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=== NH<sub>3</sub> Molecule ===

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;"|NH<sub>3</sub>
|-
| Molecule name || Ammonia
|-
| calculation method || RB3LYP
|-
| basis set || 6-31G(d,p)
|-
| final energy E in atomic units || -56.55776873
|-
| point group || C<sub>3V</sub>
|}

<jmol><jmolApplet>
  <title>NH3</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>FV3918_NH3_OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[Media:FV3918_NH3_OPT.LOG| NH<sub>3</sub> log file]]

==== Vibrational modes of NH<sub>3</sub> ====
[[File:Vibration_NH3.png|300px]]
{| class="wikitable" border="1"
! colspan="3" style="text-align: center;"|N2
|-
| Mode # || Frequency || IR
|-
| 1 || 1090 || 145
|-
| 2 || 1694 || 14
|-
| 3 || 1694 || 14
|-
| 4 || 3461 || 1
|-
| 5 || 3590 || 0
|-
| 6 || 3590 || 0
|}

Mode 1
[[File:NH3_mode1_FV.png|350px]]

Mode 2
[[File:NH3_mode2_FV.png|350px]]

Mode 3
[[File:NH3_mode3_FV.png|350px]]

Mode 4
[[File:NH3_mode4_FV.png|350px]]

Mode 5
[[File:NH3_mode5_FV.png|350px]]

Mode 6
[[File:NH3_mode6_FV.png|350px]]

:From the 3N-6 rule 6 vibrational modes are expected.
:Modes 2 and 3 and modes 5 and 6 are degenerate.
:Modes 1,2 and 3 are bond bends and modes 4,5 and 6 are bond stretches.
:Mode 4 is highly symetrical as its a symerical stretch of all bonds.
:Mode 1 is called umbrella mode.
:2 bands are expected in the vibrational spectrum of Ammonia as it has 2 IR active vibrational modes at different frequencies.
==== Partial atomic charges on NH<sub>3</sub> ====
[[File:Charges_NH3.png|350px]]
:Nitrogen has a higher electronegativity than Hydrogen so we would expect it to be partially negative and Hydrogen partially possitive. Also Nitrogen is bonded to 3 Hydrogen atoms so the negative charge on the nitrogen must be 3 times greater than the possitive charge on each hydrogen atom

=== N<sub>2</sub> Molecule ===
{| class="wikitable" border="1"
! colspan="2" style="text-align: center;"|N2
|-
| Molecule name || Nitrogen
|-
| calculation method || RB3LYP
|-
| basis set || 6-31G(d,p)
|-
| final energy E in atomic units || -109.52412868
|-
| point group ||  D<sub>∞h</sub>
|}

<jmol><jmolApplet>
  <title>N2</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>FV3918_N2_OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[Media:FV3918_N2_OPT.LOG| N<sub>2</sub> log file]]

==== Vibration of N<sub>2</sub> ====
[[File:Vibration_N2_FV.png|300px]]
:N<sub>2</sub> is a diatomic linear molecule so we expect 1 vibrational mode according to the 3N-5 rule which is what we expect.
:Nitrogen is only bonded to another nitrogen atom. They have the same electronegative so there are no partial charges or overall dipole

=== H<sub>2</sub> Molecule ===
{| class="wikitable" border="1"
! colspan="2" style="text-align: center;"|N2
|-
| Molecule name || Hydrogen
|-
| calculation method || RB3LYP
|-
| basis set || 6-31G(d,p)
|-
| final energy E in atomic units || -1.17853936
|-
| point group ||  D<sub>∞h</sub>
|}

<jmol><jmolApplet>
  <title>H2</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>FV3918_H2_OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[Media:FV3918_H2_OPT.LOG| H<sub>2</sub> log file]]

==== Vibration of H<sub>2</sub> ====
[[File:Vibration_H2_FV.png|300px]]
:Like N<sub>2</sub> H<sub>2</sub> is also diatomic and linear so has 1 vibrational mode.
:It also has no partial charges for the same reason as nitrogen

==== H<sub>2</sub> complex ====
:[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=CEJDEA&DatabaseToSearch=Published| (σ2-Dihydrogen)-tricarbonyl-bis(tri-isopropylphosphine)-tungsten]] is a crystal that complexes tungsten with hydrogen. H<sub>2</sub>'s coordination number is 2. The crystal's unique identifier is CEJDEA. The H-H bond length found in the H2 molecule is 0.74Å and the H-H bond length found on the complex is 0.76Å. This difference might be due to the fact that H<sub>2</sub> only has 2 electrons which are in the H-H bond so when it complexes the bond could loose strength. Another possible reason for this difference is that the bond length in the H<sub>2</sub> molecule was found running an optimisation and the bond length in the H2 complex was obtained from a reported structure.
=== Energy for the synthesis of ammonia ===
{| class="wikitable" border="1"
! colspan="2" style="text-align: center;"|N<sub>2</sub> + 3H<sub>2</sub> -> 2NH<sub>3</sub>
|-
| E(NH<sub>3</sub>) || -56.55776873
|-
| 2*E(NH<sub>3</sub>) || −113.1155375
|-
| E(N<sub>2</sub>)  || -109.52412868
|-
| E(H<sub>2</sub>) || -1.17853936
|-
| 3*E(H<sub>2</sub>) || −3.53561808
|-
| ΔE(Atomic units) || −0.05579074
|-
| ΔE(kJmol<sup>-1</sup>) || −146.4785879
|}
:The process is exothermic so the ammonia product is more stable than the gaseous reactants

=== CO<sub>2</sub> molecule ===
{| class="wikitable" border="1"
! colspan="2" style="text-align: center;"|CO<sub>2</sub>
|-
| Molecule name || Carbon dioxide
|-
| calculation method || RB3LYP
|-
| basis set || 6-31G(d,p)
|-
| final energy E in atomic units || -188.58093945
|-
| point group || D<sub>∞h</sub>
|}

<jmol><jmolApplet>
  <title>CO2</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>FV3918_CO2_OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
[[Media:FV3918_CO2_OPT.LOG| CO<sub>2</sub> log file]]
Vibration_CO2_FV.png
==== Vibrational modes of CO<sub>2</sub> ====
[[File:Vibration_CO2_FV.png|300px]]
{| class="wikitable" border="1"
! colspan="3" style="text-align: center;"|CO2
|-
| Mode # || Frequency || IR
|-
| 1 || 640 || 31
|-
| 2 || 640 || 31
|-
| 3 || 1372 || 0
|-
| 4 || 2436 || 546
|}

Mode 1
[[File:CO2_mode1_FV.png|350px]]


Mode 2
[[File:CO2_mode2_FV.png|350px]]


Mode 3
[[File:CO2_mode3_FV.png|350px]]


Mode 4
[[File:CO2_mode4_FV.png|350px]]

:From the 3N-5 rule 4 vibrational modes are expected.
:Modes 1 and 2 degenerate.
:Modes 1 and 2 are bond bends and modes 3 and 4 are bond stretches.
:Mode 3 is highly symetrical as its a symerical stretch.
:2 bands are expected in the vibrational spectrum of carbon dioxide as it has vibrational 2 IR active modes at different frequencies.

==== Partial atomic charges on CO<sub>2</sub> ====
[[File:Charges_CO2_FV.png|350px]]
:Although CO<sub>2</sub> has no overall dipole the C=O bonds are polar. Oxygen is more electronegative than carbon so the oxygen atoms have a partial negative charge and the carbon atom has a positive charge 2 times larger than the negative charge on the oxygen atoms.

==== Molecular orbitals of CO<sub>2</sub> ====
:The energy in a molecular orbital depends on 2 factors. How strong the overlap between the orbitals is and how many nodes there are. Molecular orbitals 2, 4, 5, 6 and 7 of CO<sub>2</sub> are shown as they illustrate very clearly the effect of both of these factors. Despite having one node, MO2 is much lower in energy than MO4 which has no nodes. This is due to the strong overlap between the atomic orbitals used to form the molecular orbitals (the pictures are to a different scale so the overlap is weaker in MO4 than it looks).  Molecular orbitals 4, 5, 6, and 7 show how an increasing number of nodes increases the energy .
MO2
[[File:CO2_MO2_FV.png|350px]]

MO4
[[File:CO2_MO4_FV.png|350px]]

MO5
[[File:CO2_MO5_FV.png|350px]]

MO6
[[File:CO2_MO6_FV.png|350px]]

MO7
[[File:CO2_MO7_FV.png|350px]]


=Marking=
 
Note: All grades and comments are provisional and subjecct 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 recieved 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 0.5/1 ==
 
Have you completed the calculation and given a link to the file?
 
YES
 
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?
 
NO -  Comment: You missed to state bond lengths every time they were asked in the whole wiki. Therefore, half a mark will be taken once in this part as it is a repeating mistake.
 
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)
 
NO - you missed give bond lengths of both optimised diatomics.
 
==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 0.5/1==
 
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?
 
NO -energies in kJ/mol should only be reported with 1 decimal place.
 
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 3/5 ==
 
Have you completed the calculation and included all relevant information?
 
YES
 
Have you added information about MOs and charges on atoms?
 
You analysis of the calculated vibrations and charges is good!
however, regarding the analysis of the MOs you just briefly commented on their energies. You missed to comment on their occupancy, if they are found in the HOMO LUMO region or deeper in energy, which AOs contribute to form the displayed MOs.
 
== Independence 0/1 ==
 
If you have finished everything else and have spare time in the lab you could:
Check one of your results against the literature, or
Do an extra calculation on another small molecule, or
Do some deeper analysis on your results so far

NO - no independent work has been identified.