair
| 33.5 ± 0.5
| 89.41804

|-
| Boat
| 44.7 ± 2.0
| 89.50550

|}
I used the zero point vibrational energy as the 6-31G optimisation activation energy. The table shows that the values between the experimental and computational activation energies are greatly different. This suggests that my computational transition states structures could have been incorrect.

Diels alder cycloaddition

Cis-butadiene HOMO:

[[Image:]]

Symmetry with respect to plane = anti-symmetric.

Cis-butadiene LUMO:

[[Image:]]

Symmetry with respect to plane = symmetric.

I attempted to create the transition state the same way that the boat transition state was created (the Q2TS calculation) but I got the structure below that could not show any MO’s, therefore, I had to create the transition state with the method used to create the chair transition state.

[[Image:]]

Transition state:

[[Image:]]

Transition state HOMO:

[[Image:]]

Symmetry with respect to plane = symmetric.

Transition state LUMO:

[[Image:]]

Symmetry with respect to plane = anti-symmetric.

Geometry and bond lengths of partly formed C-C sigma bonds:

[[Image:]]

Bond lengths of partly formed C-C sigma bonds: 4.14872A and 4.31774A.

The vibration that demonstrates the reaction pathway for the transition state is shown below:

[[Image:]]

The bond formation seems to be asynchronus.

HOMO of transition structure:

[[Image:]]

The HOMO at the transition state appears to be symmetric or “s”.

Exo maleic energy

[[Image:]]

Endo maleic energy

[[Image:]]

Exo maleic energy: -688.71418400H

Endo maleic energy: -688.64873554H

This shows that the exo configuration had more energy than the endo configuration, thus, less stable. This could be due to the strain from the two sections of the cyclic molecule that are close together, ie the parts that are pointing in the same direction.

The endo structure has the oxygen groups pointing in the opposite direction to the bridging carbons, whereas, the exo structure has both groups pointing the same way.

Ran out of time for the rest of the exercise.

Rep:Mod:dmc3

2008-11-07T15:02:38Z

Jt706:

'''Computational Inorganic Chemistry'''

Optimised B-Cl bond length = 1.86512 A

Optimised Cl-B-Cl bond angle = 120 degrees

File type = .log

Calculation type = FOPT

Calculation method = RB3LYP

Basis set = LANL2MB

Final energy = -69.43928112 au

Dipole moment = 0 Debye

Point group = D3H

Time for calculation to take place = 11 secs

'''Own molecule = H2O ([http://hdl.handle.net/10042/to-1027 http://hdl.handle.net/10042/to-1027])'''

Center Atomic Atomic Coordinates (Angstroms)

Number Number Type X Y Z

<nowiki>---------------------------------------------------------------------</nowiki>

1 8 0 0.000000 0.000000 0.000000

2 1 0 0.000000 0.000000 0.960000

3 1 0 0.904936 0.000000 -0.320455

Bond distance (H-O) = 1.02717 A

Bond angle (H-O-H) = 97.186degrees

Calculation type= FOPT

Calculation method = RB3LYP

Basis set = LANL2MB

Final energy = -75.32277388 au

Dipole moment = 1.5936 Debye

Point group = C2V

Time for calculation to take place = 16 secs

'''Vibrational analysis and confirming minima'''

{| class="prettytable"
| BH3 optimisation
| Calculation type
| FOPT

|-
|
| Calculation method
| RB3LYP

|-
|
| Basis set
| 3-21G

|-
|
| Final energy
| -26.46226436 au

|-
|
| Dipole moment
| 0 D

|-
|
| Point group
| D3H

|-
|
| Calculation time
| 10 secs

|-
| BH3 frequency
| Calculation type
| FREQ

|-
|
| Calculation method
| RB3LYP

|-
|
| Basis set
| 3-21G

|-
|
| Final energy
| -26.46226436 au

|-
|
| Dipole moment
| 0 D

|-
|
| Point group
| C3H

|-
|
| Calculation time
| 9 secs

|}
'''Animating the vibrations'''

{| class="prettytable"
| No.
| Form of vibration
| Frequency
| Intensity
| Symmetry D3h point group

|-
| 1
| [[Image:BH3-1.jpg]]

All H atoms move backwards and forwards perpendicular to the plane, B atom moves in opposite direction to H atoms.
| 1145.9
| 92.6789
| A’’2

|-
| 2
| [[Image:BH3-2.jpg]]

One H atom and B atom remain fixed but move up and down together; other two H atoms come together and away from each other.
| 1204.78
| 12.3867
| E’’

|-
| 3
| [[Image:BH3-3.jpg]]

B atom rocks from side to side, all three H atoms move, two towards each other and away, the other from side to side.
| 1204.78
| 12.3892
| E’’

|-
| 4
| [[Image:BH3-4.jpg]]

B atom is stationary, all three H atoms move in and out.
| 2592.11
| 0
| A’1

|-
| 5
| [[Image:BH3-5.jpg]]

One H atom is fixed, the other two move towards and away from the B atom (which moves towards the H atom going towards it) in opposite directions.
| 2730.57
| 103.849
| E’

|-
| 6
| [[Image:BH3-6.jpg]]

One H atom moves up and down towards the B atom, which moves towards and away from it. The other two H atoms move towards and away from the B atom in the same direction.
| 2730.57
| 103.842
| E’

|}
[[Image:BH3-ir.jpg]]

Even though there are 6 vibrations, only 3 peaks appear because there are 2 sets of redundant vibrations (i.e. each pair of vibrations vibrate at the same frequency), and thus, would not show two peaks as the vibration with the higher intensity would overshadow the other. Also, one of the vibrations has an intensity of 0, hence, it would not show in the IR spectrum.

'''Molecular orbitals of BH3'''

[[Image:BH3-MO-dia.jpg]]

[[Image:BH3-MO1.jpg]] MO1, which is the equivalent of the highest energy a’1 orbital.

[[Image:BH3-MO2.jpg]] MO2, which is the equivalent of the lowest energy a’1 orbital.

[[Image:BH3-MO3.jpg]] MO3, which is the equivalent of one of the lowest energy e’ orbitals.

[[Image:BH3-MO4.jpg]] MO4, which is the equivalent of the other lowest energy e’ orbital.

[[Image:BH3-MO5.jpg]] MO5, which is the equivalent of the pz orbital.

This shows that the qualitative MO theory has a high accuracy and it is very useful in predicting the quantitative molecular orbitals of molecules.

Part 2

Optimised geometry

Trans Mo(CO)4(P(CH3)3)2 ([http://hdl.handle.net/10042/to-1042 http://hdl.handle.net/10042/to-1042])'''

[[Image:Trans_Mo(CO)4(P(CH3)3)2.jpg]]

Cis Mo(CO)4(P(CH3)3)2 ('''unable to publish)'''

[[Image:Cis_Mo(CO)4(P(CH3)3)2.jpg]]

Trans energy – Cis energy = energy difference

-773.2781351H - -773.34681814H = 0.0686836H x 2625.5KJ/mol = 180.3287918KJ/mol.

The cis conformation has a higher final energy than the trans conformation, thus, it is less stable.

All bond angles in the Trans molecule with the Mo as the second atom (i.e. in the middle of the angle) are 90 degrees.

Trans P-C-H bond angle = 109.471 degrees

For the atoms in the Trans molecule, the bond lengths and angles seem to be the same for each species (i.e. every Mo-C bond is the same length), however, this is not the same case for the cis molecule, thus, the bond lengths below for the cis molecule are the mean values. This may have occurred because there was something wrong with the initial file or process when optimising the molecule (which could also explain why it is unable to publish the optimisation) or it could be because the two cis groups are quite large, therefore, they strain the molecule to have bond lengths and angles that are not the same as the trans molecule.

Cis P-C-H bond angle = 108.912 degrees

Cis X-Mo-X bond angle (X = C/P) = 89.5314 degrees

Literature compound is Mo(CO)4(PPh3)2.

{| class="prettytable"
| Bond
| Calculated Trans bond length (A)
| Calculated Cis bond length (A)
| Literature Trans bond length (A)
| Literature Cis bond length (A)

|-
| Mo-C
| 2.06000
| 2.00722
| 2.011
| 2.007

|-
| Mo-P
| 2.39000
| 2.648105
| 2.500
| 2.5765

|-
| C=O
| 1.25840
| 1.18983
| 1.1645
| -

|-
| P-C
| 1.87000
| 1.892355
| 1.841
| -

|-
| C-H
| 1.07000
| 1.095263
| -
| -

|}
When comparing the literature and calculated values, it can be seen that there are similarities between the two sets of values. It also shows that the average bonds in the cis conformation of the calculated molecules has results close to that of the experimental values, which could suggest the the calculated cis compound could be correct.

Nevertheless, the calculated cis compound could be wrong, as the bond lengths between same atom types varies between each bond, when it is probable that the bond lengths should not vary, however, due to the cis structure being sterically strained, it may be possible to have varying bond lengths. The cis compound was created 3 different times in the Gaussview program, with each result ending the same, thus, if the cis molecule is incorrect it can be concluded that either the method of producing the molecule is wrong or the program cannot create a cis conformation of the molecule.

'''IR analysis'''

Trans Mo(CO)4(P(CH3)3)2 ([http://hdl.handle.net/10042/to-1040 http://hdl.handle.net/10042/to-1040])

Cis Mo(CO)4(P(CH3)3)2 ([http://hdl.handle.net/10042/to-1041 http://hdl.handle.net/10042/to-1041])'''

Table of Major peaks

{| class="prettytable"
| Bond type
| Calculated peak (cm-1)
| Experimental peak (cm-1)

|-
| Trans
| 1017
| 1020

|-
| Trans
| 1839
| 1891

|-
| Cis
| 1018
| 1012

|-
| Cis
| 1027
| 1040

|-
| Cis
| 1850
| 1863

|-
| Cis
| 1870
| 1887

|-
| Cis
| 1960
| 1968

|}
Again, the calculated and experimental values are similar, thus showing that the calculate approach to an experiment is a very good prediction of the products in a reaction.

'''Ammonia'''

Symmetry

NH3

[[Image:NH3.jpg]]

Long bond NH3

[[Image:Longbond-NH3.jpg]]

High symmetry NH3

[[Image:Highsymmetry-NH3.jpg]]

The high symmetry structure has changed the ammonia molecule into a planar structure. The time taken to optimise the high symmetry ammonia was quicker than the two previous structures. The symmetry doesn’t seem to affect the time for the calculation to take place. D3h is the most symmetrical point group and has the shortest time, but C3v was the second most symmetrical group but had the longest calculation time. Symmetrical molecules can break symmetry if the optimisation provides a more stable molecule.

Lowest energy optimisation: -56.41530842 au = 148118.3923 KJ/mol

Energy differences:

-56.41530857 - -56.41530842 = -0.00000015 au = -3.93825xE-4 KJ/mol

-56.42664911 - -56.41530842 = -0.01134069 au = -29.775 KJ/mol

The energy differences are significant because they show that by slightly altering the molecules structure can affect the overall energy of the molecule and it’s point group, thus, its symmetry.

Methods

{| class="prettytable"
| Calculation Method
| Calculation time (secs)

|-
| NH3 6-31G
| 33.0

|-
| NH3 MP2
| 38.0

|-
| High Sym NH3 6-31G
| 16.0

|-
| High Sym NH3 MP2
| 22.0

|}
The higher level calculations take 5 seconds and 6 seconds longer than the lower level calculations.

MP2 calculation energy

ΔE=E(D3h)-E(C3v)

ΔE=-56.42664911 - -56.41530857 = -0.01134054 a.u. = -29.775 KJ/mol.

6-31G calculation energy = -56.56066276 - -56.56698509 = 6.32233xE-3 a.u. = 16.5993 KJ/mol.

This calculation shows that the energy difference between the two calculation methods is large, especially with the lower level calculation providing a positive energy, which would be incorrect. The value of -29.775 KJ/mol for the MP2 calculation is close to the experimentally determined value of -24.3 KJ/mol, but obviously there must be something missing from the calculation that is present in the experimental.

Inversion Mechanism

[[Image:Inversion-nh3.jpg]]

Ammonia vibrational analysis

{| class="prettytable"
| C3v NH3 frequency (cm-1)
| C3v NH3 vibrations
| D3h NH3 vibrations
| D3h NH3 frequency (cm-1)

|-
| 999.413
| [[Image:C3v-1.jpg]]
| [[Image:D3h-1.jpg]]
| -766.722

|-
| 1673.65
| [[Image:C3v-2.jpg]]
| [[Image:D3h-2.jpg]]
| 1576.99

|-
| 1673.65
| [[Image:C3v-3.jpg]]
| [[Image:D3h-3.jpg]]
| 1576.99

|-
| 3484.88
| [[Image:C3v-4.jpg]]
| [[Image:D3h-4.jpg]]
| 3623.13

|-
| 3627.94
| [[Image:C3v-5.jpg]]
| [[Image:D3h-5.jpg]]
| 3841.51

|-
| 3627.94
| [[Image:C3v-6.jpg]]
| [[Image:D3h-6.jpg]]
| 3841.51

|}
C3v NH3 IR

[[Image:C3v-ir.jpg]]

D3h NH3 IR

[[Image:D3h-ir.jpg]]

There are 6 positive frequencies for the C3v NH3 molecule, but only 5 for the D3h molecule. It has one negative frequency which is -766.722cm-1. The first vibrations in the table seem to follow the inversion mechanism, because the hydrogens move in such a way that if they had more energy, they would be able to invert the ammonia molecule.

{| class="prettytable"
| Stretch/bend
| Calculated (cm-1)
| Experimental (cm-1)

|-
| N-H symmetric stretch
| 3484.88
| 3534

|-
| N-H asymmetric stretch
| 3627.94
| 3464

|-
| N-H asymmetric stretch
| 3627.94
| 3464

|-
| H-N-H bend
| 1673.65
| 1765

|-
| H-N-H bend
| 1673.65
| 1765

|-
| H-N-H bend
| 999.413
| 1139

|}
'''Mini Project:'''

'''Fuels of the future'''

Staggered conformation (<tt>http://hdl.handle.net/10042/to-1098</tt> )

Ammonia-Borane optimisation (B3LYP 3-21G)

[[Image:Ammbor-321g.jpg]]

Ammonia-Borane optimisation (B3LYP 6-31G)

[[Image:Ammbor-631g.jpg]]

Ammonia-Borane optimisation (MP2 6-311+G(d,p))

[[Image:Ammbor-MP2.jpg]]

Ammonia-Borane Infrared (MP2 6-311+G(d,p))

[[Image:Ammbor-MP2-ir.jpg]]

Eclipsed conformation

Ammonia-Borane optimisation (B3LYP 3-21G)

[[Image:Eammbor-321g.jpg]]

Ammonia-Borane optimisation (B3LYP 6-31G)

[[Image:Eammbor-631g.jpg]]

Ammonia-Borane optimisation (MP2 6-311+G(d,p))

[[Image:Eammbor-MP2.jpg]]

Ammonia-Borane Infrared (MP2 6-311+G(d,p))

[[Image:Eammbor-MP2-ir.jpg]]

Ethane staggered

[[Image:Ethane-staggered.jpg]]

Ethane eclipsed

[[Image:ethane-ecl.jpg]]

{| class="prettytable"
| Calculation Method
| Staggered conformation energy (H)
| Eclipsed conformation energy (H)

|-
| (B3LYP 3-21G)
| -82.76661667
| -82.76331994

|-
| (B3LYP 6-31G)
| -83.22469009
| -83.19117366

|-
| (MP2 6-311+G(d,p))
| -82.99800434
| -82.99422183

|-
| Ethane (MP2 6-311+G(d,p))
| -79.60927097
| -79.80850664

|}
The results show that the median value for the energies is from the MP2 calculation method, thus, it would appear that this is the most accurate of the three calculation types and will be used for further calculations. According to the results from the table, in each comparable case, the eclipsed conformation appears to have a lower energy than its staggered counterpart, albeit, only by a small quantity. When compared to ethane, the ammonia-borane has a slightly higher energy, and with ethane it is the staggered conformation that has the lower energy.

Ethane has a covalent bond that has each carbon atom donating an election to create a σC-C single bond. With ammonia-borane, the boron atom is electron deficient (it has 6 electrons in its valent shell, 8 electrons are needed to be stable), therefore, the nitrogen atom donates one of its lone pairs into the vacant p orbital of the boron to create a dative covalent σN-B single bond.

This makes the ammonia part of the molecule more acidic and the borane part of the molecule more basic. This means that the ammonia-borane is prone to have strong intermolecular dipole-dipole interactions, which is why it has a melting point of approximately 110°C. Since ethane is not prone to having strong dipole-dipole interactions, only weaker Van der Waals forces, ethane has a melting temperature of approximately 89.87K, which is 183.13°C.

NH4Cl + NaBH4 -> NH4BH4 + NaCl

NH4BH4 -> H2 + NH3BH3

Relatively speaking, NaCl is the most stable molecule as it has a melting point of 801°C. Sodium borohydride has a melting point of less than 300°C (decomposed) and ammonium chloride has a melting point of 340°C (before it sublimes). The high melting temperature of NaCl shows that the compound has strong bonds, and therefore, it could be suggested that the formation of these bonds is the driving force of the reaction. Ammonia-borane would have to be more stable than the NH4BH4 compound because there is the formation of hydrogen gas, which is then liberated acting as the driving force of the decomposition.

References:

[http://www.ucl.ac.uk/~uccaati/Energy.html http://www.ucl.ac.uk/~uccaati/Energy.html]

'''The Heat Capacity of Ethane from 15K to the Boiling Point.'''

'''The Heat of Fusion and the Heat of Vaporization'''

BY R. K. WITT~'''AN D '''J. D. KEMP

'''Ammonium chloride'''

''Corp MSDS'' '''1''' (1), 233:D / ''IR-Spectra'' (3), 1521:D / ''RegBook'' '''1''' (3), 3325:H / ''Sax'' '''6''', 260 / ''Sigma FT-IR'' '''1''' (2), 1012:C

'''Sodium chloride'''

''Aldrich MSDS'' '''1''', 1608:C / ''Corp MSDS'' '''1''' (2), 3135:D / ''RegBook'' '''1''' (3), 3319:F / ''Sax'' '''6''', 2419

'''Sodium borohydride'''

''Aldrich MSDS'' '''1''', 1608:B / ''Corp MSDS'' '''1''' (2), 3132:B / ''Corp MSDS'' '''1''' (2), 3133:C / ''Corp MSDS'' '''1''' (2), 3132:A / ''Corp MSDS'' '''1''' (2), 3132:C / ''IR-Spectra'' (3), 1534:G / ''RegBook'' '''1''' (3), 3261:F / ''RegBook'' '''1''' (3), 3261:E / ''Sax'' '''6''', 2414

'''Synthesis of ammonia borane for hydrogen storage applicationsDavid J. Heldebrant, Abhi Karkamkar, John C. Linehan and Tom Autrey'''

'''Ir ammonia'''

[http://www.chem.purdue.edu/gchelp/vibs/nh3.html http://www.chem.purdue.edu/gchelp/vibs/nh3.html]

File:Ethane-ecl.jpg

2008-11-07T15:01:26Z

Jt706:

File:Ethane-staggered.jpg

2008-11-07T15:01:09Z

Jt706:

File:Eammbor-MP2-ir.jpg

2008-11-07T15:00:20Z

Jt706:

File:Eammbor-MP2.jpg

2008-11-07T15:00:09Z

Jt706:

File:Eammbor-631g.jpg

2008-11-07T14:59:59Z

Jt706:

File:Eammbor-321g.jpg

2008-11-07T14:59:51Z

Jt706:

File:Ammbor-MP2-ir.jpg

2008-11-07T14:58:56Z

Jt706:

File:Ammbor-MP2.jpg

2008-11-07T14:58:38Z

Jt706:

File:Ammbor-631g.jpg

2008-11-07T14:58:29Z

Jt706:

File:Ammbor-321g.jpg

2008-11-07T14:58:16Z

Jt706:

File:D3h-ir.jpg

2008-11-07T14:57:48Z

Jt706:

File:C3v-ir.jpg

2008-11-07T14:57:32Z

Jt706:

File:D3h-6.jpg

2008-11-07T14:56:30Z

Jt706:

File:D3h-5.jpg

2008-11-07T14:56:21Z

Jt706:

File:D3h-4.jpg

2008-11-07T14:56:13Z

Jt706:

File:D3h-3.jpg

2008-11-07T14:56:02Z

Jt706:

File:D3h-2.jpg

2008-11-07T14:55:54Z

Jt706:

File:D3h-1.jpg

2008-11-07T14:55:46Z

Jt706:

File:C3v-6.jpg

2008-11-07T14:54:26Z

Jt706:

File:C3v-5.jpg

2008-11-07T14:54:18Z

Jt706:

File:C3v-4.jpg

2008-11-07T14:54:09Z

Jt706: