2019-03-08T10:20:14Z

Jap18:

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 10

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<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
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is infact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1.

"Umbrella" mode = The moed at 1090cm-1

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] a mono-metallic transition metal complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly larger at 1.12Å <ref name="Bond Distance" /> . This is because the two nitrogen atoms are, similarly to N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the nitrogens and so slightly increasing the bond length. Further more, the diatomic N triple-bond N bond length was determined computationally, which uses approximations to predict the bond distance unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference. COMPUTATIONAL AND EXPERIMENTAL REASONS!

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on an H2 atom because both atoms in the diatomic are the same and hence have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribition' on the right:

Haber-Bosch reaction energy calculation

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.3*

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 Molecular Orbitals of Oxygen
|-
| || MO 1 - σ1s || MO 2 - σ*1s || MO 3 - σ2s || MO 4 - σ*2s ||MO 5 - 
|-
| '''Image'''|| [[File:JAP18_O2_MO1.jpg|100px]] || [[File:JAP18_O2_MO2.jpg|100px]]|| [[File:JAP18_O2_MO3.jpg|100px]]|| [[File:JAP18_O2_MO4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]
|-
| '''Contributing AOs'''|| The two 1s core AOs on each O-atom|| The two 1s core AOs on each O-atom|| The two 2s valence AOs on each O-atom || The two 2s valence AOs on each O-atom|| 0
|-
| '''MO type'''|| Bonding || Antibonding|| Bonding || Antibonding || 3590
|-
| '''MO energy'''|| Deep (-19.31 au) || Deep (-19.31 au) || Fairly high (-1.28 au) || Fairly high (-0.80 au) || E
|-
| '''MO occupancy'''|| Occupied || Occupied || Occupied || Occupied || 0
|-
| '''MO's contribution to bonding'''|| Very little || Very little || Large || Large || 0
|-
|}

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted 'Figure 5 - HCN Charge Distribution' on the right:

<references>

<ref name="use imerpial cway of referencing Bond Distances">This is the bond distances reference.</ref>

</references>

lighten colour of text in dipole diagrams so numbers more visible

Rep:MOD:JAP10537443

2019-03-08T10:19:52Z

Jap18:

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 10

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<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
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is infact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1.

"Umbrella" mode = The moed at 1090cm-1

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] a mono-metallic transition metal complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly larger at 1.12Å <ref name="Bond Distance" /> . This is because the two nitrogen atoms are, similarly to N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the nitrogens and so slightly increasing the bond length. Further more, the diatomic N triple-bond N bond length was determined computationally, which uses approximations to predict the bond distance unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference. COMPUTATIONAL AND EXPERIMENTAL REASONS!

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on an H2 atom because both atoms in the diatomic are the same and hence have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribition' on the right:

Haber-Bosch reaction energy calculation

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.3*

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 Molecular Orbitals of Oxygen
|-
| || MO 1 - σ1s || MO 2 - σ*1s || MO 3 - σ2s || MO 4 - σ*1s ||MO 5 - 
|-
| '''Image'''|| [[File:JAP18_O2_MO1.jpg|100px]] || [[File:JAP18_O2_MO2.jpg|100px]]|| [[File:JAP18_O2_MO3.jpg|100px]]|| [[File:JAP18_O2_MO4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]
|-
| '''Contributing AOs'''|| The two 1s core AOs on each O-atom|| The two 1s core AOs on each O-atom|| The two 2s valence AOs on each O-atom || The two 2s valence AOs on each O-atom|| 0
|-
| '''MO type'''|| Bonding || Antibonding|| Bonding || Antibonding || 3590
|-
| '''MO energy'''|| Deep (-19.31 au) || Deep (-19.31 au) || Fairly high (-1.28 au) || Fairly high (-0.80 au) || E
|-
| '''MO occupancy'''|| Occupied || Occupied || Occupied || Occupied || 0
|-
| '''MO's contribution to bonding'''|| Very little || Very little || Large || Large || 0
|-
|}

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted 'Figure 5 - HCN Charge Distribution' on the right:

<references>

<ref name="use imerpial cway of referencing Bond Distances">This is the bond distances reference.</ref>

</references>

lighten colour of text in dipole diagrams so numbers more visible

Rep:MOD:JAP10537443

2019-03-08T10:15:16Z

Jap18:

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 10

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<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
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is infact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1.

"Umbrella" mode = The moed at 1090cm-1

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] a mono-metallic transition metal complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly larger at 1.12Å <ref name="Bond Distance" /> . This is because the two nitrogen atoms are, similarly to N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the nitrogens and so slightly increasing the bond length. Further more, the diatomic N triple-bond N bond length was determined computationally, which uses approximations to predict the bond distance unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference. COMPUTATIONAL AND EXPERIMENTAL REASONS!

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on an H2 atom because both atoms in the diatomic are the same and hence have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribition' on the right:

Haber-Bosch reaction energy calculation

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.3*

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 Molecular Orbitals of Oxygen
|-
| || MO 1 - 1σ || MO 2 - 2σ* || MO 3 - 3σ || MO 4 - 4σ* ||MO 5 - 
|-
| '''Image'''|| [[File:JAP18_O2_MO1.jpg|100px]] || [[File:JAP18_O2_MO2.jpg|100px]]|| [[File:JAP18_O2_MO3.jpg|100px]]|| [[File:JAP18_O2_MO4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]
|-
| '''Contributing AOs'''|| The two 1s core AOs on each O-atom|| The two 1s core AOs on each O-atom|| The two 2s valence AOs on each O-atom || The two 2s valence AOs on each O-atom|| 0
|-
| '''MO type'''|| Bonding || Antibonding|| Bonding || Antibonding || 3590
|-
| '''MO energy'''|| Deep (-19.31 au) || Deep (-19.31 au) || Fairly high (-1.28 au) || Fairly high (-0.80 au) || E
|-
| '''MO occupancy'''|| Occupied || Occupied || Occupied || Occupied || 0
|-
| '''MO's contribution to bonding'''|| Very little || Very little || Large || Large || 0
|-
|}

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted 'Figure 5 - HCN Charge Distribution' on the right:

<references>

<ref name="use imerpial cway of referencing Bond Distances">This is the bond distances reference.</ref>

</references>

lighten colour of text in dipole diagrams so numbers more visible

File:JAP18 O2 MO4.jpg

2019-03-08T10:15:08Z

Jap18:

File:JAP18 O2 MO3.jpg

2019-03-08T10:14:24Z

Jap18:

Rep:MOD:JAP10537443

2019-03-08T10:05:30Z

Jap18:

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 10

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<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
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is infact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1.

"Umbrella" mode = The moed at 1090cm-1

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] a mono-metallic transition metal complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly larger at 1.12Å <ref name="Bond Distance" /> . This is because the two nitrogen atoms are, similarly to N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the nitrogens and so slightly increasing the bond length. Further more, the diatomic N triple-bond N bond length was determined computationally, which uses approximations to predict the bond distance unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference. COMPUTATIONAL AND EXPERIMENTAL REASONS!

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on an H2 atom because both atoms in the diatomic are the same and hence have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribition' on the right:

Haber-Bosch reaction energy calculation

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.3*

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 Molecular Orbitals of Oxygen
|-
| || MO 1 - 1σ || MO 2 - 2σ* || MO 3 - || MO 4 - ||MO 5 - 
|-
| '''Image'''|| [[File:JAP18_O2_MO1.jpg|100px]] || [[File:JAP18_O2_MO2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]
|-
| '''Contributing AOs'''|| The two core AOs on each O-atom|| The two core AOs on each O-atom|| 14 || 1 || 0
|-
| '''MO type'''|| Bonding || Antibonding|| 1694|| 3461|| 3590
|-
| '''MO energy'''|| Deep (-19.31 au) || Deep (-19.31 au) || E|| A1|| E
|-
| '''MO occupancy'''|| Occupied || Occupied || 14 || 1 || 0
|-
| '''MO's contribution to bonding'''|| Very little || Very little || 14 || 1 || 0
|-
|}

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted 'Figure 5 - HCN Charge Distribution' on the right:

<references>

<ref name="use imerpial cway of referencing Bond Distances">This is the bond distances reference.</ref>

</references>

lighten colour of text in dipole diagrams so numbers more visible

2019-03-08T09:59:36Z

Jap18:

Rep:MOD:JAP10537443

2019-03-08T09:59:10Z

Jap18:

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 10

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<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
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is infact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1.

"Umbrella" mode = The moed at 1090cm-1

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] a mono-metallic transition metal complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly larger at 1.12Å <ref name="Bond Distance" /> . This is because the two nitrogen atoms are, similarly to N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the nitrogens and so slightly increasing the bond length. Further more, the diatomic N triple-bond N bond length was determined computationally, which uses approximations to predict the bond distance unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference. COMPUTATIONAL AND EXPERIMENTAL REASONS!

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on an H2 atom because both atoms in the diatomic are the same and hence have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribition' on the right:

Haber-Bosch reaction energy calculation

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.3*

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 Molecular Orbitals of Oxygen
|-
| || MO 1 || MO 2 || MO 3 || MO 4 ||MO 5
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]
|-
| '''Contributing AOs'''|| The two core AOs on each O-atom|| 14 || 14 || 1 || 0
|-
| '''MO type'''|| Bonding || 1694|| 1694|| 3461|| 3590
|-
| '''MO energy'''|| Deep (-19.31 au) || E|| E|| A1|| E
|-
| '''MO occupancy'''|| Occupied || 14 || 14 || 1 || 0
|-
| '''MO's contribution to bonding'''|| Very little || 14 || 14 || 1 || 0
|-
|}

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted 'Figure 5 - HCN Charge Distribution' on the right:

<references>

<ref name="use imerpial cway of referencing Bond Distances">This is the bond distances reference.</ref>

</references>

lighten colour of text in dipole diagrams so numbers more visible

Rep:MOD:JAP10537443

2019-03-08T09:44:38Z

Jap18:

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 10

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<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
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is infact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1.

"Umbrella" mode = The moed at 1090cm-1

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] a mono-metallic transition metal complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly larger at 1.12Å <ref name="Bond Distance" /> . This is because the two nitrogen atoms are, similarly to N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the nitrogens and so slightly increasing the bond length. Further more, the diatomic N triple-bond N bond length was determined computationally, which uses approximations to predict the bond distance unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference. COMPUTATIONAL AND EXPERIMENTAL REASONS!

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on an H2 atom because both atoms in the diatomic are the same and hence have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribition' on the right:

Haber-Bosch reaction energy calculation

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.3*

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 Molecular Orbitals of Oxygen
|-
| || MO 1 || MO 2 || MO 3 || MO 4 ||MO 5
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]
|-
| '''Contributing AOs'''|| 145 || 14 || 14 || 1 || 0
|-
| '''MO type'''|| 1090|| 1694|| 1694|| 3461|| 3590
|-
| '''MO energy'''|| A1|| E|| E|| A1|| E
|-
| '''MO occupancy'''|| 145 || 14 || 14 || 1 || 0
|-
| '''MO's effect on bonding'''|| 145 || 14 || 14 || 1 || 0
|-
|}

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted 'Figure 5 - HCN Charge Distribution' on the right:

<references>

<ref name="use imerpial cway of referencing Bond Distances">This is the bond distances reference.</ref>

</references>

lighten colour of text in dipole diagrams so numbers more visible

Rep:MOD:JAP10537443

2019-03-08T09:42:42Z

Jap18:

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 10

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<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
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is infact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1.

"Umbrella" mode = The moed at 1090cm-1

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] a mono-metallic transition metal complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly larger at 1.12Å <ref name="Bond Distance" /> . This is because the two nitrogen atoms are, similarly to N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the nitrogens and so slightly increasing the bond length. Further more, the diatomic N triple-bond N bond length was determined computationally, which uses approximations to predict the bond distance unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference. COMPUTATIONAL AND EXPERIMENTAL REASONS!

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on an H2 atom because both atoms in the diatomic are the same and hence have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribition' on the right:

Haber-Bosch reaction energy calculation

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.3*

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 Molecular Orbitals of Oxygen
|-
| MO 1 || MO 2 || MO 3 || MO 4 || MO 5
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]
|-
| '''Contributing AOs'''|| 145 || 14 || 14 || 1 || 0
|-
| '''MO type'''|| 1090|| 1694|| 1694|| 3461|| 3590
|-
| '''MO energy'''|| A1|| E|| E|| A1|| E
|-
| '''MO occupancy'''|| 145 || 14 || 14 || 1 || 0
|-
| '''MO's effect on bonding'''|| 145 || 14 || 14 || 1 || 0
|-
|}

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted 'Figure 5 - HCN Charge Distribution' on the right:

<references>

<ref name="use imerpial cway of referencing Bond Distances">This is the bond distances reference.</ref>

</references>

lighten colour of text in dipole diagrams so numbers more visible

Rep:MOD:JAP10537443

2019-03-08T09:41:11Z

Jap18:

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 10

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<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
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is infact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1.

"Umbrella" mode = The moed at 1090cm-1

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] a mono-metallic transition metal complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly larger at 1.12Å <ref name="Bond Distance" /> . This is because the two nitrogen atoms are, similarly to N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the nitrogens and so slightly increasing the bond length. Further more, the diatomic N triple-bond N bond length was determined computationally, which uses approximations to predict the bond distance unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference. COMPUTATIONAL AND EXPERIMENTAL REASONS!

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on an H2 atom because both atoms in the diatomic are the same and hence have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribition' on the right:

Haber-Bosch reaction energy calculation

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.3*

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 Molecular Orbitals of Oxygen
|-
| MO1 || MO2 || MO3 || MO4 || MO5
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]
|-
| '''Contributing AOs'''|| 145 || 14 || 14 || 1 || 0
|-
| '''MO type'''|| 1090|| 1694|| 1694|| 3461|| 3590
|-
| '''MO energy'''|| A1|| E|| E|| A1|| E
|-
| '''MO occupancy'''|| 145 || 14 || 14 || 1 || 0
|-
| '''MO's effect on bonding'''|| 145 || 14 || 14 || 1 || 0
|-
|}

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted 'Figure 5 - HCN Charge Distribution' on the right:

<references>

<ref name="use imerpial cway of referencing Bond Distances">This is the bond distances reference.</ref>

</references>

lighten colour of text in dipole diagrams so numbers more visible

Rep:MOD:JAP10537443

2019-03-08T09:39:19Z

Jap18:

NH3 Molecule

N-H Bond Length = 1.02 Å

H-N-H Bond Angle = 10

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55776873 a.u.

RMS Gradient Norm = 0.00000485 a.u

Point Group = C3v

<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
Predicted change in Energy = -5.986283D-10</pre>

<jmol><jmolApplet>
<title> Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_NH3_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Display_Vibrations.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1090|| 1694|| 1694|| 3461|| 3590|| 3590
|-
| '''Symmetry''' || A1|| E|| E|| A1|| E || E
|-
| '''Intensity''' a.u.|| 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]|| [[File:jap_Vibration_6.jpg|100px]]
|}

I expect the nitrogen atom to have a negative charge as nitrogen is more electronegative than hydrogen. [[File:JAP18_nh3_CHARGES.jpg|thumb|right|Figure 1 - NH3 Charge Distribution]] Furthermore, I expect the 3 hydrogen atoms to have positive charges of equal value as they are less electronegative than the nitrogen atom, and are all in the same environment. This is infact true, and is highlighted by 'Figure 1 - NH3 Charge Distribution' on the right:

Expected modes = 6

Degenerate modes = The two vibrations at 1694cm-1, and the two vibrations at 3590cm-1.

"Bending" vibrations = The vibration at 1090cm-1 and both the vibrations at 1694cm-1 are "bending" vibrations.

"Bond stretch" vibrations = The vibration at 3461cm-1 and both the vibrations at 3590cm-1 are "bond stretch" vibrations.

Highly symmetric mode = The vibration at 3461cm-1.

"Umbrella" mode = The moed at 1090cm-1

Number of bands in an experimental spectrum of gaseous ammonia = 3

N2 Molecule

N-N Bond Length = 1.11 Å

N-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868 a.u.

RMS Gradient Norm = 0.00001838 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000014 0.001200 YES
Predicted change in Energy=-3.168264D-10</pre>

<jmol><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ABCJAP_N2_OPTIMISED.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:ABCJAP_N2_OPTIMISED.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that NH3 undergoes:

[[File:Vibrations_N2.jpg|200px]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:Jap18 N2 vibrations.jpg|100px]]
|}

Linked [[https://www.ccdc.cam.ac.uk/structures/Search?Compound=Dinitrogen-pentakis(trimethylphosphine)-molybdenum&DatabaseToSearch=Published | here]] a mono-metallic transition metal complex that coordinates N2 - Dinitrogen-pentakis(trimethylphosphine)-molybdenum (BIWGAP10). [[File:Jap18_n2_charges.jpg|thumb|right|Figure 2 - N2 Charge Distribution]]

The bond distance of N2 is 1.11Å. The bond distance between the two nitrogen atoms in this mono-metallic TM complex is slightly larger at 1.12Å <ref name="Bond Distance" /> . This is because the two nitrogen atoms are, similarly to N2, triple bonded to each other. However, in the mono-metallic TM complex, some of the electron density is drawn into the Mo-N bond, reducing the electron density in the triple bond between the nitrogens and so slightly increasing the bond length. Further more, the diatomic N triple-bond N bond length was determined computationally, which uses approximations to predict the bond distance unlike the bond distance determined in the mono-metallic TM complex which was determined experimentally. This could also account for the 0.01Å difference. COMPUTATIONAL AND EXPERIMENTAL REASONS!

I expect there to be no charge on either N2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true and is highlighted by 'Figure 2 - N2 Charge Distribution' on the right:

H2 Molecule

H-H Bond Length = 0.74 Å

H-H Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853929 a.u.

RMS Gradient Norm = 0.0001307 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000226 0.000450 YES
RMS Force 0.000226 0.000300 YES
Maximum Displacement 0.000298 0.001800 YES
RMS Displacement 0.000422 0.001200 YES
Predicted change in Energy=-6.751273D-08</pre>

<jmol><jmolApplet>
<title> Hydrogen Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_H2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that H2 undergoes:

[[File:JAP18 H2 VIBRATIONS.jpg|200px]]

[[File:JAP18_H2_CHARGES.jpg|thumb|right|Figure 3 - H2 Charge Distribution]]

{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 4461
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 H2 VIBRATIONS 2.jpg|100px]]
|}

I expect there to be no charge on an H2 atom because both atoms in the diatomic are the same and hence have the same electronegativity. This is in fact true as shown by 'Figure 3 - H2 Charge Distribition' on the right:

Haber-Bosch reaction energy calculation

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.11553746 a.u.3*

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853929 a.u.

3*E(H2)= -3.53561787 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -113.11553746 - [-109.52412868 + (-3.53561787)] a.u.

ΔE= -0.05579091 a.u. = -0.05579091 * 2625.5 KJ/mol = -146.479034205 KJ/mol

ΔE= -146.5 KJ/mol (1dp)

The ammonia product is more stable than the gaseous reactants as this is an exothermic reaction and the ammonia is at a lower energy.

Molecule of my own choice - O2

O-O Bond Length = 1.22 Å

O-O Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00001851 a.u.

Point Group = D*H

<pre> Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000020 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
Predicted change in Energy=-6.129527D-10</pre>

<jmol><jmolApplet>
<title> Oxygen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_O2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_O2_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that O2 undergoes:

[[File:JAP18 O2 VIBRATIONS.jpg|200px]]

[[File:JAP18 O2 DIPOLE.jpg|thumb|right|Figure 4 - O2 Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' a.u.|| 0
|-
| '''Image'''|| [[File:JAP18 O2 VIBRATIONS_VECTORS.jpg|100px]]
|}

I expect there to be no charge on either O2 atom because both atoms in the diatomic are the same and in the same environment and hence, have the same electronegativity. This is in fact true as shown by 'Figure 4 - O2 Charge Distribution' on the right:

{| class="wikitable" border="1"
|+ 5 Molecular Orbitals of Oxygen
|-
| '''Wavenumber''' cm-1|| '''''MO1''''' || '''''MO2''''' || '''''MO3''''' || '''''MO4''''' || '''''MO5'''''
|-
| '''Image'''|| [[File:jap_Vibration_1.jpg|100px]] || [[File:jap_Vibration_2.jpg|100px]]|| [[File:jap_Vibration_3.jpg|100px]]|| [[File:jap_Vibration_4.jpg|100px]]|| [[File:jap_Vibration_5.jpg|100px]]
| '''Symmetry'''|| A1|| E|| E|| A1|| E
|-
| '''Contributing AOs'''|| 145 || 14 || 14 || 1 || 0
|-
| '''MO type'''|| 1090|| 1694|| 1694|| 3461|| 3590
|-
| '''MO energy'''|| A1|| E|| E|| A1|| E
|-
| '''MO occupancy'''|| 145 || 14 || 14 || 1 || 0
|-
| '''MO's effect on bonding'''|| 145 || 14 || 14 || 1 || 0
|-
|}

 Extra Molecule - HCN

H-C Bond Length = 1.01 Å

C-N Bond Length = 1.16 Å

H-C-N Bond Angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -93.42458152 a.u.

RMS Gradient Norm = 0.00002060 a.u.

Point Group = C*V

<pre> Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000031 0.000300 YES
Maximum Displacement 0.000078 0.001800 YES
RMS Displacement 0.000049 0.001200 YES
Predicted change in Energy=-2.816950D-09</pre>

<jmol><jmolApplet>
<title> HCN Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JAP18_HCN_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

A link to the .log file can be found [[Media:JAP18_HCN_OPTIMISATION.LOG| here]].

Below is a table displaying the vibrational frequencies and corresponding intensities that HCN undergoes:

[[File:JAP18_HCN_VIBRATIONS.jpg|200px]]

[[File:JAP18_HCN_DIPOLE.jpg|thumb|right|Figure 5 - HCN Charge Distribution]]
{| class="wikitable" border="1"
|+ Table of Wavenumber, Symmetry, Intensity and Image of each vibration
|-
| '''Wavenumber''' cm-1|| 770|| 770|| 2213|| 3475
|-
| '''Symmetry''' || PI|| PI || SG || SG
|-
| '''Intensity''' a.u.|| 35|| 35|| 2 || 57
|-
| '''Image'''|| [[File:JAP18_HCN_VIBRATIONS_1.jpg|100px]] || [[File:JAP18_HCN_VIBRATIONS_2.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_3_abc.jpg|100px]]|| [[File:JAP18_HCN_VIBRATIONS_4.jpg|100px]]
|}

I expect there to be a negative charge on the nitrogen atom as this is a fairly electronegative atom. However, hydrogen and carbon are not very electronegative, hence I expect them to have positive values. This is in fact correct and is highlighted 'Figure 5 - HCN Charge Distribution' on the right:

<references>

<ref name="use imerpial cway of referencing Bond Distances">This is the bond distances reference.</ref>

</references>

lighten colour of text in dipole diagrams so numbers more visible