ChemWiki - User contributions [en]

Rep:Mod:JS5315

2016-03-04T16:46:07Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173 '''(Literature value of covalent radius = 1.02 ± 0.04Å)'''
Link: https://en.wikipedia.org/wiki/Chlorine

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

'''Frequency''' Mode 1: 520.33Hz
As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.
'''Literature value:''' "Chlorine (Cl2) has a vibrational frequency of 550 cm^-1"
Link: http://www.chegg.com/homework-help/questions-and-answers/chlorine-cl2-vibrational-frequency-550-cm-1-bond-dissociation-energy-240-kj-mol-absorption-q2899998

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]

This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

Rep:Mod:JS5315

2016-03-04T16:45:22Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173 (Literature value of covalent radius = 1.02 ± 0.04Å)
Link: https://en.wikipedia.org/wiki/Chlorine

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

'''Frequency''' Mode 1: 520.33Hz
As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.
'''Literature value:''' "Chlorine (Cl2) has a vibrational frequency of 550 cm^-1"
Link: http://www.chegg.com/homework-help/questions-and-answers/chlorine-cl2-vibrational-frequency-550-cm-1-bond-dissociation-energy-240-kj-mol-absorption-q2899998

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]

This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

Rep:Mod:JS5315

2016-03-04T16:43:15Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173 (Literature value of covalent radius = 1.02 ± 0.04Å)

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

'''Frequency''' Mode 1: 520.33Hz
As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.
"Chlorine (Cl2) has a vibrational frequency of 550 cm^-1"

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]

This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

Rep:Mod:JS5315

2016-03-04T16:40:11Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173 (Literature value of covalent radius = 1.02 ± 0.04Å)

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

'''Frequencies in Hertz''' Mode 1: 520.33
As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]

This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

Rep:Mod:JS5315

2016-03-04T15:22:48Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

'''Frequencies in Hertz''' Mode 1: 520.33
As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]

This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

Rep:Mod:JS5315

2016-03-04T15:20:57Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

'''Frequencies in Hertz''' Mode 1: 520.33
As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]
This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

Rep:Mod:JS5315

2016-03-04T15:20:20Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 520.33

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]
This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

Rep:Mod:JS5315

2016-03-04T15:10:59Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 520.33

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]
This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

Rep:Mod:JS5315

2016-03-04T15:10:20Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION 2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 520.33

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]
This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

File:JSHIMADA CL2 OPTIMISATION 2.LOG

2016-03-04T15:09:58Z

Js5315:

Rep:Mod:JS5315

2016-03-04T15:03:40Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>Cl2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 520.33

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 6.png|720px]]
This molecular orbital is 6σg. It is filled and is in phase thus overlap head-on to give a sigma bond. It is too deep in energy to contribute to the actual bond. 2p AOs contribute to create this MO.

[[File:JSHIMADA CL2 MO 10.png|720px]]

The MO 10πu is a filled, bonding orbital. However it doesn't contribute much to the actual bonding because it is too deep in energy. As the AOs are in phase, they will overlap sideways to give a pi bond. To generate this MO, the degenerate 2p orbitals that created MO 6 contributes. Thus, the energy levels are very close together (basically degenerate) with E= -7.28592 for MO 6 and E= -7.27043 for this MO.

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO. AS this is an anti-bonding orbital, it will contribute to separation of the bond, only to be prevented by the unfilled MO 18.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO 30.png|720px]]

The MO 30δg is an unfilled bonding orbital. The two delta orbitals are in phase and thus we see overlaps of the four phases seen at 90 degrees to each other. This MO is too high in energy and doesn't contribute to the bond but it is an interesting shape of MO and I have included this here. 4d AOs of both atoms contribute to create this AO. As it is unfilled, it does not affect the bonding.

File:JSHIMADA CL2 MO 30.png

2016-03-04T14:58:03Z

Js5315:

File:JSHIMADA CL2 MO 6.png

2016-03-04T14:41:33Z

Js5315:

File:JSHIMADA CL2 MO 10.png

2016-03-04T14:23:53Z

Js5315:

Rep:Mod:JS5315

2016-03-03T17:07:02Z

Js5315: /* My choice of small molecule - Cl2 */

'''
== Computational Lab part 2 ==
'''

=== Optimisation of NH3 molecule ===

Molecule: NH3

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -56.55776873

RMS gradient: 4.85x10-6

Point group of the molecule: C3V

Bond Length (in Angstroms): 1.01798

Bond Angle (in degrees): 105.741

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA NH3 OPTIMISATION 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''
https://wiki.ch.ic.ac.uk/wiki/images/e/e6/JSHIMADA_NH3_OPTIMISATION_1.LOG

[[File:JSHIMADA NH3 Vibrations Screenshot.png|360px]]
[[File:JSHIMADA NH3 Display Vibrations.png|360px]]

'''How many modes do you expect from the 3N-6 rule?'''

6

'''Which modes are degenerate (ie have the same energy)?'''

2&3 are degenerate, as well as 5&6

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Bending:1,2&3
Stretching: 4,5&6

'''Which mode is highly symmetric?'''

1&4 are highly symmetric

'''One mode is known as the "umbrella" mode, which one is this?'''

1 is known as the "umbrella" mode

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

3

'''Charges'''

On N: -1.125
On H: 0.375

We expect the charge on N to be negative and H to be positive as N is more electronegative than the surrounding H atoms, thus N attracts the negatively charged electrons towards it.

=== Optimising N2 and H2 ===
==== N2 ====

Molecule: N2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -109.52412868

RMS gradient: 4.65x10-6

Point group of the molecule: D*H

Bond Length (in Angstroms): 1.10550

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA N2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/f/f8/JSHIMADA_N2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 2457.31

==== H2 ====

Molecule: H2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -1.17853926

RMS gradient: 1.5955x10-4

Point group of the molecule: D*H

Bond Length (in Angstroms): 0.74241

Bond Angle (in degrees): 180

<pre> Item Value Threshold Converged?
Maximum Force 0.000276 0.000450 YES
RMS Force 0.000276 0.000300 YES
Maximum Displacement 0.000362 0.001800 YES
RMS Displacement 0.000513 0.001200 YES</pre>

<jmol><jmolApplet>
<title>H2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/6/6b/JSHIMADA_H2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 4471.18

==== Haber-Bosch reaction energy calculation ====

E(NH3)= -56.55776873

2*E(NH3)= -113.1155375

E(N2)= -109.52412868

E(H2)= -1.17853933

3*E(H2)= -3.53561799

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579083 =-146.4788242 kJ/mol

==== My choice of small molecule - Cl2====

Molecule: Cl2

Calculation Method: RB3LYP

Basis set: 6-31G(d,p)

Final energy E(RB3LYP) in atomic units (au): -920.34987887

RMS gradient: 2.397x10-5

Point group of the molecule: D*H

Bond Length (in Angstroms): 2.04173

Bond Angle (in degrees): 180

<pre>Item Value Threshold Converged?
Maximum Force 0.000042 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.000116 0.001800 YES
RMS Displacement 0.000164 0.001200 YES</pre>

<jmol><jmolApplet>
<title>N2</title>
<color>orange</color>
<size>300</size>
<uploadedFileContents>JSHIMADA CL2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[[Link:]]'''https://wiki.ch.ic.ac.uk/wiki/images/2/27/JSHIMADA_CL2_OPTIMISATION.LOG

'''Frequencies in Hertz''' Mode 1: 520.33

[[File:JSHIMADA CL2 Vibrations and charge distribution.png|720px]]

As the molecule is symmetrical, the charge is distributed evenly. The molecule only has one mode, and it is a stretching mode, parallel to the direction of the bond. It is also highly symmetric.

'''Molecular Orbitals'''

[[File:JSHIMADA CL2 MO 17.png|720px]]

This is MO 17πg*, the HOMO of Cl2. We can see that it is an occupied anti-bonding MO as stated and also as the p orbitals do not overlap as they are out of phase. Cl 3p orbitals contribute to this MO.

[[File:JSHIMADA CL2 MO 18.png|720px]]

This is MO 18σu*, the LUMO of Cl2. The AOs are not in phase and thus the MO is anti-bonding. This MO is formed from 3p orbitals of both chlorine atoms, but as it is not filled it means that the molecule is stable and does not dissociate on its own.

[[File:JSHIMADA CL2 MO.png|720px]]
[[File:JSHIMADA CL2 MO.png|720px]]
[[File:JSHIMADA CL2 MO.png|720px]]

File:JSHIMADA CL2 MO 18.png

2016-03-03T16:49:08Z

Js5315:

Rep:Mod:JS5315

2016-03-03T16:35:06Z

Js5315: /* My choice of small molecule - Cl2 */

File:JSHIMADA CL2 MO 17.png

2016-03-03T16:34:11Z

Js5315:

File:JSHIMADA CL2 OPTIMISATION.LOG

2016-03-03T16:02:57Z

Js5315: Js5315 uploaded a new version of File:JSHIMADA CL2 OPTIMISATION.LOG

Rep:Mod:JS5315

2016-03-03T16:02:13Z

Js5315: /* Computational Lab part 2 */

Rep:Mod:JS5315

2016-03-03T16:01:40Z

Js5315: /* My choice of small molecule - Cl2 */

Rep:Mod:JS5315

2016-03-03T15:50:46Z

Js5315: /* Optimisation of NH3 molecule */

Rep:Mod:JS5315

2016-03-03T15:50:19Z

Js5315: /* My choice of small molecule - Cl2 */

Rep:Mod:JS5315

2016-03-03T15:31:57Z

Js5315: /* My choice of small molecule - Cl2 */

Rep:Mod:JS5315

2016-03-03T15:23:05Z

Js5315: /* My choice of small molecule - Cl2 */

File:JSHIMADA CL2 Vibrations and charge distribution.png

2016-03-03T15:22:22Z

Js5315: Js5315 uploaded a new version of File:JSHIMADA CL2 Vibrations and charge distribution.png

Rep:Mod:JS5315

2016-03-03T15:20:17Z

Js5315: /* Computational Lab part 2 */

File:JSHIMADA CL2 Vibrations and charge distribution.png

2016-03-03T15:19:19Z

Js5315:

File:JSHIMADA CL2 OPTIMISATION.LOG

2016-03-03T15:09:40Z

Js5315: Js5315 uploaded a new version of File:JSHIMADA CL2 OPTIMISATION.LOG

Rep:Mod:JS5315

2016-03-03T15:08:20Z

Js5315: /* My choice of small molecule - Cl2 */

Rep:Mod:JS5315

2016-03-03T15:07:46Z

Js5315: /* Computational Lab part 2 */

File:JSHIMADA CL2 OPTIMISATION.LOG

2016-03-03T15:06:42Z

Js5315:

Rep:Mod:JS5315

2016-03-03T15:04:36Z

Js5315: /* Computational Lab part 2 */

Rep:Mod:JS5315

2016-03-03T14:53:27Z

Js5315: /* Computational Lab part 2 */

Rep:Mod:JS5315

2016-03-03T14:52:50Z

Js5315: /* My choice of small molecule - Cl2 */

Rep:Mod:JS5315

2016-03-03T14:44:59Z

Js5315: /* My choice of small molecule - Cl2 */

Rep:Mod:JS5315

2016-03-03T14:26:00Z

Js5315: /* Computational Lab part 2 */

Rep:Mod:JS5315

2016-03-03T14:21:15Z

Js5315: /* Optimising N2 and H2 */

Rep:Mod:JS5315

2016-03-03T14:20:30Z

Js5315: /* Optimising N2 and H2 */

Rep:Mod:JS5315

2016-03-03T14:18:06Z

Js5315: /* Optimisation of NH3 molecule */

Rep:Mod:JS5315

2016-03-03T14:17:04Z

Js5315: /* H2 */

Rep:Mod:JS5315

2016-02-29T17:36:07Z

Js5315: /* Computational Lab part 2 */

Rep:Mod:JS5315

2016-02-29T17:28:29Z

Js5315: /* Computational Lab part 2 */

Rep:Mod:JS5315

2016-02-29T17:26:53Z

Js5315: /* Computational Lab part 2 */

File:JSHIMADA H2 OPTIMISATION.LOG

2016-02-29T17:26:20Z

Js5315:

Rep:Mod:JS5315

2016-02-29T17:16:44Z

Js5315: /* Computational Lab part 2 */

Rep:Mod:JS5315

2016-02-29T17:12:17Z

Js5315: /* Computational Lab part 2 */

File:JSHIMADA N2 Display Vibrations.png

2016-02-29T17:11:42Z

Js5315:

Rep:Mod:JS5315

2016-02-29T17:08:11Z

Js5315: /* Computational Lab part 2 */

Rep:Mod:JS5315

2016-02-29T17:07:23Z

Js5315: /* Optimising N2 and H2 */