ChemWiki - User contributions [en]

Rep:Mod3:jib09

2012-02-17T15:43:45Z

Jib09: /* Optimizing the Reactants and Products */

== Cope Rearrangement of 1,5-Hexadiene ==
===Aims===

===Introduction===

===Optimizing the Reactants and Products===

The ease of rotation about the carbon-carbon single bonds in 1,5-Hexadiene makes it possible for it to have many conformational isomers. To determine which is the most stable each of the conformers will be optimized using the Hartree-Fock method and a 3-21G basis set. This level of analysis is relatively low but it should be able to provide a guided to the potential energies of the conformers and indicate which is the most stable.

'''Table 1. HF/3-21G Optimization of 1,5-Hexadiene conformers'''

{| class="wikitable"
|-
| || || ||
|-
|'''Conformation''' || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point Group'''
|-
| <jmolFile text="Gauche 1"> 10030.mol </jmolFile><ref> [[File:10020.LOG]] </ref> || -231.68772 || 3.10 || C2
|-
| <jmolFile text="Gauche 2"> 10031.mol </jmolFile><ref> [[File:10021.LOG]]</ref> || -231.69166 || 0.62 || C2
|-
| <jmolFile text="Gauche 3"> 10032.mol </jmolFile><ref> [[File:10022.LOG]] </ref> || -231.69266 || 0.00 || C1
|-
| <jmolFile text="Gauche 4"> 10033.mol </jmolFile> <ref> [[File:10023.LOG]] </ref> || -231.69153 || 0.71 || C2
|-
| <jmolFile text="Gauche 5"> 10034.mol </jmolFile> <ref> [[File:10024.LOG]] </ref> || -231.68962 || 1.91 || C1
|-
| <jmolFile text="Gauche 6"> 10035.mol </jmolFile> <ref> [[File:10025.LOG]] </ref> || -231.68916 || 2.20 || C1
|-
| <jmolFile text="Anti 1"> 10036.mol </jmolFile> <ref> [[File:10026.LOG]] </ref> || -231.69260 || 0.04 || C2
|-
| <jmolFile text="Anti 2"> 10037.mol </jmolFile> <ref> [[File:10027.LOG]] </ref> || -231.69254 || 0.08 || Ci
|-
| <jmolFile text="Anti 3"> 10038.mol </jmolFile> <ref> [[File:10028.LOG]] </ref> || -231.68907 || 2.25 || C2H
|-
| <jmolFile text="Anti 4"> 10039.mol </jmolFile> <ref> [[File:10029.LOG]] </ref> || -231.69097 || 1.06 || C1
|}
*The 3DJmol structures can be viewed by following the corresponding link and the LOG files located in the references.

Prior to running the calculations it was expected that the most stable conformer would have a ''anti'' conformation, as it would have lower energy steric interactions, but as can be seen form the data the most stable conformer is ''gauche 3''. This result could be due to the fact that a low level method of analysis was used (HF/3-21G), which is not accurate enough, or some other factor is also playing a role in determining the energy of the conformers.

To obtain more accurate calculations, the 3 most stable conformers were re-optimized using a higher level of analysis. The method used was DFT/B3YLP with a 6-31G basis set, this should yield a more accurate optimization and a better approximation to optimized geometry.

'''Table 2. Optimization of most stable 1,5-Hexadiene conformers using DFT/6-31G '''

{| class="wikitable"
|-
| || || ||
|-
|Conformer || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point group'''
|-
| <jmolFile text="Gauche 3"> 10057.mol </jmolFile> <ref> [[File:10058.LOG]] </ref> || -234.55934 || 0.29 || C1
|-
| <jmolFile text="Anti 1"> 10055.mol </jmolFile> <ref> [[File:10059.LOG]] </ref> || -234.55978 || 0.00 || C2
|-
| <jmolFile text="Anti 2"> 10056.mol </jmolFile> <ref> [[File:10060.LOG]] </ref> || -234.55970 || 0.05 || Ci
|}
*The 3DJmol structures can be viewed by following the corresponding link and the LOG files located in the references.

The higher level of optimization resulted in both ''anti'' conformers being more stable than the ''gauche'', which was the expected result, even though the resulting geometries for the DFT-method did not vary significantly form the Hartree-Frock method.

===Frequency and Thermochemical Analysis ===

*'''Sum of Electronic and Zero-Point Energies (E = E0 + ZPE )''': The potential energy at 0K including the zero point vibrational energy.
*'''Sum of Electronic and Thermal Energies (E = E0 + Etot''' ): The total electronic energy + the total internal thermal energy, consisting of the vibrational, rotational and translational energy.
* '''Sum of electronic and Thermal Enthalpies''' '''(E = E0 + Hcorrected)''': The total electronic energy + the correction to enthalpy due to room temperature.
*'''Sum of Electronic and Thermal Free Energies (E= E0 + Gcorrected'''): The total electronic energy + the correction to Gibbs free energy due to internal energy.

===References===
<references/>

Rep:Mod3:jib09

2012-02-17T12:46:19Z

Jib09: /* Optimizing the Reactants and Products */

== Cope Rearrangement of 1,5-Hexadiene ==
===Aims===

===Introduction===

===Optimizing the Reactants and Products===

The ease of rotation about the carbon-carbon single bonds in 1,5-Hexadiene makes it possible for it to have many conformational isomers. To determine which is the most stable each of the conformers will be optimized using the Hartree-Fock method and a 3-21G basis set. This level of analysis is relatively low but it should be able to provide a guided to the potential energies of the conformers and indicate which is the most stable.

'''Table 1. HF/3-21G Optimization of 1,5-Hexadiene conformers'''

{| class="wikitable"
|-
| || || ||
|-
|'''Conformation''' || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point Group'''
|-
| <jmolFile text="Gauche 1"> 10030.mol </jmolFile><ref> [[File:10020.LOG]] </ref> || -231.68772 || 3.10 || C2
|-
| <jmolFile text="Gauche 2"> 10031.mol </jmolFile><ref> [[File:10021.LOG]]</ref> || -231.69166 || 0.62 || C2
|-
| <jmolFile text="Gauche 3"> 10032.mol </jmolFile><ref> [[File:10022.LOG]] </ref> || -231.69266 || 0.00 || C1
|-
| <jmolFile text="Gauche 4"> 10033.mol </jmolFile> <ref> [[File:10023.LOG]] </ref> || -231.69153 || 0.71 || C2
|-
| <jmolFile text="Gauche 5"> 10034.mol </jmolFile> <ref> [[File:10024.LOG]] </ref> || -231.68962 || 1.91 || C1
|-
| <jmolFile text="Gauche 6"> 10035.mol </jmolFile> <ref> [[File:10025.LOG]] </ref> || -231.68916 || 2.20 || C1
|-
| <jmolFile text="Anti 1"> 10036.mol </jmolFile> <ref> [[File:10026.LOG]] </ref> || -231.69260 || 0.04 || C2
|-
| <jmolFile text="Anti 2"> 10037.mol </jmolFile> <ref> [[File:10027.LOG]] </ref> || -231.69254 || 0.08 || Ci
|-
| <jmolFile text="Anti 3"> 10038.mol </jmolFile> <ref> [[File:10028.LOG]] </ref> || -231.68907 || 2.25 || C2H
|-
| <jmolFile text="Anti 4"> 10039.mol </jmolFile> <ref> [[File:10029.LOG]] </ref> || -231.69097 || 1.06 || C1
|}
*The 3DJmol structures can be viewed by following the corresponding link and the LOG files located in the references.

Prior to running the calculations it was expected that the most stable conformer would have a ''anti'' conformation, as it would have lower energy steric interactions, but as can be seen form the data the most stable conformer is ''gauche 3''. This result could be due to the fact that a low level method of analysis was used (HF/3-21G), which is not accurate enough, or some other factor is also playing a role in determining the energy of the conformers.

To obtain more accurate calculations, the 3 most stable conformers were re-optimized using a higher level of analysis. The method used was DFT/B3YLP with a 6-31G basis set.

'''Table 2. Optimization of most stable 1,5-Hexadiene conformers using DFT/6-31G '''

{| class="wikitable"
|-
| || || ||
|-
|Conformer || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point group'''
|-
| <jmolFile text="Gauche 3"> 10057.mol </jmolFile> <ref> [[File:10058.LOG]] </ref> || -234.55934 || 0.29 || C1
|-
| <jmolFile text="Anti 1"> 10055.mol </jmolFile> <ref> [[File:10059.LOG]] </ref> || -234.55978 || 0.00 || C2
|-
| <jmolFile text="Anti 2"> 10056.mol </jmolFile> <ref> [[File:10060.LOG]] </ref> || -234.55970 || 0.05 || Ci
|}
*The 3DJmol structures can be viewed by following the corresponding link and the LOG files located in the references.

The higher level of optimization resulted in both ''anti'' conformers being more stable than the ''gauche'', which was the expected result. Even though the resulting geometries for the DFT-method did not vary significantly form the Hartree-Frock method

===Frequency and Thermochemical Analysis ===

*'''Sum of Electronic and Zero-Point Energies (E = E0 + ZPE )''': The potential energy at 0K including the zero point vibrational energy.
*'''Sum of Electronic and Thermal Energies (E = E0 + Etot''' ): The total electronic energy + the total internal thermal energy, consisting of the vibrational, rotational and translational energy.
* '''Sum of electronic and Thermal Enthalpies''' '''(E = E0 + Hcorrected)''': The total electronic energy + the correction to enthalpy due to room temperature.
*'''Sum of Electronic and Thermal Free Energies (E= E0 + Gcorrected'''): The total electronic energy + the correction to Gibbs free energy due to internal energy.

===References===
<references/>

File:10060.LOG

2012-02-17T12:46:13Z

Jib09:

File:10059.LOG

2012-02-17T12:45:54Z

Jib09:

File:10058.LOG

2012-02-17T12:44:43Z

Jib09:

File:10057.mol

2012-02-17T12:43:46Z

Jib09:

File:10056.mol

2012-02-17T12:43:16Z

Jib09:

File:10055.mol

2012-02-17T12:42:04Z

Jib09:

Rep:Mod3:jib09

2012-02-17T12:29:35Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

== Cope Rearrangement of 1,5-Hexadiene ==
===Aims===

===Introduction===

===Optimizing the Reactants and Products===

The ease of rotation about the carbon-carbon single bonds in 1,5-Hexadiene makes it possible for it to have many conformational isomers. To determine which is the most stable each of the conformers will be optimized using the Hartree-Fock method and a 3-21G basis set. This level of analysis is relatively low but it should be able to provide a guided to the potential energies of the conformers and indicate which is the most stable.

'''Table 1. HF/3-21G Optimization of 1,5-Hexadiene conformers'''

{| class="wikitable"
|-
| || || ||
|-
|'''Conformation''' || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point Group'''
|-
| <jmolFile text="Gauche 1"> 10030.mol </jmolFile><ref> [[File:10020.LOG]] </ref> || -231.68772 || 3.10 || C2
|-
| <jmolFile text="Gauche 2"> 10031.mol </jmolFile><ref> [[File:10021.LOG]]</ref> || -231.69166 || 0.62 || C2
|-
| <jmolFile text="Gauche 3"> 10032.mol </jmolFile><ref> [[File:10022.LOG]] </ref> || -231.69266 || 0.00 || C1
|-
| <jmolFile text="Gauche 4"> 10033.mol </jmolFile> <ref> [[File:10023.LOG]] </ref> || -231.69153 || 0.71 || C2
|-
| <jmolFile text="Gauche 5"> 10034.mol </jmolFile> <ref> [[File:10024.LOG]] </ref> || -231.68962 || 1.91 || C1
|-
| <jmolFile text="Gauche 6"> 10035.mol </jmolFile> <ref> [[File:10025.LOG]] </ref> || -231.68916 || 2.20 || C1
|-
| <jmolFile text="Anti 1"> 10036.mol </jmolFile> <ref> [[File:10026.LOG]] </ref> || -231.69260 || 0.04 || C2
|-
| <jmolFile text="Anti 2"> 10037.mol </jmolFile> <ref> [[File:10027.LOG]] </ref> || -231.69254 || 0.08 || Ci
|-
| <jmolFile text="Anti 3"> 10038.mol </jmolFile> <ref> [[File:10028.LOG]] </ref> || -231.68907 || 2.25 || C2H
|-
| <jmolFile text="Anti 4"> 10039.mol </jmolFile> <ref> [[File:10029.LOG]] </ref> || -231.69097 || 1.06 || C1
|}
*The 3DJmol structures can be viewed by following the corresponding link and the LOG files located in the references.

Prior to running the calculations it was expected that the most stable conformer would have a ''anti'' conformation, as it would have lower energy steric interactions, but as can be seen form the data the most stable conformer is ''gauche 3''. This result could be due to the fact that a low level method of analysis was used (HF/3-21G), which is not accurate enough, or some other factor is also playing a role in determining the energy of the conformers.

To obtain more accurate calculations, the 3 most stable conformers were re-optimized using a higher level of analysis. The method used was DFT/B3YLP with a 6-31G basis set.

'''Table 2. Optimization of most stable 1,5-Hexadiene conformers using DFT/6-31G '''

{| class="wikitable"
|-
| || || ||
|-
|Conformer || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point group'''
|-
|Gauche 3 || -234.55934 || 0.29 || C1
|-
|Anti 1 || -234.55978 || 0.00 || C2
|-
|Anti 2 || -234.55970 || 0.05 || Ci
|}

===Frequency and Thermochemical Analysis ===

*'''Sum of Electronic and Zero-Point Energies (E = E0 + ZPE )''': The potential energy at 0K including the zero point vibrational energy.
*'''Sum of Electronic and Thermal Energies (E = E0 + Etot''' ): The total electronic energy + the total internal thermal energy, consisting of the vibrational, rotational and translational energy.
* '''Sum of electronic and Thermal Enthalpies''' '''(E = E0 + Hcorrected)''': The total electronic energy + the correction to enthalpy due to room temperature.
*'''Sum of Electronic and Thermal Free Energies (E= E0 + Gcorrected'''): The total electronic energy + the correction to Gibbs free energy due to internal energy.

===References===
<references/>

Rep:Mod3:jib09

2012-02-15T18:34:56Z

Jib09: /* Frequency and Thermochemical Analysis */

== Cope Rearrangement of 1,5-Hexadiene ==
===Aims===

===Introduction===

===Optimizing the Reactants and Products===

The ease of rotation about the carbon-carbon single bonds in 1,5-Hexadiene makes it possible for it to have many conformational isomers. To determine which is the most stable each of the conformers will be optimized using the Hartree-Fock method and a 3-21G basis set. This level of analysis is relatively low but it should be able to provide a guided to the potential energies of the conformers and indicate which is the most stable.

'''Table 1. HF/3-21G Optimization of 1,5-Hexadiene conformers'''

{| class="wikitable"
|-
| || || ||
|-
|'''Conformation''' || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point Group'''
|-
| <jmolFile text="Gauche 1"> 10030.mol </jmolFile><ref> [[File:10020.LOG]] </ref> || -231.68772 || 3.10 || C2
|-
| <jmolFile text="Gauche 2"> 10031.mol </jmolFile><ref> [[File:10021.LOG]]</ref> || -231.69166 || 0.62 || C2
|-
| <jmolFile text="Gauche 3"> 10032.mol </jmolFile><ref> [[File:10022.LOG]] </ref> || -231.69266 || 0.00 || C1
|-
| <jmolFile text="Gauche 4"> 10033.mol </jmolFile> <ref> [[File:10023.LOG]] </ref> || -231.69153 || 0.71 || C2
|-
| <jmolFile text="Gauche 5"> 10034.mol </jmolFile> <ref> [[File:10024.LOG]] </ref> || -231.68962 || 1.91 || C1
|-
| <jmolFile text="Gauche 6"> 10035.mol </jmolFile> <ref> [[File:10025.LOG]] </ref> || -231.68916 || 2.20 || C1
|-
| <jmolFile text="Anti 1"> 10036.mol </jmolFile> <ref> [[File:10026.LOG]] </ref> || -231.69260 || 0.04 || C2
|-
| <jmolFile text="Anti 2"> 10037.mol </jmolFile> <ref> [[File:10027.LOG]] </ref> || -231.69254 || 0.08 || Ci
|-
| <jmolFile text="Anti 3"> 10038.mol </jmolFile> <ref> [[File:10028.LOG]] </ref> || -231.68907 || 2.25 || C2H
|-
| <jmolFile text="Anti 4"> 10039.mol </jmolFile> <ref> [[File:10029.LOG]] </ref> || -231.69097 || 1.06 || C1
|}
*The 3DJmol structures can be viewed by following the corresponding link and the LOG files located in the references.

Prior to running the calculations it was expected that the most stable conformer would have a ''anti'' conformation, as it would have lower energy steric interactions, but as can be seen form the data the most stable conformer is ''gauche''. This result could be due to the fact that a low level method of analysis was used which is not accurate enough, or another factor

{| class="wikitable"
|-
| || || ||
|-
|Conformer || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point group'''
|-
|Gauche 3 || -234.55934 || 0.29 || C1
|-
|Anti 1 || -234.55978 || 0.00 || C2
|-
|Anti 2 || -234.55970 || 0.05 || Ci
|}

===Frequency and Thermochemical Analysis ===

*'''Sum of Electronic and Zero-Point Energies (E = E0 + ZPE )''': The potential energy at 0K including the zero point vibrational energy.
*'''Sum of Electronic and Thermal Energies (E = E0 + Etot''' ): The total electronic energy + the total internal thermal energy, consisting of the vibrational, rotational and translational energy.
* '''Sum of electronic and Thermal Enthalpies''' '''(E = E0 + Hcorrected)''': The total electronic energy + the correction to enthalpy due to room temperature.
*'''Sum of Electronic and Thermal Free Energies (E= E0 + Gcorrected'''): The total electronic energy + the correction to Gibbs free energy due to internal energy.

===References===
<references/>

Rep:Mod3:jib09

2012-02-15T18:14:54Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

Rep:Mod3:jib09

2012-02-15T17:13:13Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

Rep:Mod3:jib09

2012-02-15T17:12:24Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

Rep:Mod3:jib09

2012-02-15T16:59:20Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

Rep:Mod3:jib09

2012-02-15T15:59:25Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

Rep:Mod3:jib09

2012-02-15T15:46:03Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

Rep:Mod3:jib09

2012-02-15T15:40:34Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

Rep:Mod3:jib09

2012-02-15T15:32:40Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

== Cope Rearrangement of 1,5-Hexadiene ==
===Aims===

===Introduction===
[[File:Cope_rearrangement_mech.jpg|thumb|Figure 1. Cope Rearrangment‎]]

===Optimizing the Reactants and Products===
{| class="wikitable"
|-
| || || ||
|-
|'''Conformation''' || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point Group'''
|-
| <jmolFile text="Gauche 1"> 10030.mol </jmolFile><ref> [[File:10020.LOG]] </ref> || -231.68772 || 3.10 || C2
|-
| <jmolFile text="Gauche 2"> 10031.mol </jmolFile><ref> [[File:10021.LOG]]</ref> || -231.69166 || 0.62 || C2
|-
| <jmolFile text="Gauche 3"> 10032.mol </jmolFile><ref> [[File:10022.LOG]] </ref> || -231.69266 || 0.00 || C1
|-
| <jmolFile text="Gauche 4"> 10033.mol </jmolFile> <ref> [[File:10023.LOG]] </ref> || -231.69153 || 0.71 || C2
|-
| <jmolFile text="Gauche 5"> 10034.mol </jmolFile> <ref> [[File:10024.LOG]] </ref> || -231.68962 || 1.91 || C1
|-
| <jmolFile text="Gauche 6"> 10035.mol </jmolFile> <ref> [[File:10025.LOG]] </ref> || -231.68916 || 2.20 || C1
|-
| <jmolFile text="Anti 1"> 10036.mol </jmolFile> <ref> [[File:10026.LOG]] </ref> || -231.69260 || 0.04 || C2
|-
| <jmolFile text="Anti 2"> 10037.mol </jmolFile> <ref> [[File:10027.LOG]] </ref> || -231.69254 || 0.08 || Ci
|-
| <jmolFile text="Anti 3"> 10038.mol </jmolFile> <ref> [[File:10028.LOG]] </ref> || -231.68907 || 2.25 || C2H
|-
| <jmolFile text="Anti 4"> 10039.mol </jmolFile> <ref> [[File:10029.LOG]] </ref> || -231.69097 || 1.06 || C1
|}
*The 3DJmol structures can be viewed by following the corresponding link and the LOG files located in the references.

Prior to running the calculations it was expected that the most stable conformer would have a ''anti'' conformation, as it would have lower energy steric interactions, but as can be seen form the data the most stable conformer is ''gauche''.

<references/>

File:10023.LOG

2012-02-14T16:22:47Z

Jib09:

Rep:Mod3:jib09

2012-02-14T16:22:07Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

== Cope Rearrangement of 1,5-Hexadiene ==
===Aims===

===Introduction===
[[File:Cope_rearrangement_mech.jpg|thumb|Figure 1. Cope Rearrangment‎]]

===Optimizing the Reactants and Products===
{| class="wikitable"
|-
| || || ||
|-
|'''Conformation''' || '''Total Energy/ Hartrees''' || '''Relative energy/ kcal/mol''' || '''Point Group'''
|-
| <jmolFile text="Gauche 1"> 10030.mol </jmolFile><ref> Gauche 1 [[File:10020.LOG]] </ref> || -231.68772 || 3.10 || C2
|-
| <jmolFile text="Gauche 2"> 10031.mol </jmolFile><ref> [[File:10021.LOG]]</ref> || -231.69166 || 0.62 || C2
|-
| <jmolFile text="Gauche 3"> 10032.mol </jmolFile><ref> [[File:10022.LOG]] </ref> || -231.69266 || 0.00 || C1
|-
| <jmolFile text="Gauche 4"> 10033.mol </jmolFile> <ref> [[File:10023.LOG]] </ref> || -231.69153 || 0.71 || C2
|-
| <jmolFile text="Gauche 5"> 10034.mol </jmolFile> <ref> [[File:10024.LOG]] </ref> || -231.68962 || 1.91 || C1
|-
| <jmolFile text="Gauche 6"> 10035.mol </jmolFile> <ref> [[File:10025.LOG]] </ref> || -231.68916 || 2.20 || C1
|-
| <jmolFile text="Anti 1"> 10036.mol </jmolFile> <ref> [[File:10026.LOG]] </ref> || -231.69260 || 0.04 || C2
|-
| <jmolFile text="Anti 2"> 10037.mol </jmolFile> <ref> [[File:10027.LOG]] </ref> || -231.69254 || 0.08 || Ci
|-
| <jmolFile text="Anti 3"> 10038.mol </jmolFile> <ref> [[File:10028.LOG]] </ref> || -231.68907 || 2.25 || C2H
|-
| <jmolFile text="Anti 4"> 10039.mol </jmolFile> <ref> [[File:10029.LOG]] </ref> || -231.69097 || 1.06 || C1
|}

<references/>

File:10029.LOG

2012-02-14T16:21:57Z

Jib09: uploaded a new version of "File:10029.LOG"

File:10028.LOG

2012-02-14T16:21:42Z

Jib09:

File:10027.LOG

2012-02-14T16:21:15Z

Jib09:

File:10026.LOG

2012-02-14T16:20:54Z

Jib09:

File:10025.LOG

2012-02-14T16:20:33Z

Jib09:

File:10024.LOG

2012-02-14T16:20:10Z

Jib09:

Rep:Mod3:jib09

2012-02-14T16:17:38Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

File:10022.LOG

2012-02-14T16:16:05Z

Jib09:

File:10021.LOG

2012-02-14T16:12:02Z

Jib09:

File:10020.LOG

2012-02-14T16:08:19Z

Jib09:

Rep:Mod3:jib09

2012-02-14T16:03:18Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

Rep:Mod3:jib09

2012-02-14T16:01:47Z

Jib09: /* Cope Rearrangement of 1,5-Hexadiene */

File:10039.mol

2012-02-14T16:01:28Z

Jib09:

File:10038.mol

2012-02-14T16:01:13Z

Jib09:

File:10037.mol

2012-02-14T16:00:36Z

Jib09:

File:10036.mol

2012-02-14T15:59:47Z

Jib09:

File:10035.mol

2012-02-14T15:58:55Z

Jib09:

File:10034.mol

2012-02-14T15:58:21Z

Jib09:

File:10033.mol

2012-02-14T15:58:02Z

Jib09:

File:10032.mol

2012-02-14T15:55:14Z

Jib09:

File:10031.mol

2012-02-14T15:51:30Z

Jib09:

File:10030.mol

2012-02-14T15:50:09Z

Jib09:

Rep:Mod3:jib09

2012-02-14T15:44:22Z

Jib09:

Rep:Mod3:jib09

2012-02-13T18:48:43Z

Jib09: Created page with "== Cope Rearrangement of 1,5-Hexadiene == ===Aims=== ===Introduction=== Figure 1. Cope Rearrangment‎ ===Optimizing the Reactants ..."

== Cope Rearrangement of 1,5-Hexadiene ==
===Aims===

===Introduction===
[[File:Cope_rearrangement_mech.jpg|thumb|Figure 1. Cope Rearrangment‎]]

===Optimizing the Reactants and Products===

Rep:Mod2:jib09

2012-02-06T16:26:49Z

Jib09: /* Frequency Analysis */

== Computational Analysis of BH3 ==
===Aims===
The aim is to use Gaussian Quantum Mechanical calculations to optimized the geometry of BH3 molecule, determine its modes of vibration and predict its Molecular Orbitals.

===Structure Optimization===
Using the program GaussView a molecule of trigonal planar Boron trihydride (BH3) was drawn and its B-H bond lengths were set to 1.5 A. The method used for the optimization is the Density Functional Theory (DFT) using the B3LYP hybrid functional and the basis 3-21G.

The results of the optimisation are summarised below:

Summary:

File type: .log
Calculation Type: FOPT
Calculation Method: RB3LYP
Basis Set: 3-21G
E(RB+HF-LYP): -26.46226438 a.u.
RMS Gradient Norm: 0.00000294 a.u.
Imaginary Freq:
Dipole Moment 0.0000 Debye
Point Group: D3H

The complete results are referenced as a .log file<ref> [[File: BH3_OPTJIB09.LOG‎ ]]</ref>

The optimisation generated a (BH3) molecule with an optimised B-H bond length of 1.19A and a bond angle of 120⁰. This bond angle is in accordance with a trigonal planar molecule and is in good agreement with literature. The point group is also correctly assigned to D3H with a dipole moment of zero (given that the molecule is symmetrical a zero dipole moment is expected).

Apart from the data agreeing with literature it can also be seen that the optimisation is a correct one given that the gradient is very small (less than 0.001). This indicates that a stationary point was found in the first derivative of energy against internuclear distance. The .log file was also checked to make sure all the parameters converged successfully:

Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000352 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.580915D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,4) 1.1945 -DE/DX = -0.0001 !
! R2 R(2,4) 1.1945 -DE/DX = -0.0001 !
! R3 R(3,4) 1.1945 -DE/DX = -0.0001 !
! A1 A(1,4,2) 120.0 -DE/DX = 0.0 !
! A2 A(1,4,3) 120.0 -DE/DX = 0.0 !
! A3 A(2,4,3) 120.0 -DE/DX = 0.0 !
! A4 L(2,4,3,1,-2) 180.0 -DE/DX = 0.0 !

Each parameter converged successfully and every bond length and bond angle is satisfactory. The graphs below show each step in the optimisation. The first graph shows how the energy of the molecule changed after each step (5) in the optimisation, also the root mean squared gradient is shown.
[[File:Bh3optgraphs.png|500 px|]]

==Frequency Analysis==
A frequency analysis is run to make sure that the stationary point found in the optimisation is a minimum, as opposed to a maximum which would be a transition state. The analysis was run with the same method and basis set, the summary of the results <ref> [[File: 10029.LOG‎ ]]</ref> are shown below:

File Type: .log
Calculation Type: FREQ
Calculation Method: RB3LYP
Basis Set: 3-21G
E(RB+HF-LYP): -26.46226438
RMS Gradient Norm: 0.00000294
Imaginary Freq: 0
Dipole Moment : 0.0000 Debye
Point Group: D3H

As can be seen the total energy obtained is the same as in the optimisation, which indicates that there is no change in geometry, also there are no negative vibrational frequencies indicating that the molecule is in the ground state. The analysis also generated a predicted IR spectrum which is shown below:

''Figure 2. Predicted IR spectrum''

[[file:332256.png‎]]

The predicted IR spectrum shows 3 peaks, but BH3 has 6 vibrational modes. The vibrational modes of the BH3 molecule are discussed and displayed in the Table below:

{| class="wikitable"
|-
| || || || || ||
|-
|'''no.''' || '''Frequency/ cm''' || '''Description''' || || '''Symmetry D3H point group''' || '''Form of Vibration'''
|-
|1 || 1146.03 || '''Umbrella motion:'''All 3 H move symmetrically above and below the boron centre. The boron is also slightly displaced up and down. || || '''A2''' || [[file: 100023.png|thumb|Umbrella motion‎ ]]
|-
|2 || 1204.86 || '''Scissor motion:''' Two H move in a concerted manner inwards and outwards, with the remaining H and Boron slightly displaced up and down. || || '''E'''' || [[file: 10024.png|thumb|Scissor Motion‎ ]]
|-
|3 || 1204.86 || '''Rocking motion:''' Two H undergo a rocking motion with a constant angle between the bonds, the remaining H has a motion opposed to the rocking. || || '''E'''' || [[file: 10025.png|thumb|Rocking Motion‎ ]]
|-
|4 || 2591.65 || '''Symmetric Stretch:''' All H's stretch symmetrically in the plane of the molecule. || || '''A1'''' || [[file: 10026.png|thumb|Symmetric Stretch‎ ]]
|-
|5 || 2730.07 || '''Asymmetric Stretch:'''A H stretch in as the other stretch out. || || '''E'''' || [[file: 10027.png|thumb|Antisymmetric Stretch‎ ]]
|-
|6 || 2730.07 || '''Asymmetric Stretch'''Two H's stretch along their bonds as the other H counters this motion by stretching || ||'''E'''' || [[file: 10028.png|thumb|Antisymmetric Stretch‎ ]]
|}

The discrepancy between the predicted IR spectrum and the modes of vibration can be rationalised by the fact that there are two sets of degenerate stretching frequencies at 1204 and 2730 cm-1 which only generate one peak each.Also, the symmetric stretching mode (A1) which has a predicted frequency of 2591 cm-1 will not be seen in the IR as it does not generate a change in dipole moment as it vibrates.
{{DOI|10042/to-12002}}
==NBO Analysis==

==References==

<references/>

Rep:Mod2:jib09

2012-02-06T15:40:33Z

Jib09:

== Computational Analysis of BH3 ==
===Aims===
The aim is to use Gaussian Quantum Mechanical calculations to optimized the geometry of BH3 molecule, determine its modes of vibration and predict its Molecular Orbitals.

===Structure Optimization===
Using the program GaussView a molecule of trigonal planar Boron trihydride (BH3) was drawn and its B-H bond lengths were set to 1.5 A. The method used for the optimization is the Density Functional Theory (DFT) using the B3LYP hybrid functional and the basis 3-21G.

The results of the optimisation are summarised below:

Summary:

File type: .log
Calculation Type: FOPT
Calculation Method: RB3LYP
Basis Set: 3-21G
E(RB+HF-LYP): -26.46226438 a.u.
RMS Gradient Norm: 0.00000294 a.u.
Imaginary Freq:
Dipole Moment 0.0000 Debye
Point Group: D3H

The complete results are referenced as a .log file<ref> [[File: BH3_OPTJIB09.LOG‎ ]]</ref>

The optimisation generated a (BH3) molecule with an optimised B-H bond length of 1.19A and a bond angle of 120⁰. This bond angle is in accordance with a trigonal planar molecule and is in good agreement with literature. The point group is also correctly assigned to D3H with a dipole moment of zero (given that the molecule is symmetrical a zero dipole moment is expected).

Apart from the data agreeing with literature it can also be seen that the optimisation is a correct one given that the gradient is very small (less than 0.001). This indicates that a stationary point was found in the first derivative of energy against internuclear distance. The .log file was also checked to make sure all the parameters converged successfully:

Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000352 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.580915D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,4) 1.1945 -DE/DX = -0.0001 !
! R2 R(2,4) 1.1945 -DE/DX = -0.0001 !
! R3 R(3,4) 1.1945 -DE/DX = -0.0001 !
! A1 A(1,4,2) 120.0 -DE/DX = 0.0 !
! A2 A(1,4,3) 120.0 -DE/DX = 0.0 !
! A3 A(2,4,3) 120.0 -DE/DX = 0.0 !
! A4 L(2,4,3,1,-2) 180.0 -DE/DX = 0.0 !

Each parameter converged successfully and every bond length and bond angle is satisfactory. The graphs below show each step in the optimisation. The first graph shows how the energy of the molecule changed after each step (5) in the optimisation, also the root mean squared gradient is shown.
[[File:Bh3optgraphs.png|500 px|]]

==Frequency Analysis==
A frequency analysis is run to make sure that the stationary point found in the optimisation is a minimum, as opposed to a maximum which would be a transition state. The analysis was run with the same method and basis set, the summary of the results <ref> [[File: 10029.LOG‎ ]]</ref> are shown below:

File Type: .log
Calculation Type: FREQ
Calculation Method: RB3LYP
Basis Set: 3-21G
E(RB+HF-LYP): -26.46226438
RMS Gradient Norm: 0.00000294
Imaginary Freq: 0
Dipole Moment : 0.0000 Debye
Point Group: D3H

As can be seen the total energy obtained is the same as in the optimisation, which indicates that there is no change in geometry, also there are no negative vibrational frequencies indicating that the molecule is in the ground state. The analysis also generated a predicted IR spectrum which is shown below:

''Figure 2. Predicted IR spectrum''

[[file:332256.png‎]]

The predicted IR spectrum shows 3 peaks, but BH3 has 6 vibrational modes. The vibrational modes of the BH3 molecule are discussed and displayed in the Table below:

{| class="wikitable"
|-
| || || || || ||
|-
|'''no.''' || '''Frequency/ cm''' || '''Description''' || || '''Symmetry D3H point group''' || '''Form of Vibration'''
|-
|1 || 1146.03 || '''Umbrella motion:'''All 3 H move symmetrically above and below the boron centre. The boron is also slightly displaced up and down. || || '''A2''' || [[file: 100023.png|thumb|Umbrella motion‎ ]]
|-
|2 || 1204.86 || '''Scissor motion:''' Two H move in a concerted manner inwards and outwards, with the remaining H and Boron slightly displaced up and down. || || '''E'''' || [[file: 10024.png|thumb|Scissor Motion‎ ]]
|-
|3 || 1204.86 || '''Rocking motion:''' Two H undergo a rocking motion with a constant angle between the bonds, the remaining H has a motion opposed to the rocking. || || '''E'''' || [[file: 10025.png|thumb|Rocking Motion‎ ]]
|-
|4 || 2591.65 || '''Symmetric Stretch:''' All H's stretch symmetrically in the plane of the molecule. || || '''A1'''' || [[file: 10026.png|thumb|Symmetric Stretch‎ ]]
|-
|5 || 2730.07 || '''Asymmetric Stretch:'''A H stretch in as the other stretch out. || || '''E'''' || [[file: 10027.png|thumb|Antisymmetric Stretch‎ ]]
|-
|6 || 2730.07 || '''Asymmetric Stretch'''Two H's stretch along their bonds as the other H counters this motion by stretching || ||'''E'''' || [[file: 10028.png|thumb|Antisymmetric Stretch‎ ]]
|}

The discrepancy between the predicted IR spectrum and the modes of vibration can be rationalised by the fact that there are two sets of degenerate stretching frequencies at 1204 and 2730 cm-1. Also, the symmetric stretching mode (A1) which has a predicted frequency of 2591 cm-1 will not be seen in the IR as it does not generate a change in dipole moment as it vibrates.

==References==

<references/>

Rep:Mod2:jib09

2012-02-06T15:08:29Z

Jib09:

== Computational Analysis of BH3 ==
===Aims===
The aim is to use Gaussian Quantum Mechanical calculations to optimized the geometry of BH3 molecule, determine its modes of vibration and predict its Molecular Orbitals.

===Structure Optimization===
Using the program GaussView a molecule of trigonal planar Boron trihydride (BH3) was drawn and its B-H bond lengths were set to 1.5 A. The method used for the optimization is the Density Functional Theory (DFT) using the B3LYP hybrid functional and the basis 3-21G.

The results of the optimisation are summarised below:

Summary:

File type: .log
Calculation Type: FOPT
Calculation Method: RB3LYP
Basis Set: 3-21G
E(RB+HF-LYP): -26.46226438 a.u.
RMS Gradient Norm: 0.00000294 a.u.
Imaginary Freq:
Dipole Moment 0.0000 Debye
Point Group: D3H

The complete results are referenced as a .log file<ref> [[File: BH3_OPTJIB09.LOG‎ ]]</ref>

The optimisation generated a (BH3) molecule with an optimised B-H bond length of 1.19A and a bond angle of 120⁰. This bond angle is in accordance with a trigonal planar molecule and is in good agreement with literature. The point group is also correctly assigned to D3H with a dipole moment of zero (given that the molecule is symmetrical a zero dipole moment is expected).

Apart from the data agreeing with literature it can also be seen that the optimisation is a correct one given that the gradient is very small (less than 0.001). This indicates that a stationary point was found in the first derivative of energy against internuclear distance. The .log file was also checked to make sure all the parameters converged successfully:

Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000352 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.580915D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,4) 1.1945 -DE/DX = -0.0001 !
! R2 R(2,4) 1.1945 -DE/DX = -0.0001 !
! R3 R(3,4) 1.1945 -DE/DX = -0.0001 !
! A1 A(1,4,2) 120.0 -DE/DX = 0.0 !
! A2 A(1,4,3) 120.0 -DE/DX = 0.0 !
! A3 A(2,4,3) 120.0 -DE/DX = 0.0 !
! A4 L(2,4,3,1,-2) 180.0 -DE/DX = 0.0 !

Each parameter converged successfully and every bond length and bond angle is satisfactory. The graphs below show each step in the optimisation. The first graph shows how the energy of the molecule changed after each step (5) in the optimisation, also the root mean squared gradient is shown.
[[File:Bh3optgraphs.png|500 px|]]

==Frequency Analysis==
A frequency analysis is run to make sure that the stationary point found in the optimisation is a minimum, as opposed to a maximum which would be a transition state. The analysis was run with the same method and basis set, the summary of the results <ref> [[File: 10029.LOG‎ ]]</ref> are shown below:

File Type: .log
Calculation Type: FREQ
Calculation Method: RB3LYP
Basis Set: 3-21G
E(RB+HF-LYP): -26.46226438
RMS Gradient Norm: 0.00000294
Imaginary Freq: 0
Dipole Moment : 0.0000 Debye
Point Group: D3H

As can be seen the total energy obtained is the same as in the optimisation, which indicates that there is no change in geometry. The predicted IR spectrum from this analysis is shown below:

[[file:332256.png|thumb|Predicted IR Spectrum‎]]

{| class="wikitable"
|-
| || || || || ||
|-
|'''no.''' || '''Frequency''' || '''Description''' || || '''Symmetry D3H point group''' || '''Form of Vibration'''
|-
|1 || 1146.03 || '''Umbrella motion:'''All 3 H move symmetrically above and below the boron centre. The boron is also slightly displaced up and down. || || '''A2''' || [[file: 100023.png|thumb|Umbrella motion‎ ]]
|-
|2 || 1204.86 || '''Scissor motion:''' Two H move in a concerted manner inwards and outwards, with the remaining H and Boron slightly displaced up and down. || || '''E'''' || [[file: 10024.png|thumb|Scissor Motion‎ ]]
|-
|3 || 1204.86 || '''Rocking motion:''' Two H undergo a rocking motion with a constant angle between the bonds, the remaining H has a motion opposed to the rocking. || || '''E'''' || [[file: 10025.png|thumb|Rocking Motion‎ ]]
|-
|4 || 2591.65 || '''Symmetric Stretch:''' All H's stretch symmetrically in the plane of the molecule. || || '''A1'''' || [[file: 10026.png|thumb|Symmetric Stretch‎ ]]
|-
|5 || 2730.07 || '''Asymmetric Stretch:'''A H stretch in as the other stretch out. || || '''E'''' || [[file: 10027.png|thumb|Antisymmetric Stretch‎ ]]
|-
|6 || 2730.07 || '''Asymmetric Stretch'''Two H's stretch along their bonds as the other H counters this motion by stretching || ||'''E'''' || [[file: 10028.png|thumb|Antisymmetric Stretch‎ ]]
|}

==References==

<references/>

Rep:Mod2:jib09

2012-02-06T15:04:35Z

Jib09: /* Frequency Analysis */

== Computational Analysis of BH3 ==
===Aims===
The aim is to use Gaussian Quantum Mechanical calculations to optimized the geometry of BH3 molecule, determine its modes of vibration and predict its Molecular Orbitals.

===Structure Optimization===
Using the program GaussView a molecule of trigonal planar Boron trihydride (BH3) was drawn and its B-H bond lengths were set to 1.5 A. The method used for the optimization is the Density Functional Theory (DFT) using the B3LYP hybrid functional and the basis 3-21G.

The results of the optimisation are summarised below:

Summary:

File type: .log
Calculation Type: FOPT
Calculation Method: RB3LYP
Basis Set: 3-21G
E(RB+HF-LYP): -26.46226438 a.u.
RMS Gradient Norm: 0.00000294 a.u.
Imaginary Freq:
Dipole Moment 0.0000 Debye
Point Group: D3H

The complete results are referenced as a .log file<ref> [[File: BH3_OPTJIB09.LOG‎ ]]</ref>

The optimisation generated a (BH3) molecule with an optimised B-H bond length of 1.19A and a bond angle of 120⁰. This bond angle is in accordance with a trigonal planar molecule and is in good agreement with literature. The point group is also correctly assigned to D3H with a dipole moment of zero (given that the molecule is symmetrical a zero dipole moment is expected).

Apart from the data agreeing with literature it can also be seen that the optimisation is a correct one given that the gradient is very small (less than 0.001). This indicates that a stationary point was found in the first derivative of energy against internuclear distance. The .log file was also checked to make sure all the parameters converged successfully:

Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000352 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.580915D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,4) 1.1945 -DE/DX = -0.0001 !
! R2 R(2,4) 1.1945 -DE/DX = -0.0001 !
! R3 R(3,4) 1.1945 -DE/DX = -0.0001 !
! A1 A(1,4,2) 120.0 -DE/DX = 0.0 !
! A2 A(1,4,3) 120.0 -DE/DX = 0.0 !
! A3 A(2,4,3) 120.0 -DE/DX = 0.0 !
! A4 L(2,4,3,1,-2) 180.0 -DE/DX = 0.0 !

Each parameter converged successfully and every bond length and bond angle is satisfactory. The graphs below show each step in the optimisation. The first graph shows how the energy of the molecule changed after each step (5) in the optimisation, also the root mean squared gradient is shown.
[[File:Bh3optgraphs.png|500 px|]]

==Frequency Analysis==
A frequency analysis is run to make sure that the stationary point found in the optimisation is a minimum, as opposed to a maximum which would be a transition state. The analysis was run with the same method and basis set, the summary of the results are shown below:

File Type: .log
Calculation Type: FREQ
Calculation Method: RB3LYP
Basis Set: 3-21G
E(RB+HF-LYP): -26.46226438
RMS Gradient Norm: 0.00000294
Imaginary Freq: 0
Dipole Moment : 0.0000 Debye
Point Group: D3H

As can be seen the total energy obtained is the same as in the optimisation, which indicates that there is no change in geometry

[[file:332256.png‎]]

{| class="wikitable"
|-
| || || || || ||
|-
|'''no.''' || '''Frequency''' || '''Description''' || || '''Symmetry D3H point group''' || '''Form of Vibration'''
|-
|1 || 1146.03 || '''Umbrella motion:'''All 3 H move symmetrically above and below the boron centre. The boron is also slightly displaced up and down. || || '''A2''' || [[file: 100023.png|thumb|Umbrella motion‎ ]]
|-
|2 || 1204.86 || '''Scissor motion:''' Two H move in a concerted manner inwards and outwards, with the remaining H and Boron slightly displaced up and down. || || '''E'''' || [[file: 10024.png|thumb|Scissor Motion‎ ]]
|-
|3 || 1204.86 || '''Rocking motion:''' Two H undergo a rocking motion with a constant angle between the bonds, the remaining H has a motion opposed to the rocking. || || '''E'''' || [[file: 10025.png|thumb|Rocking Motion‎ ]]
|-
|4 || 2591.65 || '''Symmetric Stretch:''' All H's stretch symmetrically in the plane of the molecule. || || '''A1'''' || [[file: 10026.png|thumb|Symmetric Stretch‎ ]]
|-
|5 || 2730.07 || '''Asymmetric Stretch:'''A H stretch in as the other stretch out. || || '''E'''' || [[file: 10027.png|thumb|Antisymmetric Stretch‎ ]]
|-
|6 || 2730.07 || '''Asymmetric Stretch'''Two H's stretch along their bonds as the other H counters this motion by stretching || ||'''E'''' || [[file: 10028.png|thumb|Antisymmetric Stretch‎ ]]
|}

==References==

<references/>

File:10029.LOG

2012-02-06T15:04:12Z

Jib09:

File:10028.png

2012-02-06T14:45:57Z

Jib09: