ChemWiki - User contributions [en]

Rep:Mod:boredofcomplabs

2011-02-18T17:04:38Z

Ckw08: /* Diels Alder */

=Module 3: Christopher Wood=

Apologies for the size of the pictures, time is an issue.

==Introduction==

In this module, GausView was used not only to optimise and analyse various molecules as before, but now expanded to study transition states. Transition states are states of maximum energy along a reaction path from reactants to products. The structure and geometry of the transition states can significantly determine the structure of the product of the reaction. This is a highly useful tool for chemists and therefore will be investigated in this module

==The Cope Rearrangement==

In this section, the Cope rearrangement of 1,5-hexadiene will be studied. First of all, the low energy minima were determined for the structural arrangements of 1,5-hexadiene.

The structures were made in GaussView and "Cleaned". The job type was '''Optimization''' and the default method was left unchanged, '''Hartree Fock'' with basis set '''3-21G'''. The size of the output files were also limited to a maximum of 250 MB. The resultant molecule's symmetry was noted after selecting '''Symmetrize'''. The table below shows the various minima in the structure of 1,5-hexadiene.

{| border="1" cellpadding="5"
|- align="center"
| width="150" | '''Conformer'''
| width="150" | '''Structure'''
| width="100" | '''Point Group'''
| width="200" | '''Energy/Hartrees <br />HF/3-21G'''
| width="200" | '''Relative Energy/kcal/mol'''
|- align="center"
| ''gauche1''
|
<jmol>
<jmolApplet>
<title>Gauche 1</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche1.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7224}}
| C<sub>2</sub>
| -231.68772
| 3.10
|- align="center"
| ''gauche2''
|
<jmol>
<jmolApplet>
<title>Gauche 2</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche2.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7225}}
| C<sub>2</sub>
| -231.69167
| 0.62
|- align="center"
| ''gauche3''
|
<jmol>
<jmolApplet>
<title>Gauche 3</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche3.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7226}}
| C<sub>1</sub>
| -231.69266
| 0.00
|- align="center"
| ''gauche4''
|
<jmol>
<jmolApplet>
<title>Gauche 4</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche4.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7227}}
| C<sub>2</sub>
| -231.69153
| 0.71
|- align="center"
| ''gauche5''
|
<jmol>
<jmolApplet>
<title>Gauche 5</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche5.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7228}}
| C<sub>1</sub>
| -231.68962
| 1.91
|- align="center"
| ''gauche6''
|
<jmol>
<jmolApplet>
<title>Gauche 6</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche6.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7229}}
| C<sub>1</sub>
| -231.68916
| 2.20
|- align="center"
| ''anti1''
|
<jmol>
<jmolApplet>
<title>Anti 1</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Anti1.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7230}}
| C<sub>2</sub>
| -231.69260
| 0.04
|- align="center"
| ''anti2''
|
<jmol>
<jmolApplet>
<title>Anti 2</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Anti2.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7232}}
| C<sub>i</sub>
| -231.69254
| 0.08
|- align="center"
| ''anti3''
|
<jmol>
<jmolApplet>
<title>Anti 3</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Anti3.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7231}}
| C<sub>2h</sub>
| -231.68907
| 2.25
|- align="center"
| ''anti4''
|
ANTI 4
{{DOI|10042/to-7233}}
| C<sub>1</sub>
| -231.69097
| 1.06
|}

The relative energies are taken in comparison to the lowest energy minima, which was determined to be '''gauche 3'''.

To compare the energy outcomes of different optimisation methods, the C<sub>i</sub> minima structure was reoptimised using '''B3LYP/3-21G''' and then '''6-31G'''. There was no observable change in structure, but the energies that were computed were -233.33634 Au and -234.55970 Au respectively.

A frequency job was then run on the optimised structure with the following results: {{DOI|10042/to-7236}}

{|
|-
|
| Hatree
|-
| Sum of electronic and zero-point Energies
| -234.416244
|-
| Sum of electronic and thermal Energies
| -234.408953
|-
| Sum of electronic and thermal Enthalpies
| -234.408009
|-
| Sum of electronic and thermal Free Energies
| -234.447848
|-
|}

===Optimising the "Chair" and "Boat" Transition Structures"===

The Cope rearrange is a [3,3]-sigmatropic shift rearrangement. it is generally accepted that the reaction occurs in a concerted fashion via either a "chair" or "boat" transition structure. In this section, both structure shall be analysed to a '''B3LYP/6-31G''' level of theory, which has been shown to give good agreement to experimental data.

====Chair====

The first method used to determine the transition structure involved the placement of 2 allyl fragments positioned approximately 2.2 Å apart. They were first optimised using '''HF/3-21G''' level of theory. Once the transition structure was approximately made, a '''Opt+Freq''' calculation was set up and was optimised '''to a TS (Berry)'''. The force constants were calculated '''Once''' and '''Opt=NoEigen''' was added to the ''Additional keyword'' box. {{DOI|10042/to-7246}}

There was an imaginary frequency observed at -817.89 cm<sup>-1</sup> and this corresponded to the bonds forming/breaking in this rearrangement reaction. (Jmol unable to show vibration...)

<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 1;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>Chair_1_log.out</uploadedFileContents> </jmolApplet></jmol>

On examining the structure, the C-C separations, at the sites of the new forming C-C bonds, were observed to be 2.01954 and 2.01999 Å.

The next method investigated involved fixing the C-C separtions mentioned above. First of all, the C-C separations (where the new bonds would form) were fixed at 2.2 Å. An optimisation calculation was run then the separations were then optimised in a second calculation by running an '''Opt+Freq to a TS (Berry)'''. {{DOI|10042/to-7267}}

The C-C separations were noted to be 2.01998 Å. This is similar to the previous method. The structures resulting from both methods were both the same.

====Boat====

For the boat transition structure a different method had to be employed. this involved mapping the reactants and products and letting the program determine the structure. Initially, a chair TS was given, as below, but after tweaking the geometry of both the reagents and products the boat was achieved. {{DOI|10042/to-7274}} and {{DOI|10042/to-7275}}

<jmol> <jmolAppletButton> <uploadedFileContents>Boat_failed_opt_mol.mol</uploadedFileContents> <text>Failed Boat</text> </jmolAppletButton> </jmol>
<jmol> <jmolAppletButton> <uploadedFileContents>Boat_opt_mol.mol</uploadedFileContents> <text>Successful boat</text> </jmolAppletButton> </jmol>

Again there is only 1 imaginary frequency observed and this corresponds to the desired rearrangement reaction.

====Intrinsic Reaction Coordinate====

Using IRC, this allows us to follow the minimum energy path from a transition structure down to its local minimum on a potential energy surface. This confirmed that my input chair structure was and TS in accordance to the IRC plot. {{DOI|10042/to-7277}}

====Energy workup====

In this section, the TS's were optimised to '''B3LYP/6-31G''' level of theory. The resultant geometries were extremely similar to those already determined above.
Chair {{DOI|10042/to-7280}}, Boat {{DOI|10042/to-7281}}.

Unfortunately, due to calculation errors, the energies could not be determined for unknown reasons, even after countless repeats.

==Exercise==

In this exercise, specific Diels Alder reactions shall be investigated using the methods described above.

===Cis-butadiene and Ethylene===

Both the molecules were first made separately and optimised to a '''B3LYP/6-31G''' level. Their HOMO/LUMO's are as shown:

{|
|-
| Molecule
| MO
| MO visualised
| Symmetry
|-
| Cis-butadiene
| LUMO
| [[Image:LUMO_cis_butadiene.gif|frame|centre|]]
| Symmetric
|-
| Cis-butadiene
| HOMO
|[[Image:HOMO_cis_butadiene.gif|frame|centre|]]
| Anti-symmetric
|-
| Ethylene
| LUMO
|[[Image:LUMO_ethene.gif|frame|centre|]]
| Anti-symmetric
|-
| Ethylene
| HOMO
|[[Image:HOMO_ethene.gif|frame|centre|]]
| Symmetric
|-
|}

The two molecules were then combined and using the bond fixing method, the transition state was determined. {{DOI|10042/to-7282}}

The following MO's were achieved:
[[Image:HOMO_TS_GIFF.gif|frame|centre|HOMO TS]]
[[Image:LUMO_TS_GIF.gif|frame|centre|LUMO TS]]

As you can see the HOMO is anti-symmetric and LUMO is symmetric, which agrees with the discussion in the given task.

The TS was confirmed by running a IRC calculation in both directions, and the above TS was indeed the maximum on the reaction coordinate graph.

[[Image:IRC_graphs.tif|frame|centre|LUMO TS]]

The HOMO of the TS is the combination of the HOMO of the cis-butadiene and the LUMO of the ethylene, and the LUMO is the opposite.

The C-C separation at the new bonding sites was noted to be 2.26354 and 2.26297 Å. The double bonds on the cis-butadiene are 1.38880 Å, single C-C bond is 1.40798 Å and the ethylene double bond is 1.39274 Å.

===Diels Alder===

TS1 optimisation fixed

{{DOI|10042/to-7286}}

TS2 optimisation

{{DOI|10042/to-7287}}

TS1 failed final opt

{{DOI|10042/to-7288}}

TS2 failed final opt

{{DOI|10042/to-7289}}

<jmol> <jmolAppletButton> <uploadedFileContents>TS1_fixed_opt_mol.mol</uploadedFileContents> <text>TS1</text> </jmolAppletButton> </jmol>
<jmol> <jmolAppletButton>

<jmol> <jmolAppletButton> <uploadedFileContents>TS2_fixed_opt_mol.mol</uploadedFileContents> <text>TS2</text> </jmolAppletButton> </jmol>
<jmol> <jmolAppletButton>

In this exercise, I was unable to get a fully optimised transition structure. tried various methods, but the best was the bond fixing. The above are the structure of the exo and endo TS's. But on final optimisations, the structure would distort unrealistically.

File:TS2 fixed opt mol.mol

2011-02-18T17:00:42Z

Ckw08:

File:TS1 fixed opt mol.mol

2011-02-18T17:00:23Z

Ckw08:

Rep:Mod:boredofcomplabs

2011-02-18T16:58:12Z

Ckw08: /* Cis-butadiene and Ethylene */

=Module 3: Christopher Wood=

Apologies for the size of the pictures, time is an issue.

==Introduction==

In this module, GausView was used not only to optimise and analyse various molecules as before, but now expanded to study transition states. Transition states are states of maximum energy along a reaction path from reactants to products. The structure and geometry of the transition states can significantly determine the structure of the product of the reaction. This is a highly useful tool for chemists and therefore will be investigated in this module

==The Cope Rearrangement==

In this section, the Cope rearrangement of 1,5-hexadiene will be studied. First of all, the low energy minima were determined for the structural arrangements of 1,5-hexadiene.

The structures were made in GaussView and "Cleaned". The job type was '''Optimization''' and the default method was left unchanged, '''Hartree Fock'' with basis set '''3-21G'''. The size of the output files were also limited to a maximum of 250 MB. The resultant molecule's symmetry was noted after selecting '''Symmetrize'''. The table below shows the various minima in the structure of 1,5-hexadiene.

{| border="1" cellpadding="5"
|- align="center"
| width="150" | '''Conformer'''
| width="150" | '''Structure'''
| width="100" | '''Point Group'''
| width="200" | '''Energy/Hartrees <br />HF/3-21G'''
| width="200" | '''Relative Energy/kcal/mol'''
|- align="center"
| ''gauche1''
|
<jmol>
<jmolApplet>
<title>Gauche 1</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche1.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7224}}
| C<sub>2</sub>
| -231.68772
| 3.10
|- align="center"
| ''gauche2''
|
<jmol>
<jmolApplet>
<title>Gauche 2</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche2.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7225}}
| C<sub>2</sub>
| -231.69167
| 0.62
|- align="center"
| ''gauche3''
|
<jmol>
<jmolApplet>
<title>Gauche 3</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche3.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7226}}
| C<sub>1</sub>
| -231.69266
| 0.00
|- align="center"
| ''gauche4''
|
<jmol>
<jmolApplet>
<title>Gauche 4</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche4.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7227}}
| C<sub>2</sub>
| -231.69153
| 0.71
|- align="center"
| ''gauche5''
|
<jmol>
<jmolApplet>
<title>Gauche 5</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche5.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7228}}
| C<sub>1</sub>
| -231.68962
| 1.91
|- align="center"
| ''gauche6''
|
<jmol>
<jmolApplet>
<title>Gauche 6</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche6.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7229}}
| C<sub>1</sub>
| -231.68916
| 2.20
|- align="center"
| ''anti1''
|
<jmol>
<jmolApplet>
<title>Anti 1</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Anti1.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7230}}
| C<sub>2</sub>
| -231.69260
| 0.04
|- align="center"
| ''anti2''
|
<jmol>
<jmolApplet>
<title>Anti 2</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Anti2.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7232}}
| C<sub>i</sub>
| -231.69254
| 0.08
|- align="center"
| ''anti3''
|
<jmol>
<jmolApplet>
<title>Anti 3</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Anti3.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7231}}
| C<sub>2h</sub>
| -231.68907
| 2.25
|- align="center"
| ''anti4''
|
ANTI 4
{{DOI|10042/to-7233}}
| C<sub>1</sub>
| -231.69097
| 1.06
|}

The relative energies are taken in comparison to the lowest energy minima, which was determined to be '''gauche 3'''.

To compare the energy outcomes of different optimisation methods, the C<sub>i</sub> minima structure was reoptimised using '''B3LYP/3-21G''' and then '''6-31G'''. There was no observable change in structure, but the energies that were computed were -233.33634 Au and -234.55970 Au respectively.

A frequency job was then run on the optimised structure with the following results: {{DOI|10042/to-7236}}

{|
|-
|
| Hatree
|-
| Sum of electronic and zero-point Energies
| -234.416244
|-
| Sum of electronic and thermal Energies
| -234.408953
|-
| Sum of electronic and thermal Enthalpies
| -234.408009
|-
| Sum of electronic and thermal Free Energies
| -234.447848
|-
|}

===Optimising the "Chair" and "Boat" Transition Structures"===

The Cope rearrange is a [3,3]-sigmatropic shift rearrangement. it is generally accepted that the reaction occurs in a concerted fashion via either a "chair" or "boat" transition structure. In this section, both structure shall be analysed to a '''B3LYP/6-31G''' level of theory, which has been shown to give good agreement to experimental data.

====Chair====

The first method used to determine the transition structure involved the placement of 2 allyl fragments positioned approximately 2.2 Å apart. They were first optimised using '''HF/3-21G''' level of theory. Once the transition structure was approximately made, a '''Opt+Freq''' calculation was set up and was optimised '''to a TS (Berry)'''. The force constants were calculated '''Once''' and '''Opt=NoEigen''' was added to the ''Additional keyword'' box. {{DOI|10042/to-7246}}

There was an imaginary frequency observed at -817.89 cm<sup>-1</sup> and this corresponded to the bonds forming/breaking in this rearrangement reaction. (Jmol unable to show vibration...)

<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 1;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>Chair_1_log.out</uploadedFileContents> </jmolApplet></jmol>

On examining the structure, the C-C separations, at the sites of the new forming C-C bonds, were observed to be 2.01954 and 2.01999 Å.

The next method investigated involved fixing the C-C separtions mentioned above. First of all, the C-C separations (where the new bonds would form) were fixed at 2.2 Å. An optimisation calculation was run then the separations were then optimised in a second calculation by running an '''Opt+Freq to a TS (Berry)'''. {{DOI|10042/to-7267}}

The C-C separations were noted to be 2.01998 Å. This is similar to the previous method. The structures resulting from both methods were both the same.

====Boat====

For the boat transition structure a different method had to be employed. this involved mapping the reactants and products and letting the program determine the structure. Initially, a chair TS was given, as below, but after tweaking the geometry of both the reagents and products the boat was achieved. {{DOI|10042/to-7274}} and {{DOI|10042/to-7275}}

<jmol> <jmolAppletButton> <uploadedFileContents>Boat_failed_opt_mol.mol</uploadedFileContents> <text>Failed Boat</text> </jmolAppletButton> </jmol>
<jmol> <jmolAppletButton> <uploadedFileContents>Boat_opt_mol.mol</uploadedFileContents> <text>Successful boat</text> </jmolAppletButton> </jmol>

Again there is only 1 imaginary frequency observed and this corresponds to the desired rearrangement reaction.

====Intrinsic Reaction Coordinate====

Using IRC, this allows us to follow the minimum energy path from a transition structure down to its local minimum on a potential energy surface. This confirmed that my input chair structure was and TS in accordance to the IRC plot. {{DOI|10042/to-7277}}

====Energy workup====

In this section, the TS's were optimised to '''B3LYP/6-31G''' level of theory. The resultant geometries were extremely similar to those already determined above.
Chair {{DOI|10042/to-7280}}, Boat {{DOI|10042/to-7281}}.

Unfortunately, due to calculation errors, the energies could not be determined for unknown reasons, even after countless repeats.

==Exercise==

In this exercise, specific Diels Alder reactions shall be investigated using the methods described above.

===Cis-butadiene and Ethylene===

Both the molecules were first made separately and optimised to a '''B3LYP/6-31G''' level. Their HOMO/LUMO's are as shown:

{|
|-
| Molecule
| MO
| MO visualised
| Symmetry
|-
| Cis-butadiene
| LUMO
| [[Image:LUMO_cis_butadiene.gif|frame|centre|]]
| Symmetric
|-
| Cis-butadiene
| HOMO
|[[Image:HOMO_cis_butadiene.gif|frame|centre|]]
| Anti-symmetric
|-
| Ethylene
| LUMO
|[[Image:LUMO_ethene.gif|frame|centre|]]
| Anti-symmetric
|-
| Ethylene
| HOMO
|[[Image:HOMO_ethene.gif|frame|centre|]]
| Symmetric
|-
|}

The two molecules were then combined and using the bond fixing method, the transition state was determined. {{DOI|10042/to-7282}}

The following MO's were achieved:
[[Image:HOMO_TS_GIFF.gif|frame|centre|HOMO TS]]
[[Image:LUMO_TS_GIF.gif|frame|centre|LUMO TS]]

As you can see the HOMO is anti-symmetric and LUMO is symmetric, which agrees with the discussion in the given task.

The TS was confirmed by running a IRC calculation in both directions, and the above TS was indeed the maximum on the reaction coordinate graph.

[[Image:IRC_graphs.tif|frame|centre|LUMO TS]]

The HOMO of the TS is the combination of the HOMO of the cis-butadiene and the LUMO of the ethylene, and the LUMO is the opposite.

The C-C separation at the new bonding sites was noted to be 2.26354 and 2.26297 Å. The double bonds on the cis-butadiene are 1.38880 Å, single C-C bond is 1.40798 Å and the ethylene double bond is 1.39274 Å.

===Diels Alder===

TS1 optimisation fixed
{{DOI|10042/to-7286}}
TS2 optimisation
{{DOI|10042/to-7287}}
TS1 failed final opt
{{DOI|10042/to-7288}}
TS2 failed final opt
{{DOI|10042/to-7289}}

Rep:Mod:boredofcomplabs

2011-02-18T15:58:55Z

Ckw08: /* Optimising the "Chair" and "Boat" Transition Structures" */

=Module 3: Christopher Wood=

==Introduction==

In this module, GausView was used not only to optimise and analyse various molecules as before, but now expanded to study transition states. Transition states are states of maximum energy along a reaction path from reactants to products. The structure and geometry of the transition states can significantly determine the structure of the product of the reaction. This is a highly useful tool for chemists and therefore will be investigated in this module

==The Cope Rearrangement==

In this section, the Cope rearrangement of 1,5-hexadiene will be studied. First of all, the low energy minima were determined for the structural arrangements of 1,5-hexadiene.

The structures were made in GaussView and "Cleaned". The job type was '''Optimization''' and the default method was left unchanged, '''Hartree Fock'' with basis set '''3-21G'''. The size of the output files were also limited to a maximum of 250 MB. The resultant molecule's symmetry was noted after selecting '''Symmetrize'''. The table below shows the various minima in the structure of 1,5-hexadiene.

{| border="1" cellpadding="5"
|- align="center"
| width="150" | '''Conformer'''
| width="150" | '''Structure'''
| width="100" | '''Point Group'''
| width="200" | '''Energy/Hartrees <br />HF/3-21G'''
| width="200" | '''Relative Energy/kcal/mol'''
|- align="center"
| ''gauche1''
|
<jmol>
<jmolApplet>
<title>Gauche 1</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche1.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7224}}
| C<sub>2</sub>
| -231.68772
| 3.10
|- align="center"
| ''gauche2''
|
<jmol>
<jmolApplet>
<title>Gauche 2</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche2.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7225}}
| C<sub>2</sub>
| -231.69167
| 0.62
|- align="center"
| ''gauche3''
|
<jmol>
<jmolApplet>
<title>Gauche 3</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche3.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7226}}
| C<sub>1</sub>
| -231.69266
| 0.00
|- align="center"
| ''gauche4''
|
<jmol>
<jmolApplet>
<title>Gauche 4</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche4.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7227}}
| C<sub>2</sub>
| -231.69153
| 0.71
|- align="center"
| ''gauche5''
|
<jmol>
<jmolApplet>
<title>Gauche 5</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche5.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7228}}
| C<sub>1</sub>
| -231.68962
| 1.91
|- align="center"
| ''gauche6''
|
<jmol>
<jmolApplet>
<title>Gauche 6</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Gauche6.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7229}}
| C<sub>1</sub>
| -231.68916
| 2.20
|- align="center"
| ''anti1''
|
<jmol>
<jmolApplet>
<title>Anti 1</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Anti1.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7230}}
| C<sub>2</sub>
| -231.69260
| 0.04
|- align="center"
| ''anti2''
|
<jmol>
<jmolApplet>
<title>Anti 2</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Anti2.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7232}}
| C<sub>i</sub>
| -231.69254
| 0.08
|- align="center"
| ''anti3''
|
<jmol>
<jmolApplet>
<title>Anti 3</title><color>white</color>
<size>200</size>
<script>zoom 150</script>
<uploadedFileContents>Anti3.mol</uploadedFileContents>
</jmolApplet>
</jmol>
{{DOI|10042/to-7231}}
| C<sub>2h</sub>
| -231.68907
| 2.25
|- align="center"
| ''anti4''
|
ANTI 4
{{DOI|10042/to-7233}}
| C<sub>1</sub>
| -231.69097
| 1.06
|}

The relative energies are taken in comparison to the lowest energy minima, which was determined to be '''gauche 3'''.

To compare the energy outcomes of different optimisation methods, the C<sub>i</sub> minima structure was reoptimised using '''B3LYP/3-21G''' and then '''6-31G'''. There was no observable change in structure, but the energies that were computed were -233.33634 Au and -234.55970 Au respectively.

A frequency job was then run on the optimised structure with the following results: {{DOI|10042/to-7236}}

{|
|-
|
| Hatree
|-
| Sum of electronic and zero-point Energies
| -234.416244
|-
| Sum of electronic and thermal Energies
| -234.408953
|-
| Sum of electronic and thermal Enthalpies
| -234.408009
|-
| Sum of electronic and thermal Free Energies
| -234.447848
|-
|}

===Optimising the "Chair" and "Boat" Transition Structures"===

The Cope rearrange is a [3,3]-sigmatropic shift rearrangement. it is generally accepted that the reaction occurs in a concerted fashion via either a "chair" or "boat" transition structure. In this section, both structure shall be analysed to a '''B3LYP/6-31G''' level of theory, which has been shown to give good agreement to experimental data.

====Chair====

The first method used to determine the transition structure involved the placement of 2 allyl fragments positioned approximately 2.2 Å apart. They were first optimised using '''HF/3-21G''' level of theory. Once the transition structure was approximately made, a '''Opt+Freq''' calculation was set up and was optimised '''to a TS (Berry)'''. The force constants were calculated '''Once''' and '''Opt=NoEigen''' was added to the ''Additional keyword'' box. {{DOI|10042/to-7246}}

There was an imaginary frequency observed at -817.89 cm<sup>-1</sup> and this corresponded to the bonds forming/breaking in this rearrangement reaction. (Jmol unable to show vibration...)

<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 1;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>Chair_1_log.out</uploadedFileContents> </jmolApplet></jmol>

On examining the structure, the C-C separations, at the sites of the new forming C-C bonds, were observed to be 2.01954 and 2.01999 Å.

The next method investigated involved fixing the C-C separtions mentioned above. First of all, the C-C separations (where the new bonds would form) were fixed at 2.2 Å. An optimisation calculation was run then the separations were then optimised in a second calculation by running an '''Opt+Freq to a TS (Berry)'''. {{DOI|10042/to-7267}}

The C-C separations were noted to be 2.01998 Å. This is similar to the previous method. The structures resulting from both methods were both the same.

====Boat====

For the boat transition structure a different method had to be employed. this involved mapping the reactants and products and letting the program determine the structure. Initially, a chair TS was given, as below, but after tweaking the geometry of both the reagents and products the boat was achieved. {{DOI|10042/to-7274}} and {{DOI|10042/to-7275}}

<jmol> <jmolAppletButton> <uploadedFileContents>Boat_failed_opt_mol.mol</uploadedFileContents> <text>Failed Boat</text> </jmolAppletButton> </jmol>
<jmol> <jmolAppletButton> <uploadedFileContents>Boat_opt_mol.mol</uploadedFileContents> <text>Successful boat</text> </jmolAppletButton> </jmol>

Again there is only 1 imaginary frequency observed and this corresponds to the desired rearrangement reaction.

====Intrinsic Reaction Coordinate====

Using IRC, this allows us to follow the minimum energy path from a transition structure down to its local minimum on a potential energy surface. This confirmed that my input chair structure was and TS in accordance to the IRC plot. {{DOI|10042/to-7277}}

=Exercise=

If the same method were undertaken as above, the resultant transition structure resembled a chair and not a boat.

File:Boat opt mol.mol

2011-02-18T15:45:46Z

Ckw08:

File:Boat failed opt mol.mol

2011-02-18T15:45:20Z

Ckw08:

Rep:Mod:boredofcomplabs

2011-02-18T15:25:28Z

File:NEW trans freq OUT.out

2011-02-10T01:59:56Z

Ckw08:

Rep:Mod:ckw082

2011-02-10T01:49:52Z

Ckw08: /* Isomers of Mo(CO)<sub>4</sub>L<sub>2</sub> */

=Module 2: Christopher Wood=

==Introduction==

In this module, various computational methods are going to be explored to help analyse various inorganic structures. The chosen software is GaussView due to its appropriateness to the problems and the ability to a take a problem further and take a much deeper analysis. Using GaussView, one can create a molecule and design a calculation that would be run by a sister program Gaussian. Once your calculation is complete, you get a combination of various files which can be viewed as a log in many word editing softwares and all the calculated values can be noted. If the results were then open once again in GaussView, and visual representation of your data will be shown.

This is a very powerful tool as this allows for visual representation of a multitude of data. MOs and vibrations can be visualised and spectra can be calculated. This type of computational chemistry can greatly help chemists in the understanding of reactions and properties of various molecules and this in turn can be used to along side practical experiments to compare your actual and predicted products. Comparison of the two could give surprising results.

==GaussView Analysis of BH<sub>3</sub>==

In this section the GaussView software was investigated using a simple molecule of BH<sub>3</sub>. The molecule was made and the bonds adjusted to a length of 1.50 Å. The molecule was then optimised using '''DFT''', with the '''B3LYP''' method and '''3-21G''' basis set. These parameters are used due to fast calculation time, but this affects the accuracy of the results. Since BH<sub>3</sub> is a simple small molecule, these parameters are sufficient enough to achieve credible results.

In the calculation, the intermediates can be viewed. For those with a relatively large bond distance, GaussView would not display a bond. This is due to the program's settings and defaults for bonds with the corresponding atoms. With this in mind, the program would define bonds to be within a specific distance even though a bond of a longer length can exist. BH<sub>3</sub> exists as a trigonal planar molecule, with D<sub>3h</sub> symmetry. The bond angles between the B-H bonds are 120.0<sup>o</sup> (1d.p.) with a bond length of 1.19 Å (2d.p.).

Once the molecule was optimized, the MO's can be calculated from the checkpoint file. In this calculation, '''pop=full''' was added to additional keywords and '''Full NBO''' was selected. These results can then be compared to LCAO for each of the MO's. Below is a diagram illustrating the LCAO and computed molecular orbitals for the first 8 MO's of BH<sub>3</sub>. The calculation file is located here: {{DOI|10042/to-6892}}

[[Image:Mo_diagram_small_gif.gif|frame|centre|Figure 1: MO diagram of BH<sub>3</sub>]]

[[Image:MO_energies.gif|frame|right|Figure 2: Calculated MO energies for BH<sub>3</sub>]]
[[Image:Formal_charges_gif.gif|thumb|200px|Figure 3: Formal charges within BH<sub>3</sub>]]
As you can see from the figure above, the shapes of the orbitals in LCAO fit well to the calculated MO's. The main difference between the two would be that overlapping lobes would either form an constructive or destructive interaction. With a constructive overlap, the lobes would combine to form a seamless lobe. For destructive overlaps, a nodal plane would form. This would exert a "pressure" on the lobes, squishing and distorting their shapes, like balloons packed into a confined and competing space. This is shown well by the 3a<sub>1</sub>' orbital. The inner boron s orbital is spherical, but since it is in an opposite phase to the surrounding hydrogen s orbitals, nodal planes form between them, and this highly distorts the once spherical boron orbital to more of a triangular prism in shape.

The big difference between the two methods however is the ordering of the MO energies. Using computational methods, the 3a<sub>1</sub>' MO is higher in energy in comparison to the 2e' MOs. This shown by figure 2 and contradicts LCAO theory. LCAO is only an approximation to determine MOs and cannot predict entirely relative energies. This is due to complex electrostatic interactions of the orbitals and their relative orientation and spacing.

Another useful tool in using GaussView is the NBO analysis. This gives us information on the "atomic charges" of the individual atoms in the molecule. Figure 3 shows the pictorial results given by GaussView.

This leads onto one final very useful computational calculation and that determines the frequencies of various vibrations within the molecule. The software can then animate the vibrations to show visually what happens so that various movements of specific groups can be isolated, for example a distinction between stretching and scissoring motions can be identified. The same method was basis sets were applied, the only thing changed was the job type to '''frequency''' and in additional key words '''pop=(full,nbo)'''. Below is a table that summarises the calculated vibrations.

{| class="wikitable" border="1"
|'''No.'''
|'''Mode of Vibration'''
|'''Description'''
|'''Frequency/cm<sup>-1</sup>''' (to the nearest 10 cm<sup>-1</sup>)
|'''Intensity'''
|'''Symmetry (D<sub>3h</sub> Point Group)'''
|----
|1
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 3;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Synchronised wagging of the hydrogen atoms in the same direction, with slight movement of the boron centre.
|1140
|93
|a<sub>2</sub>"
|----
|2
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 4;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Bottom 2 hydrogen atoms scissor in-plane. The bond between the boron and the third hydrogen looks to remain at a fixed length, and the two atoms bob up and down very slightly.
|1200
|12
|e'
|----
|3
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 5;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Rocking motion in-plane. The bottom 3 hydrogens appear to stay a at fixed distance from the boron and it looks to just rotate, whilst the top hyrogen rocks in the opposite direction in a much larger amplitude.
|1200
|12
|e'
|----
|4
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 6;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Symmetric stretching of all 3 hydrogen atoms in relation to a fixed hydrogen.
|2600
|0
|a<sub>1</sub>'
|----
|5
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 7;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Assymetric stretch where the bottom 2 hydrogens are alternating their streches, whist the boron wags very slightly in relation to the third, fixed, hydrogen.
|2740
|104
|e'
|----
|6
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 8;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Asymmetric stretch where the bottom 2 hydrogens now in synchronised stretching motions whilst the third is dramatically stretching in response to the other 2.
|2740
|104
|e'
|----
|}

[[Image:Ir_spectrum.gif|thumb|200px|Figure 4: Calculated IR spectrum of BH<sub>3</sub>]]
Using this data the IR spectrum can be predicted. Figure 4 shows the predicted spectrum. The biggest point to take from this is the number of observed peaks in comparison to the number calculated. There are 6 calculated vibrations and yet there are only 3 distinct peaks. There are two reasons for this, Firstly, 2 is degenerate with 3 whilst 5 is degenerate with 6. This means that their peaks combine since it is at the same frequency. And lastly, vibration 4 is a completely symmetric stretch. This means that it cannot be observed under IR due to there being no change in overall dipole in the vibration.

Now that the basics have been applied to a relatively simple molecule, the same analysis shall be applied to a much heavier molecule, using appropriate approximations to aid in the calculations.

==GaussView Analysis of TlBr<sub>3</sub>==

[[Image:TlBr3_opt_data.jpg|thumb|200px|Figure 5: Summary of results for optimisation of TlBr<sub>3</sub>]]
TlBr<sub>3</sub> was modelled in GaussView as before, but now the symmetry was restricted to its D<sub>3h</sub> symmetry group and the tolerance was set to '''Very tight (0.0001)'''. Again, an optimisation was run using '''DFT''' and '''B3LYP'''. This time the basis set of choice was '''LanL2DZ''' and this would yield far more accurate results than if the same calculation was run using the previous method set. The summary of the results are shown in figure 5. The optimisation data can be found here: https://wiki.ch.ic.ac.uk/wiki/images/f/f1/TLBR3_FREQ.LOG (this was not run on SCAN due to queue issues).

The optimised TlBr<sub>3</sub> molecule had equilibrium bond lengths of 2.65 Å (2d.p.) which compares well to the literature of 2.762 Å<ref>A. Linden et al., ''Inorganica Chimica Acta'', '''2002''', 332, 61-71.</ref>. The corresponding bond angles between the Tl-Br bonds were all 120.0<sup>o</sup> (1d.p.). To check that this is indeed the optimised structure, frequency analysis can be undertaken. This can determine whether your structure is indeed optimum by looking in the log file and examining the low frequencies. If the 6 low frequencies are within the range of <sup>+</sup><sub>-</sub>10 cm<sup>-1</sup> then the structure has be optimised to a reasonable degree. The closer the values to zero, the more accurate the optimisation.

To run the frequency analysis, the same method and basis set were used, but the job type now changed to frequency (as before with BH<sub>3</sub>). The same basis set has to be used because the molecule has been preoptimised using the previous set. If you change the basis set, the structure may not be optimised for the new set and this can drastically effect the frequency results. When considering molecular vibrations, a molecule can have 3N-6 vibrational frequencies. The "-6" are due to motions of the core. It is for this reason that they must be minimised in the optimised structure. The first "real" virbration is observed at 46.4289 cm<sup>-1</sup>. One major point to make is that with computational analysis and especially with the methods and basis sets I have used in this experiment, the frequencies '''cannot''' be expressed to this accuracy.

==Isomers of Mo(CO)<sub>4</sub>L<sub>2</sub>==

In this part of the module, the cis and trans isomers of MO(CO)<sub>4</sub>(PCl<sub>3</sub>)<sub>2</sub> shall be investigated. First of all, both structures have to be optimized before any analysis can be taken. The method used for the calculations was'''B3LYP''' with a pseudo-potential of '''LANL2MB''' and '''opt=loose''' in "Additional keywords".

This gave a partially optimised structures were then altered by instruction:
for the cis conformer ensure that one Cl points up parallel to the axial bond, and that one Cl of the other group points down. Make sure you rotate the whole group and not just a single Cl atom
for the trans conformer ensure that both PCl3 groups are eclipsed and that one Cl of each group lies parallel to one Mo-C bond

The optimisation was then run again but with a far more accurate basis set of '''LANL2DZ''' and '''int=ultrafine scf=conver=9''' replaced opt=loose in the "Additional keywords". Once the molecules were fully optimised, the IR frequencies can be calculated. To do so, the job was changed to frequency and the additional keywords were kept the same to avoid negative frequencies. My calculations for both can be found here: cis ({{DOI|10042/to-6968}}), trans ({{DOI|10042/to-7080}}). Below are the fully optimized structures on which the frequency analysis was run.

<jmol> <jmolAppletButton> <uploadedFileContents>Cis_freq_mol.mol</uploadedFileContents> <text>Cis geometry</text> </jmolAppletButton> </jmol>
<jmol> <jmolAppletButton> <uploadedFileContents>NEW_trans_final_opt_mol.mol</uploadedFileContents> <text>Trans geometry</text> </jmolAppletButton> </jmol>

When comparing the two structures, there aren't that many differences between the two (despite the obvious cis and trans). But the biggest difference, even though it is small, is the angle of the two trans CO ligands. Due to the two large ligands being cis to each other, this puts strain on the other CO ligands and pushes them away slightly. This changes the angle from 180.0<sup>o</sup> to 178.3<sup>o</sup> (1d.p.). This is not observed in the trans complex.

The energies of the cis and trans complex are calculated to be: -1637201.602 kJ/mol and -1637198.869 kJ/mol respectively. This is a difference of 2.733 kJ/mol, in favour of forming the cis complex. This contradicts literature, where the trans is favoured<ref>D. Darensbourg, ''Inorg. Chem.'', '''1979''', ''18'', 14-17. {{DOI|10.1021/ic50191a003}}</ref>. This would make more sense due to the larger separation of the bulky groups. The strain is observed in the structure of the cis, as mentioned above.

When undertaking vibrational analysis it was observed that there were vibrations of a very low frequency, ranging from frequencies of 4 to 18 cm<sup>-1</sup>. Below is a table to illustrate these vibrations.

{| class="wikitable" border="1"
|'''No.'''
|'''Mode of Vibration'''
|'''Description'''
|'''Frequency/cm<sup>-1</sup>''' (to the nearest 10 cm<sup>-1</sup>)
|'''Intensity'''
|----
|1
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 1;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>Cis_freq_log.out</uploadedFileContents> </jmolApplet></jmol>
|Synchronised wagging of the hydrogen atoms in the same direction, with slight movement of the boron centre.
|1140
|93
|----
|2
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 2;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>Cis_freq_log.out</uploadedFileContents> </jmolApplet></jmol>
|Bottom 2 hydrogen atoms scissor in-plane. The bond between the boron and the third hydrogen looks to remain at a fixed length, and the two atoms bob up and down very slightly.
|1200
|12
|----
|}

==Project==

For my project I have decided to investigate Al2Br2Cl4. Due to massive queues of up to 16 hours or so, I havent had time to fully analyse everything but all my calculations I shall post as soon as I get them and I shall endevour to finish everything ASAP.

The molecules were preoptimised using DFT, B3LYP and 3-21G. Then optimised with LanL2DZ with int=ultrafine scf=conver=9. Finally frequency analysis adding pop=full.

Al2Cl6 frequency/MO result calculation
<jmol> <jmolAppletButton> <uploadedFileContents>Al2cl6_mol.mol</uploadedFileContents> <text>Al2Cl6</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7016

Al2Cl4Br2 frequency/MO result calculation (Br2 bridging)
<jmol> <jmolAppletButton> <uploadedFileContents>Centre_freq_mol.mol</uploadedFileContents> <text>Al2Cl4Br2 (bridging)</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7048

Al2Cl4Br2 frequency/MO result calculation (Br's diagonal)
<jmol> <jmolAppletButton> <uploadedFileContents>Freq_mol_diagonal.mol</uploadedFileContents> <text>Al2Cl4Br2 (diagonal)</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7046

Al2Cl4Br2 frequency/MO result calculation (one side)
<jmol> <jmolAppletButton> <uploadedFileContents>Br2_one_side_mol.mol</uploadedFileContents> <text>Al2Cl4Br2 (one side)</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7050

Al2Cl4Br2 frequency/MO result calculation (cis)
<jmol> <jmolAppletButton> <uploadedFileContents>Cis_freq_mol2.mol</uploadedFileContents> <text>Al2Cl4Br2 (cis)</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7051

Al2Cl4Br2 frequency/MO result calculation (in and up)
<jmol> <jmolAppletButton> <uploadedFileContents>In_and_up_freq_mol.mol</uploadedFileContents> <text>Al2Cl4Br2 (in and up)</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7063

Al2Cl4Br2 frequency/MO result calculation (in and down)
<jmol> <jmolAppletButton> <uploadedFileContents>In_and_down_freq_mol.mol</uploadedFileContents> <text>Al2Cl4Br2 (in and down)</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7062

==References==
<references />

Rep:Mod:ckw082

2011-02-08T16:44:48Z

Ckw08: /* Project */

=Module 2: Christopher Wood=

==Introduction==

In this module, various computational methods are going to be explored to help analyse various inorganic structures. The chosen software is GaussView due to its appropriateness to the problems and the ability to a take a problem further and take a much deeper analysis. Using GaussView, one can create a molecule and design a calculation that would be run by a sister program Gaussian. Once your calculation is complete, you get a combination of various files which can be viewed as a log in many word editing softwares and all the calculated values can be noted. If the results were then open once again in GaussView, and visual representation of your data will be shown.

This is a very powerful tool as this allows for visual representation of a multitude of data. MOs and vibrations can be visualised and spectra can be calculated. This type of computational chemistry can greatly help chemists in the understanding of reactions and properties of various molecules and this in turn can be used to along side practical experiments to compare your actual and predicted products. Comparison of the two could give surprising results.

==GaussView Analysis of BH<sub>3</sub>==

In this section the GaussView software was investigated using a simple molecule of BH<sub>3</sub>. The molecule was made and the bonds adjusted to a length of 1.50 Å. The molecule was then optimised using '''DFT''', with the '''B3LYP''' method and '''3-21G''' basis set. These parameters are used due to fast calculation time, but this affects the accuracy of the results. Since BH<sub>3</sub> is a simple small molecule, these parameters are sufficient enough to achieve credible results.

In the calculation, the intermediates can be viewed. For those with a relatively large bond distance, GaussView would not display a bond. This is due to the program's settings and defaults for bonds with the corresponding atoms. With this in mind, the program would define bonds to be within a specific distance even though a bond of a longer length can exist. BH<sub>3</sub> exists as a trigonal planar molecule, with D<sub>3h</sub> symmetry. The bond angles between the B-H bonds are 120.0<sup>o</sup> (1d.p.) with a bond length of 1.19 Å (2d.p.).

Once the molecule was optimized, the MO's can be calculated from the checkpoint file. In this calculation, '''pop=full''' was added to additional keywords and '''Full NBO''' was selected. These results can then be compared to LCAO for each of the MO's. Below is a diagram illustrating the LCAO and computed molecular orbitals for the first 8 MO's of BH<sub>3</sub>. The calculation file is located here: {{DOI|10042/to-6892}}

[[Image:Mo_diagram_small_gif.gif|frame|centre|Figure 1: MO diagram of BH<sub>3</sub>]]

[[Image:MO_energies.gif|frame|right|Figure 2: Calculated MO energies for BH<sub>3</sub>]]
[[Image:Formal_charges_gif.gif|thumb|200px|Figure 3: Formal charges within BH<sub>3</sub>]]
As you can see from the figure above, the shapes of the orbitals in LCAO fit well to the calculated MO's. The main difference between the two would be that overlapping lobes would either form an constructive or destructive interaction. With a constructive overlap, the lobes would combine to form a seamless lobe. For destructive overlaps, a nodal plane would form. This would exert a "pressure" on the lobes, squishing and distorting their shapes, like balloons packed into a confined and competing space. This is shown well by the 3a<sub>1</sub>' orbital. The inner boron s orbital is spherical, but since it is in an opposite phase to the surrounding hydrogen s orbitals, nodal planes form between them, and this highly distorts the once spherical boron orbital to more of a triangular prism in shape.

The big difference between the two methods however is the ordering of the MO energies. Using computational methods, the 3a<sub>1</sub>' MO is higher in energy in comparison to the 2e' MOs. This shown by figure 2 and contradicts LCAO theory. LCAO is only an approximation to determine MOs and cannot predict entirely relative energies. This is due to complex electrostatic interactions of the orbitals and their relative orientation and spacing.

Another useful tool in using GaussView is the NBO analysis. This gives us information on the "atomic charges" of the individual atoms in the molecule. Figure 3 shows the pictorial results given by GaussView.

This leads onto one final very useful computational calculation and that determines the frequencies of various vibrations within the molecule. The software can then animate the vibrations to show visually what happens so that various movements of specific groups can be isolated, for example a distinction between stretching and scissoring motions can be identified. The same method was basis sets were applied, the only thing changed was the job type to '''frequency''' and in additional key words '''pop=(full,nbo)'''. Below is a table that summarises the calculated vibrations.

{| class="wikitable" border="1"
|'''No.'''
|'''Mode of Vibration'''
|'''Description'''
|'''Frequency/cm<sup>-1</sup>''' (to the nearest 10 cm<sup>-1</sup>)
|'''Intensity'''
|'''Symmetry (D<sub>3h</sub> Point Group)'''
|----
|1
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 3;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Synchronised wagging of the hydrogen atoms in the same direction, with slight movement of the boron centre.
|1140
|93
|a<sub>2</sub>"
|----
|2
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 4;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Bottom 2 hydrogen atoms scissor in-plane. The bond between the boron and the third hydrogen looks to remain at a fixed length, and the two atoms bob up and down very slightly.
|1200
|12
|e'
|----
|3
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 5;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Rocking motion in-plane. The bottom 3 hydrogens appear to stay a at fixed distance from the boron and it looks to just rotate, whilst the top hyrogen rocks in the opposite direction in a much larger amplitude.
|1200
|12
|e'
|----
|4
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 6;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Symmetric stretching of all 3 hydrogen atoms in relation to a fixed hydrogen.
|2600
|0
|a<sub>1</sub>'
|----
|5
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 7;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Assymetric stretch where the bottom 2 hydrogens are alternating their streches, whist the boron wags very slightly in relation to the third, fixed, hydrogen.
|2740
|104
|e'
|----
|6
|<jmol><jmolApplet>
<title>Vibration</title><color>white</color><size>150</size>
<script>zoom 100;frame 8;vectors 4;vectors scale 2.0;color vectors blue; vibration 2;
</script><uploadedFileContents>CHRISWOOD_BH3_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol>
|Asymmetric stretch where the bottom 2 hydrogens now in synchronised stretching motions whilst the third is dramatically stretching in response to the other 2.
|2740
|104
|e'
|----
|}

[[Image:Ir_spectrum.gif|thumb|200px|Figure 4: Calculated IR spectrum of BH<sub>3</sub>]]
Using this data the IR spectrum can be predicted. Figure 4 shows the predicted spectrum. The biggest point to take from this is the number of observed peaks in comparison to the number calculated. There are 6 calculated vibrations and yet there are only 3 distinct peaks. There are two reasons for this, Firstly, 2 is degenerate with 3 whilst 5 is degenerate with 6. This means that their peaks combine since it is at the same frequency. And lastly, vibration 4 is a completely symmetric stretch. This means that it cannot be observed under IR due to there being no change in overall dipole in the vibration.

Now that the basics have been applied to a relatively simple molecule, the same analysis shall be applied to a much heavier molecule, using appropriate approximations to aid in the calculations.

==GaussView Analysis of TlBr<sub>3</sub>==

[[Image:TlBr3_opt_data.jpg|thumb|200px|Figure 5: Summary of results for optimisation of TlBr<sub>3</sub>]]
TlBr<sub>3</sub> was modelled in GaussView as before, but now the symmetry was restricted to its D<sub>3h</sub> symmetry group and the tolerance was set to '''Very tight (0.0001)'''. Again, an optimisation was run using '''DFT''' and '''B3LYP'''. This time the basis set of choice was '''LanL2DZ''' and this would yield far more accurate results than if the same calculation was run using the previous method set. The summary of the results are shown in figure 5. The optimisation data can be found here: https://wiki.ch.ic.ac.uk/wiki/images/f/f1/TLBR3_FREQ.LOG (this was not run on SCAN due to queue issues).

The optimised TlBr<sub>3</sub> molecule had equilibrium bond lengths of 2.65 Å (2d.p.) which compares well to the literature of 2.762 Å<ref>A. Linden et al., ''Inorganica Chimica Acta'', '''2002''', 332, 61-71.</ref>. The corresponding bond angles between the Tl-Br bonds were all 120.0<sup>o</sup> (1d.p.). To check that this is indeed the optimised structure, frequency analysis can be undertaken. This can determine whether your structure is indeed optimum by looking in the log file and examining the low frequencies. If the 6 low frequencies are within the range of <sup>+</sup><sub>-</sub>10 cm<sup>-1</sup> then the structure has be optimised to a reasonable degree. The closer the values to zero, the more accurate the optimisation.

To run the frequency analysis, the same method and basis set were used, but the job type now changed to frequency (as before with BH<sub>3</sub>). The same basis set has to be used because the molecule has been preoptimised using the previous set. If you change the basis set, the structure may not be optimised for the new set and this can drastically effect the frequency results. When considering molecular vibrations, a molecule can have 3N-6 vibrational frequencies. The "-6" are due to motions of the core. It is for this reason that they must be minimised in the optimised structure. The first "real" virbration is observed at 46.4289 cm<sup>-1</sup>. One major point to make is that with computational analysis and especially with the methods and basis sets I have used in this experiment, the frequencies '''cannot''' be expressed to this accuracy.

==Isomers of Mo(CO)<sub>4</sub>L<sub>2</sub>==

In this part of the module, the cis and trans isomers of MO(CO)<sub>4</sub>(PCl<sub>3</sub>)<sub>2</sub> shall be investigated. First of all, both structures have to be optimized before any analysis can be taken. The method used for the calculations was'''B3LYP''' with a pseudo-potential of '''LANL2MB''' and '''opt=loose''' in "Additional keywords".

This gave a partially optimised structures were then altered by instruction:
for the cis conformer ensure that one Cl points up parallel to the axial bond, and that one Cl of the other group points down. Make sure you rotate the whole group and not just a single Cl atom
for the trans conformer ensure that both PCl3 groups are eclipsed and that one Cl of each group lies parallel to one Mo-C bond

The optimisation was then run again but with a far more accurate basis set of '''LANL2DZ''' and '''int=ultrafine scf=conver=9''' replaced opt=loose in the "Additional keywords". Once the molecules were fully optimised, the IR frequencies can be calculated. To do so, the job was changed to frequency and the additional keywords were kept the same to avoid negative frequencies. My calculations for both can be found here: cis ({{DOI|10042/to-6968}}), trans ({{DOI|10042/to-6969}}). Below are the fully optimized structures on which the frequency analysis was run.

<jmol> <jmolAppletButton> <uploadedFileContents>Cis_freq_mol.mol</uploadedFileContents> <text>Cis geometry</text> </jmolAppletButton> </jmol>
<jmol> <jmolAppletButton> <uploadedFileContents>Trans_freq_mol.mol</uploadedFileContents> <text>Trans geometry</text> </jmolAppletButton> </jmol>

==Project==

For my project I have decided to investigate Al2Br2Cl4. Due to massive queues of up to 16 hours or so, I havent had time to fully analyse everything but all my calculations I shall post as soon as I get them and I shall endevour to finish everything ASAP.

Al2Cl6 frequency/MO result calculation
<jmol> <jmolAppletButton> <uploadedFileContents>Al2cl6_mol.mol</uploadedFileContents> <text>Al2Cl6</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7016

Al2Cl4Br2 frequency/MO result calculation (Br2 bridging)
<jmol> <jmolAppletButton> <uploadedFileContents>Centre_freq_mol.mol</uploadedFileContents> <text>Al2Cl4Br2 (bridging)</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7048

Al2Cl4Br2 frequency/MO result calculation (Br's diagonal)
<jmol> <jmolAppletButton> <uploadedFileContents>Freq_mol_diagonal.mol</uploadedFileContents> <text>Al2Cl4Br2 (diagonal)</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-7046

==References==
<references />

File:Centre freq mol.mol

2011-02-08T16:44:39Z

Ckw08:

File:Freq mol diagonal.mol

2011-02-08T16:44:21Z

Ckw08:

File:Al2cl6 mol.mol

2011-02-08T16:38:35Z

Ckw08: