View source for Mod01559535

==NH<sub>3</sub>==
<pre> 
Molecule: ammonia

Calculation method: RB3LYP

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

Final energy E(RB3LYP):-56.55776873 au

RMS gradient: 0.00000485 au

Point group: C3V

N-H bond length: 1.02 Angstroms

H-N-H bond angle: 106°
</pre>

<jmol><jmolApplet>
  <title>Interactive ammonia molecule</title>
  <color>black</color>
  <size>400</size>
  <uploadedFileContents>CKERWIN_NH3_OPTIMISATION.LOG</uploadedFileContents>   
</jmolApplet></jmol>

[[File:optimised nh3 image.png|400px|thumb|left|Optimised ammonia structure]]



















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

[[File:vibrational table.png|600px|thumb|left|Initial table displaying the vibrational modes data for ammonia]]





































{| class="wikitable" border="1"
|+ Vibrational frequencies of NH<sub>3</sub>
! Vibration number !! Frequency (cm<sup>-1</sup>) !! Intensity (arbitrary units) !! Symmetry !! Image
|-
| 1 || 1090 || 145 || A1 || [[File:Vibration image 1.png|200px|thumb|left|]]
|-
| 2 || 1694 || 14 || E || [[File:Vibration image 2.png|200px|thumb|left|]]
|-
| 3 || 1694 || 14 || E || [[File:Vibration image 3.png|200px|thumb|left|]]
|-
| 4 || 3461 || 1 || A1 || [[File:Vibrational image 4.png|200px|thumb|left|]]
|-
| 5 || 3590 || 0 || E || [[File:Vibrational image 5.png|200px|thumb|left|]]
|-
| 6 || 3590 || 0 || E || [[File:Vibrational image 6.png|200px|thumb|left|]]
|}

<pre>
Using the 3N-6 rule, 6 vibrational modes are expected, as 3(4)-6=6.
There are two sets of degenerate modes; one set is at 1694 wavenumbers (modes 2 & 3) and the other set is at 3590 wavenumbers (modes 5 & 6)
The modes at 1090 wavenumbers and 1694 wavenumbers (modes 1, 2 & 3) are bending vibrations and the modes at 3461 wavenumbers and 3590 wavenumbers (modes 4, 5 & 6) are stretching.
The mode at 3461 wavenumbers (mode 4) is highly symmetric.
The "umbrella" mode is at 1090 wavenumbers (mode 1)
Two bands would be observed in an experimental spectrum of gaseous ammonia - although four different frequencies are observed in total, the stretching frequencies are of much lower intensity, therefore meaning only 
two bands would be observed.
</pre>

[[File:ammonia charge image 2.png|600px|thumb|centre|Image displaying the charge distribution on an ammonia molecule]]

<pre>
Shown above is an image of the charge distribution on an ammonia molecule. It is expected that the nitrogen is negatively charged and the hydrogens are positively charged - this is because nitrogen is much more
electronegative than hydrogen, therefore nitrogen pulls the electron density towards itself.
</pre>
Optimisation file can be found [[Media:CKERWIN_N2_OPTIMISATION.LOG|here]]

==N<sub>2</sub>==

<pre>
Molecule: nitrogen

Calculation method: RB3LYP

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

Final energy E(RB3LYP): -109.52359111 au

RMS gradient: 0.02473091 au

Point group: D∞H

N-N bond length: 1.11 Angstroms
The charges on both atoms are the same (0) because they have the same electronegativity, therefore the overall charge on the molecule is zero.

</pre>

<jmol><jmolApplet>
  <title>Interactive nitrogen molecule</title>
  <color>black</color>
  <size>400</size>
  <uploadedFileContents>CKERWIN_N2_OPTIMISATION.LOG</uploadedFileContents>   
</jmolApplet></jmol>

[[File:n2 optimised image.png|400px|thumb|left|Optimised nitrogen structure]]





















<pre>

         Item               Value     Threshold  Converged?
 Maximum Force            0.000001     0.000450     YES
 RMS     Force            0.000001     0.000300     YES
 Maximum Displacement     0.000000     0.001800     YES
 RMS     Displacement     0.000000     0.001200     YES
</pre>

[[File:vibrations table n2.png|600px|thumb|left|Initial table displaying the vibrational modes data  for nitrogen]]


The optimisation file can be found [[Media:CKERWIN_N2_OPTIMISATION.LOG|here]]


































==H<sub>2</sub>==

<pre>
Molecule: hydrogen

Calculation method: RB3LYP

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

Final energy E(RB3LYP): -1.17853936 au

RMS gradient: 0.00000017 au

Point group: D∞H

H-H bond length: 0.74 Angstroms
The charges on both atoms are the same (0) because they have the same electronegativity, therefore the overall charge on the molecule is zero.

</pre>



<jmol><jmolApplet>
  <title>Interactive hydrogen molecule</title>
  <color>black</color>
  <size>400</size>
  <uploadedFileContents>CKERWIN_H2_OPTIMISATION.LOG</uploadedFileContents>   
</jmolApplet></jmol>

[[File:h2 optimised image.png|400px|thumb|left|Optimised hydrogen structure]]






















         Item               Value     Threshold  Converged?
 Maximum Force            0.000000     0.000450     YES
 RMS     Force            0.000000     0.000300     YES
 Maximum Displacement     0.000000     0.001800     YES
 RMS     Displacement     0.000001     0.001200     YES

[[File:h2 vibrational table.png|600px|thumb|left|Initial table displaying the vibrational modes data  for hydrogen]]






































The optimisation file can be found [[Media:CKERWIN_H2_OPTIMISATION.LOG|here]]


==The Haber Bosch Process==
<pre>
The Haber Bosch Process is a process in which ammonia is formed from nitrogen and hydrogen. The equation for the reaction is shown below:

N2 +3H2 --> 2NH3
E(NH3)= -56.55776873 au
2*E(NH3)= -113.1155375 au
E(N2)= -109.52359111 au
E(H2)= -1.17853936 au
3*E(H2)= -3.53561808
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05632831 au
ΔE=-147.9kJ/mol]
</pre>
This process is exothermic, meaning the product (ammonia) is more stable as it is at a lower energy.
A literature value for ΔE was found to be -92kJ/mol<ref> name="chemguide"[https://www.chemguide.co.uk/physical/equilibria/haber.html]</ref> - although this is exothermic and is similar to the value 
calculated in this aspect, the literature value and the value obtained from calculations still differ by approximately 55kJ/mol.

==CH<sub>4</sub>==
<pre>
Molecule: methane

Calculation method: RB3LYP

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

Final energy E(RB3LYP):-40.52401404 au

RMS gradient: 0.00003263 au

Point group: Td

C-H bond length: 1.09 Angstroms

H-C-H bond angle: 109°
</pre>

<jmol><jmolApplet>
  <title>Interactive methane molecule</title>
  <color>black</color>
  <size>400</size>
  <uploadedFileContents>CKERWIN_CH4_OPTIMISATION.LOG</uploadedFileContents>   
</jmolApplet></jmol>

[[File:ch4 optimised image.png|400px|thumb|left|Optimised methane structure]]


















<pre>
         Item               Value     Threshold  Converged?
 Maximum Force            0.000063     0.000450     YES
 RMS     Force            0.000034     0.000300     YES
 Maximum Displacement     0.000179     0.001800     YES
 RMS     Displacement     0.000095     0.001200     YES
</pre>

[[File:ch4 vibrations table.png|600px|thumb|left|Initial table displaying the vibrational modes data for methane]]




































{| class="wikitable" border="1"
|+ Vibrational frequencies of CH<sub>4</sub>
! Vibration number !! Frequency (cm<sup>-1</sup>) !! Intensity (arbitrary units) !! Symmetry !! Image
|-
| 1 || 1356 || 14 || T2 || [[File:ch4 vibration 1.png|200px|thumb|left|]]
|-
| 2 || 1356 || 14 || T2 || [[File:ch4 vibration 2.png|200px|thumb|left|]]
|-
| 3 || 1356 || 14 || T2 || [[File:ch4 vibration 3.png|200px|thumb|left|]]
|-
| 4 || 1579 || 0 || E || [[File:ch4 vibration 4.png|200px|thumb|left|]]
|-
| 5 || 1579 || 0 || E || [[File:ch4 vibration 5.png|200px|thumb|left|]]
|-
| 6 || 3046 || 0 || A1 || [[File:ch4 vibration 6.png|200px|thumb|left|]]
|-
| 7 || 3162 || 25 || T2 || [[File:ch4 vibration 4.png|200px|thumb|left|]]
|-
| 8 || 3162 || 25 || T2 || [[File:ch4 vibration 5.png|200px|thumb|left|]]
|-
| 9 || 3162 || 25 || T2 || [[File:ch4 vibration 6.png|200px|thumb|left|]]
|}

[[File:ch4 charge image.png|400px|thumb|left|Charge distribution of methane]]


















<pre>
This charge distribution is as expected, as carbon is more electronegative than hydrogen and therefore pulls the electron density towards itself, creating a negative charge on the carbon and a positive 
charge on the hydrogen atoms.
</pre>
Optimisation file can be found [[Media:CKERWIN_CH4_OPTIMISATION.LOG|here]]

====Molecular orbitals of CH<sub>4</sub>====

<pre>
Methane has 4 bonding and 4 antibonding molecular orbitals. The third, fourth and 5th molecular orbitals are all degenerate with energies of -0.38831. The HOMO is the sigma bonding orbital and has
energy of -0.38831 and consists of 1s orbitals from hydrogen and 2sp3 orbitals from carbon. The HOMO can be considered to be any of the three degenerate occupied orbitals.
The LUMO is the sigma star anti bonding orbital and has an energy of 0.11824 As the three orbitals (Figures 3, 4 and 5) are all degenerate, any may be considered the HOMO.
All of the electrons occupy the bonding orbitals, therefore the antibonding orbitals do not contribute to the bond order. Methane has a bond order of 4, as 0.5(8)-0=4.
</pre>

[[File:ch4 mo 1.png|600px|thumb|left|Figure 1 - Image of the first MO of methane]]

[[File:ch4 lumo.png|600px|thumb|left|Figure 2 - Image of the LUMO for methane]]

[[File:ch4 homo.png|600px|thumb|left|Figure 3 - Image of the HOMO for methane (degenerate)]]

[[File:ch4 mo 3.png|600px|thumb|left|Figure 4 - Image of the third MO for methane (degenerate)]]
 
[[File:ch4 mo 4.png|600px|thumb|left|Figure 5 - Image of the fourth MO for methane (degenerate)]]

The optimisation file can be found [[Media:CKERWIN_CH4_OPTIMISATION.LOG|here]]

























































































































==Frequency tables for N<sub>2</sub> and H<sub>2</sub>==

{| class="wikitable" border="1"
|+ Vibrational frequencies of N<sub>2</sub>
! Vibration number !! Frequency (cm<sup>-1</sup>) !! Intensity (arbitrary units) !! Symmetry !! Image
|-
| 1 || 2457 || 0 || SGG || [[File:n2 vibrational mode.png|200px|thumb|centre|]]
|-


{| class="wikitable" border="1"
|+ Vibrational frequencies of H<sub>2</sub>
! Vibration number !! Frequency (cm<sup>-1</sup>) !! Intensity (arbitrary units) !! Symmetry !! Image
|-
| 1 || 4466 || 0 || SGG || [[File:h2 vibration image.png|200px|thumb|centre|]]
|-


=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 0/1 ==

Have you completed the calculation and given a link to the file?

NO - Your given link redirects to the .log file of an optimised N2 molecule

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0.5/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 2/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES

You could have analysed the calculated vibrations as you did for NH3.
You missed to explicitly state the occupancy and effect on bonding of all MOs.
You correctly identified the contributing AOs for the HOMO. You commented on the LUMO without showing it. You showed two MOs which you never mentioned in your description (Figure 1 & 2).
You missed to give the relative MO energies and to explain these as well.


== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

YES - you could have tried to explain why there is such a difference between experimental and computational values for the reaction energy of the Haber-Bosch-process.

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far