View source for Rep:Mod:IAB


= Ignacy Bartnik's Wiki Page =

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

=== Results of Gaussian calculations ===
{| class="wikitable"
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-56.5577687 a.u.</nowiki>
|-
|RMS Gradient Norm
|0.00000485 a.u.
|-
|Point Group
|C3V
|-
|N-H bond length
|1.02 Å
|-
|H-N-H bond angle
|106°
|}

==== Final results table from .log file ====
<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=-5.986274D-10
Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.018          -DE/DX =    0.0                 !
 ! R2    R(1,3)                  1.018          -DE/DX =    0.0                 !
 ! R3    R(1,4)                  1.018          -DE/DX =    0.0                 !
 ! A1    A(2,1,3)              105.7412         -DE/DX =    0.0                 !
 ! A2    A(2,1,4)              105.7412         -DE/DX =    0.0                 !
 ! A3    A(3,1,4)              105.7412         -DE/DX =    0.0                 !
 ! D1    D(2,1,4,3)           -111.8571         -DE/DX =    0.0                 !
 --------------------------------------------------------------------------------

</pre>

==== .log File of NH<sub>3</sub> Molecule ====
[[File:IAB18_NH3_OPTIMISATION.LOG]]

==== Interactive model of NH<sub>3</sub> Molecule ====
<jmol><jmolApplet>
  <title>NH3 molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>IAB18_NH3_OPTIMISATION.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

=== NH<sub>3</sub> Vibrations ===

==== Screen Shot of calculated Vibrations ====
[[File:IAB_NH3_Vibrations_screen.png]]

==== Calculated Vibrations of NH<sub>3</sub> ====
{| class="wikitable"
|'''Mode'''
|1
|2
|3
|4
|5
|6
|-
|'''wavenumber'''<br>
cm<sup>-1</sup>
|1090
|1694
|1694
|3461
|3590
|3590
|-
|'''symmetry'''
|A1
|E
|E
|A1
|E
|E
|-
|'''intensity''' <br>
arbitrary units
|145
|14
|14
|1
|0
|0
|-
|'''image'''
|[[File:IAB NH3 image1.png|120px]]
|[[File:IAB NH3 image2.png|120px]]
|[[File:IAB NH3 image3.png|120px]]
|[[File:IAB NH3 image4.png|120px]]
|[[File:IAB NH3 image5.png|120px]]
|[[File:IAB NH3 image6.png|120px]]
|}

Modes 2 and 3 are degenerated with respect to each other and modes 5 and 6 are also degenerated with respect to each other.
6 modes of vibrations would be expected of NH<sub>3</sub> using the 3N-6 rule and indeed 6 modes were calculated.
Modes 1, 2, and 3 are bending vibration modes, while modes 4, 5, and 6 and bond stretching vibration modes.
Mode 4 is highly symmetric.
2 bands would be expected in an IR spectrum, corresponding to absoptions for 1 and 2 & 3. 2 & 3 would be indistinguishable as they are degenerate, vibrational mode 4 does not have a change in dipole, so it would not be visible in an IR spectrum and mode 5 & 6 have a very low intensity so they could be seen in a very delicate spectrometer but most of the time, they too would be undetectable.
Vibration mode 1 is the so called umbrella motion vibration.

==== Charge Distribution of NH<sub>3</sub> ====
{| class="wikitable"
!Atom
!N
!H
|-
|Charge (elementary charge)
|<nowiki>-1.125</nowiki>
|0.375
|}
It would be expected for the nitrogen to have a negative charge and hydrogen to have a partial positve charge as the nitrogen is more electronegative and indeed, this is also found in the calculations.

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

=== Results of Gaussian calculations ===
{| class="wikitable"
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-109.5241287 a.u.</nowiki>
|-
|RMS Gradient Norm
|0.00000060 a.u.
|-
|Point Group
|D*H
|-
|N-N bond length
|1.11 Å
|-
|N-N bond angle
|180°
|}

==== Final results table from .log file ====
<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
 Predicted change in Energy=-3.401096D-13
 Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.1055         -DE/DX =    0.0                 !
 --------------------------------------------------------------------------------


</pre>



==== .log File of N<sub>2</sub> Molecule ====
[[File:IAB18_N2_OPTIMISATION.LOG]]

==== Interactive model of N<sub>2</sub> Molecule ====
<jmol><jmolApplet>
  <title>N<sub>2</sub> molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>IAB18_N2_OPTIMISATION.LOG</uploadedFileContents>
<script>frame 1.11</script>
</jmolApplet></jmol>

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

==== Screen Shot of calculated Vibrations ====
[[File:IAB_N2_Vibrations_screen.png]]

==== Calculated Vibrations of N<sub>2</sub> ====
{| class="wikitable"
|'''Mode'''
|1
|-
|'''wavenumber'''<br>
cm<sup>-1</sup>
|2457
|-
|'''symmetry'''
|SGG
|-
|'''intensity''' <br>
arbitrary units
|0
|-
|'''image'''
|[[File:IAb N2 image1.png|200px]]
|}


For the N<sub>2</sub> molecule, only 1 mode of vibration would be expected from the 3N-5 rule (not 3N-6 as it is a linear molecule), and indeed only 1 vibrational mode is predicted by the calculations. Since there is only one mode, there is no degeneracy possible. The one mode is a bond stretch vibration. It would not be IR active as it does not change the dipole of the molecule, so N<sub>2</sub> would not be visible in an IR spectrum.

====== Charge Distribution of N<sub>2</sub> ======
{| class="wikitable"
!Atom
!N
|-
|Charge (elementary charge)
|<nowiki>0</nowiki>
|}

It would be expected that there is equal charge distribution over the whole N<sub>2</sub> molecule as it is a elementary diatomic molecule, meaning it is purely covalent and both the nitrogens are identical in their electronegativity. Therefore, their electron attraction cancels each other out completely. This is also what was calculated, resulting in no charge on the individual atoms and no dipole.

== H2 Molecule ==

=== Results of Gaussian calculations ===
{| class="wikitable"
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-1.1785394 a.u.</nowiki>
|-
|RMS Gradient Norm
|0.00000017 a.u.
|-
|Point Group
|D*H
|-
|H-H bond length
|0.74 Å
|-
|H-H bond angle
|180°
|}

==== Final results table from .log file ====
<pre>
       
         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
 Predicted change in Energy=-1.164080D-13
 Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  0.7428         -DE/DX =    0.0                 !
 --------------------------------------------------------------------------------

</pre>

==== .log File of H<sub>2</sub> Molecule ====
[[File:IAB18_H2_OPTIMISATION.LOG]]

==== Interactive model of H<sub>2</sub> Molecule ====
<jmol><jmolApplet>
  <title>H<sub>2</sub> molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>H2struvcture.xyz</uploadedFileContents>
</jmolApplet></jmol>

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

==== Screen Shot of calculated Vibrations ====
[[File:IAB_H2_Vibrations_screen.png]]

==== Calculated Vibrations of H<sub>2</sub> ====
{| class="wikitable"
|'''Mode'''
|1
|-
|'''wavenumber'''<br>
cm<sup>-1</sup>
|4466
|-
|'''symmetry'''
|SGG
|-
|'''intensity''' <br>
arbitrary units
|0
|-
|'''image'''
|[[File:IAB H2 image1.png|200px]]
|}


For the H<sub>2</sub> molecule, only 1 mode of vibration would be expected from the 3N-5 rule (not 3N-6 as it is a linear molecule), and indeed only 1 vibrational mode is predicted by the calculations. Since there is only one mode, there is no degeneracy possible. The one mode is a bond stretch vibration. It would not be IR active as it does not change the dipole of the molecule, so H<sub>2</sub> would not be visible in an IR spectrum. In this aspect the H<sub>2</sub> molecule is very similar to the N<sub>2</sub> molecule.

====== Charge Distribution of H<sub>2</sub> ======
{| class="wikitable"
!Atom
!H
|-
|Charge (elementary charge)
|<nowiki>0</nowiki>
|}

It would be expected that there is equal charge distribution over the whole H<sub>2</sub> molecule as it is a elementary diatomic molecule, meaning it is purely covalent and both the hydrogens are identical in their electronegativity. Therefore, their electron attraction cancels each other out completely. This is also what was calculated, resulting in no charge on the individual atoms and no dipole.

== <br>Bond Length of N<sub>2 </sub> in mono-metallic transition metal complex ==

<jmol><jmolApplet>
  <title>Interactive model of MABVER Molecule </title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>MABVER.sd</uploadedFileContents>

</jmolApplet></jmol>
<ref name="LazyDog" />

{| class="wikitable"
!Complex
!N-N bond length(Å) 
|-
|MABVER
|<nowiki>1.08</nowiki><ref name="LazyDog" />
|}

The transition metal complex with N<sub>2 </sub> can be found here [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=MABVER&DatabaseToSearch=Published]

The bond length of the N<sub>2 </sub> in the MABVER complex is shorter than the calculated bond length of N<sub>2 </sub>. This is not expected as the N<sub>2 </sub> would donate some of its electrons from its bonding orbitals to the metal (as it has none in non-bonding orbitals), and then there would be some overlap of its non bonding orbitals and the metal electrons orbitals, so the N<sub>2 </sub> bond should be weaker resulting in a longer bond. However, this is not necessarily true, and it is possible that if the whole complex and not just N<sub>2 </sub> was calculated, the same bond length would be found. Even if it was not, this can still be explained by the fact that a simplified theory is being used to reduce compute time, and it also does not incorporate packing effects, which could well result in a shorter bond length as well.

==Calculating the energy of Haber Bosch Process==

{| class="wikitable"
!
!E(NH<sub>3</sub>)
!2*E(NH<sub>3</sub>)
!E(N<sub>2</sub>)
!E(H<sub>2</sub>)
!3*E(H<sub>2</sub>)
!ΔE=2*E(NH<sub>3</sub>)-[E(N<sub>2</sub>)+3*E(H<sub>2</sub>)]=
|-
|Energy (au)
|<nowiki>-56.5577687</nowiki>
|<nowiki>-113.1155375</nowiki>
|<nowiki>-109.5241287</nowiki>
|<nowiki>-1.1785394</nowiki>
|<nowiki>-3.5356181</nowiki>
|<nowiki>-0.0557907</nowiki>
|-
|Energy (kJ mol <sup>-1</sup>)
|<nowiki>-148492.4</nowiki>
|<nowiki>-296984.8</nowiki>
|<nowiki>-287555.6</nowiki>
|<nowiki>-3094.3</nowiki>
|<nowiki>-9282.8</nowiki>
|<nowiki>-146.5</nowiki>
|}

In terms of energy, N<sub>2</sub> is most stable, NH<sub>3</sub> is less stable and H<sub>2</sub> is least stable. Even though N<sub>2</sub> is very stable, the reaction of 3H<sub>2</sub> + N<sub>2</sub> → 2NH<sub>3</sub> is energetically favorable, as NH<sub>3</sub> is also quite stable and H<sub>2</sub> has a reltively low stability.

== CN<sup>-</sup> Molecule ==

=== Results of Gaussian calculations ===
{| class="wikitable"
|Calculation Method
|RB3LYP
|-
|Basis Set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-92.8245315 a.u.</nowiki>
|-
|RMS Gradient Norm
|0.00000704 a.u.
|-
|Point Group
|C<sub>inf</sub>V
|-
|C-N bond length
|1.18 Å
|-
|C-N bond angle
|180°
|}

==== Final results table from .log file ====
<pre>
       
         Item               Value     Threshold  Converged?
 Maximum Force            0.000012     0.000450     YES
 RMS     Force            0.000012     0.000300     YES
 Maximum Displacement     0.000005     0.001800     YES
 RMS     Displacement     0.000008     0.001200     YES
 Predicted change in Energy=-6.650397D-11
 Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.1841         -DE/DX =    0.0                 !
 --------------------------------------------------------------------------------

</pre>

==== .log File of CN<sup>-</sup> Molecule ====
[[File:IAB18 CN- OPTIMISATION.LOG]]

==== Interactive model of CN<sup>-</sup> Molecule ====
<jmol><jmolApplet>
  <title>CN- molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>IAB18 CN- OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== CN<sup>-</sup> Vibrations ===

==== Screen Shot of calculated Vibrations ====
[[IMAGE:IAB CN- Vibrations screen.png]]

==== Calculated Vibrations of CN<sup>-</sup> ====
{| class="wikitable"
|'''Mode'''
|1
|-
|'''wavenumber'''<br>
cm<sup>-1</sup>
|2139
|-
|'''symmetry'''
|SG
|-
|'''intensity''' <br>
arbitrary units
|8
|-
|'''image'''
|[[File:IAB CN- image1.png|200px]]
|}




For the CN<sup>-</sup> molecule, only 1 mode of vibration would be expected from the 3N-5 rule (not 3N-6 as it is a linear molecule), and indeed only 1 vibrational mode is predicted by the calculations. Since there is only one mode, there is no degeneracy possible. The one mode is a bond stretch vibration. Unlike the other diatomics analysed on this wiki page, the CN<sup>-</sup> would be IR active as it does change its dipole of the molecule with the vibration, as it has an overall dipole and the distance between the charges changes as it vibrates.

====== Charge Distribution of CN<sup>-</sup> ======
{| class="wikitable"
!Atom
!C
!N
|-
|Charge (elementary charge)
|<nowiki>-0.246</nowiki>
|<nowiki>-0.754</nowiki>
|}

It would be expected that there is an unequal charge distribution that is overall negative for the CN<sup>-</sup> molecule as it is a simple diatomic with a negative charge. Indeed, the calculations show that both the nitrogen and carbon have negative charges, with the nitrogen having more of the negative charge, which again agrees with expectations as nitrogen is more electronegative and more electron rich, starting in its elemental state with a lone pair.

=== MOs of CN<sup>-</sup> ===


{| class="wikitable"
|'''Arbitrary MO number'''
|1
|2
|3
|4
|5
|-
|'''image'''
|[[File:IAB CN- MO image1.png|300px]]
|[[File:IAB CN- MO image2.png|300px]]
|[[File:IAB CN- MO image3.png|300px]]
|[[File:IAB CN- MO image4.png|300px]]
|[[File:IAB CN- MO image5.png|300px]]
|-
|'''MO number as seen in gaussian'''
|1
|6
|7
|8
|10
|-
|'''Energy'''<br>
au
|<nowiki>-14.00393</nowiki>
|<nowiki>-0.01696</nowiki>
|<nowiki>0.01857</nowiki>
|<nowiki>0.35435</nowiki>
|<nowiki>0.59206</nowiki>
|-
|'''Occupied?'''
|Occupied
|Occupied
|Occupied
|Unoccupied
|Unoccupied
|-
|'''Bonding?''' <br>
|Bonding
|Bonding
|Bonding
|Anti bonding
|Anti bonding
|-
|'''AO contribution'''  <br>
|According to a traditional MO diagram, this orbital consists of 1s AOs of C and N combinding to make a σ bonding orbital, but gaussian predicts that this will be practically just the 1s nitrogen AO which is also what it displays in the image.
|According to a traditional MO diagram, this orbital consists of 2p AOs of C and N combinding to make a π bonding orbital. According to the calculations,2p<sub>x</sub> orbitals of both the N and C are the major contributors while the 3p<sub>x</sub> also play a role. The other AOs do not play a relevant role. Both C and N contribute more or less equally.
|According to a traditional MO diagram, this orbital consists of 2p AOs of C and N combinding to make a σ bonding orbital. According to the calculations, the major positively contributing AOs are the 3s orbital from the carbon and the 2p<sub>z</sub> from the nitrogen. The negative contributers are the carbon 3p<sub>z</sub> and 2p<sub>z</sub>.
|According to a traditional MO diagram, this orbital consists of 2p AOs of C and N combinding to make a π* anti-bonding orbital. According to the calculations,3p<sub>y</sub> orbitals of both the N and C are the major contributors while the 2p<sub>y</sub> also play a role. The other AOs do not play a relevant role. Both C and N contribute equally.
|According to a traditional MO diagram, this orbital consists of 2p AOs of C and N combinding to make a σ* anti-bonding orbital. According to the calculations, the nitrogen 3s orbital has a large positive contribution while the carbon 3s has an equal but negative contribution and then, the C 3p<sub>z</sub> also has a large negative contribution. This is very interesting as for the 4th MO, the traditional understanding fit very well with the calculations, while here it does not. This is probably partly due to the "traditional understanding" being referenced being quite simplistic and also, gaussian not being as reliable in calculating energetically high unoccupied MOs.
|-
|'''General comment?''' <br>
|This is an orbital that is increadibly deep in energy and will therefore being practically completely inert. Nitrogen is more electronegative, so it makes sense that it will be the major contributor to the MO, although it is suprising to see just how much of the MO is due to the N and how little the C contributes. 
|This orbital is one level below the HOMO, so it is not as relevant for reactions, but could still concievable affect them. It is bonding and occupied, so it contributes to the bonding. It is well predicted by a traditional MO diagram, with the 2p orbitals being the largest contributing AOs. It is also degenerate with what gaussian would call MO 5, as that one is just shifted by 90° as it is made of p<sub>x</sub> orbitals instead of p<sub>y</sub>.
|This is a very relevant orbital as it is the HOMO. It is occupied and bonding so it adds to the C-N bond. It is quite high in energy, and accessible, so it will participate in reactions whenever the molecule acts as a nucleophile. This is the orbital that will "attack" the LUMO of whatever it is reacting with. It is worthy to note that this σ orbital is higher in energy than the corresponding π orbitals, which only happens for atoms with low atomic numbers (the π/σ switch occurs for only a few compounds).
|This is an unoccupied bond so it does not play a role in the bond of the molecule. However, it is the LUMO, degenerate with what gaussian labeled MO number 9, which is the other π* anti-bonding orbital. That one was not included as it is the same, just shifted 90° as it is made of p<sub>x</sub> orbitals instead of p<sub>y</sub>. Both of these orbitals might seem quite important, as being the LUMO, they will take part in reactions where CN<sup>-</sup> acts as an electrophile, but CN<sup>-</sup> rarely acts as an electrophile, so they are not as important. It is interesting that the 3p orbitals contribute more than the 2p orbitals. This is further evidence for it being unoccupied and being quite high in energy.
|This is an unoccupied bond so it does not play a role in the bond of the molecule. Additionally, there are two other energetically lower unoccupied orbital, so it is also unlikely to take part in things lewis acid base reactions, as there the LUMO orbital will be more relevant.
|-
|}

=== Independence Mark: CN<sup>-</sup> bond length ===

For my independece mark, I decided to investigate the literature value of CN- bond lengths, but because it is an ion, I decided to look at it bonded in a transition metal complex. I looked at 3 different complexes, taken from here [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=AVARUM&DatabaseToSearch=Published] [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEHMIP&DatabaseToSearch=Published] [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=FILDEL01&DatabaseToSearch=Published]

<jmol><jmolApplet>
  <title>Interactive model of AVARUM Molecule </title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>AVARUM.mol2</uploadedFileContents>

</jmolApplet></jmol>
<ref name="LazyDog2" />

<jmol><jmolApplet>
  <title>Interactive model of DEHMIP Molecule </title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>DEHMIP.mol2</uploadedFileContents>

</jmolApplet></jmol>
<ref name="LazyDog3" />

<jmol><jmolApplet>
  <title>Interactive model of FILDEL01 Molecule </title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>FILDEL01.mol2</uploadedFileContents>

</jmolApplet></jmol>
<ref name="LazyDog4" />

{| class="wikitable"
!Complex
!Average C-N bond length(Å) 
|-
|AVARUM
|<nowiki>1.12</nowiki><ref name="LazyDog2" />
|-
|DEHMIP
|<nowiki>1.15</nowiki><ref name="LazyDog3" />
|-
|FILDEL01
|<nowiki>1.14</nowiki><ref name="LazyDog4" />
|-
|}

All of these bond lengths are shorter than the 1.18 Å bond length calculated in gaussian for the ion in a vacuum. This is again, similar to what was observed for the N<sub>2</sub> molecule. CN<sup>-</sup> and N<sub>2</sub> are isoelectronic and have all their electrons in bonding orbitals, so when they bond to something else, like in the transition metal complexes, their bond should become weaker and therefore longer, however the opposite is observed in the examples shown above. It is impossible to tell if this is due to too many approximations in the calculation made with gaussian, or if it due to the packing effects from just this information. However, a literature value was found to be 1.14  Å <ref name="LazyDog5" />, suggesting that it is not the packing effects that make the bond length shorted in the transition metal complexes, but that it is the gaussian calculations which wrongly predict a longer bond than is found in nature. The fact that gaussian, with the method of calculation that was used, does not meet reality exactly, should not be suprising as it is a computationally much simplified method, again, to enable performing it on a regular PC by students, and requiring hours and days of CPU time. If a different method of calculations was used, it well maybe that the correct bond length would be calculated, but then students would not be able to perform these calculations on regular PCs.








<references>
<ref name="LazyDog"> S.M.P.R.M.Cunha, M.F.C.G.da Silva, A.J.L.Pombeiro, Inorganic Chemistry, 2003, 42, 2157, DOI: 10.1021/ic026176e </ref>


<ref name="LazyDog2"> Zong-xin Pi, Jian-Hong Bi, Hua-Ze Dong, Asian Journal of Chemistry, 2015, 27, 2729, DOI: 10.14233/ajchem.2015.17812 </ref>


<ref name="LazyDog3">  Maria-Gabriela Alexandru, Diana Visinescu, Sergiu Shova, Francesc Lloret, Miguel Julve, Inorganic Chemistry, 2017, 56, 12594, DOI: 10.1021/acs.inorgchem.7b02050  </ref>


<ref name="LazyDog4">  Mohammed A. Abbas, Colin D. McMillen, Julia L. Brumaghim, Inorganica Chimica Acta, 2017, 468, 308, DOI: 10.1016/j.ica.2017.07.003  </ref>

<ref name="LazyDog5">   F. H. Allen, O. Kennard, D. G. Watson, L. Brammer, A. G. Orpen. Tables of bond Lengths determined by X-Ray and Neutron Diffraction. Part 1. Bond Lengths in Organic Compounds. J. Chem. Soc. Perkin Trans. II 1987, S1-S19. </ref>

</references>

=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 1/1 ==

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?

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, good explanations and sentence structure well done!

== N2 and H2 0/0.5 ==

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

YES, However you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==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 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES, you lost the half mark for giving the bond angle - invalid for a diatomic.

Have you added information about MOs and charges on atoms?

YES, good job on the MO analysis, very detailed explanations! On MO 1 there is not much C contribution because MO 2 contains the C 1s, the AOs are too localised to interact and forming a bonding anti-bonding pair so instead you get two MOs, each with just one AO.

== 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

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far


You looked up some crystal structures and analysed the different C-N bond lengths, well done!