View source for Rep:Mod:01576020dp3618

==Introduction==
Gaussian was used to optimize the structures of several molecules using the RB3LYP calculation method and the 6-31G(d,p) basis set. Another calculation method was also used to explore its effects on the obtained results. The findings are discussed below. NH<sub>3</sub>, N<sub>2</sub>, H<sub>2</sub>, CO and SF<sub>4</sub> were studied using the aforementioned program. Molecular orbitals of the latter molecule were also studied and discussed. Comparison to other studies of these molecules can also be found below. 

==NH<sub>3</sub> molecule==
===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || NH<sub>3</sub>
|-
| File name || dp3618_nh3_optf_pop
|-
| File type || .log
|-
| Calculation Type || FREQ
|-
| Calculation Method || RB3LYP
|-
| Basis set || 6-31G(d,p)
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -56.55776873 a.u.
|-
| RMS Gradient Norm || 0.00000485 a.u.
|-
| Dipole Moment || 1.8466 Debye
|-
| Point group || C<sub>3V</sub>
|}

N-H bond lengths: 1.02 Å

H-N-H bond angles: 106°

"Item" table:
<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=-5.986275D-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                 !
 --------------------------------------------------------------------------------
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

<jmol><jmolApplet>
  <title>NH<sub>3</sub>molecule</title>
  <color>black</color>
  <size>300</size>
  <uploadedFileContents>DP3618 NH3 OPTF POP.LOG</uploadedFileContents>
  <script>frame 1.16</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 NH3 OPTF POP.LOG| here]]


===Vibrational analysis===

[[File: DP3618 screenshot DisplayVibrations.png]]



{| class="wikitable" border="1"
|+ Vibrational modes of the NH<sub>3</sub> molecule
!  !! Vibration 1 !! Vibration 2 !! Vibration 3 !! Vibration 4 !! Vibration 5 !! Vibration 6
|-
| '''Wavenumber''' [cm-1] || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''IR Intensity''' || 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image''' || [[File: DP3618 screenshot vibration1.png|200 px]] || [[File: DP3618 screenshot vibration2.png|200 px]] || [[File: DP3618 screenshot vibration3.png|200 px]] || [[File: DP3618 screenshot vibration4.png|200 px]] || [[File: DP3618 screenshot vibration5.png|200 px]] || [[File: DP3618 screenshot vibration6.png|200 px]]
|-
|}


There are 3N-6 expected vibrational modes in a non-linear molecule. Since our molecule consists of 4 atoms, we would expect 6 vibrational modes to exist and that is confirmed by the quantum calculation.

There are 2 degenerate vibrational modes with a wavenumber of 1693.95 cm<sup>-1</sup> and 2 degenerate modes with a wavenumber of 3589.82 cm<sup>-1</sup>.

Two types of vibrations exist; "bending" and "stretching". Vibrations with wavenumbers 1089.54 cm<sup>-1</sup> and the two with 1693.95 cm<sup>-1</sup> fall in the former category, whilst the other 3 fall in the latter. This is in agreement with the generally accepted fact that bending vibrations have smaller frequencies/wavenumbers than stretching vibrations.<ref name="vibrations" />

The stretching mode with the wavenumber 3461.29 cm<sup>-1</sup> is highly symmetric.

The symmetric bending mode (1089.54 cm<sup>-1</sup>) is known as the "umbrella" mode.

Based on the calculated wavenumbers of the different vibrations, we would expect to see 3 bands in the experimental spectrum of gaseous ammonia (Vibration 4 is highly symmetric and therefore not IR active), but two of them are degenerate, so we only see 2 bands.

Predicted IR spectrum:

[[File: DP3618 screenshot ir.png|450 px]]


===Charge analysis===
Taking into account the electronegativities of the constituent atoms of ammonia, we would expect the nitrogen atom to be negatively charged and the 3 hydrogen atoms to be positively charged. Since ammonia is neutral overall, the sum of the individual charges on atoms should be 0. This is confirmed by the results of the calculation.

The charge on the nitrogen atom is -1.125 and the charge on each of the hydrogen atoms is 0.375.

[[File: DP3618 screenshot charges.png|300px]]

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

===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || N<sub>2</sub>
|-
| File name || dp3618_n2_optf_pop
|-
| File type || .log
|-
| Calculation Type || FREQ
|-
| Calculation Method || RB3LYP
|-
| Basis set || 6-31G(d,p)
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -109.52412868 a.u.
|-
| RMS Gradient Norm || 0.00000158 a.u.
|-
| Dipole Moment || 0.0000 Debye
|-
| Point group || D<sub>∞h</sub>
|}

N-N bond length: 1.11 Å

"Item" table:
<pre>
        Item               Value     Threshold  Converged?
 Maximum Force            0.000003     0.000450     YES
 RMS     Force            0.000003     0.000300     YES
 Maximum Displacement     0.000001     0.001800     YES
 RMS     Displacement     0.000001     0.001200     YES
 Predicted change in Energy=-2.352265D-12
 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                 !
 --------------------------------------------------------------------------------
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

<jmol><jmolApplet>
  <title>N<sub>2</sub>molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>DP3618 N2 OPTF POP.LOG</uploadedFileContents>
  <script>frame 1.12</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 N2 OPTF POP.LOG| here]].

===Vibrational analysis===

[[File: DP3618 screenshot DisplayVibrations n2.png]]


{| class="wikitable" border="1"
|+ Vibrational mode of the N<sub>2</sub> molecule
!  !! Vibration 1
|-
| '''Wavenumber''' [cm-1] || 2457
|-
| '''Symmetry''' || SGG
|-
| ''' IR Intensity''' || 0
|-
| '''Image''' || [[File: DP3618 screenshot vibration1 n2.png|200 px]]
|-
|}

There are 3N-5 expected vibrational modes in a linear molecule. Since our molecule consists of 2 atoms, we would expect 1 vibrational mode to exist and that is confirmed by the quantum calculation.

The vibrational mode is the "stretching" type and is symmetric.

There is no change in dipole moment and the molecule shows no bands in the IR spectrum, this is also predicted by our calculation (IR Intensity = 0).

===Charge analysis===
This molecule consists of two identical atoms with same electronegativities. We expect a purely covalent bond with charge 0 on both atoms. This is exactly what we see from the results of the calculation.

[[File: DP3618 screenshot charges n2.png|300 px]]



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

===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || H<sub>2</sub>
|-
| File name || dp3618_h2_optf_pop
|-
| File type || .log
|-
| Calculation Type || FREQ
|-
| Calculation Method || RB3LYP
|-
| Basis set || 6-31G(d,p)
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -1.17853936 a.u.
|-
| RMS Gradient Norm || 0.00000204 a.u.
|-
| Dipole Moment || 0.0000 Debye
|-
| Point group || D<sub>∞h</sub>
|}

H-H bond length: 0.74 Å

"Item" table:
<pre>
         Item               Value     Threshold  Converged?
 Maximum Force            0.000004     0.000450     YES
 RMS     Force            0.000004     0.000300     YES
 Maximum Displacement     0.000005     0.001800     YES
 RMS     Displacement     0.000007     0.001200     YES
 Predicted change in Energy=-1.634290D-11
 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                 !
 --------------------------------------------------------------------------------
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
</pre>

<jmol><jmolApplet>
  <title>H<sub>2</sub>molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>DP3618 H2 OPTF POP.LOG</uploadedFileContents>
  <script>frame 1.10</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 H2 OPTF POP.LOG| here]].

===Vibrational analysis===

[[File: DP3618 screenshot DisplayVibrations h2.png]]


{| class="wikitable" border="1"
|+ Vibrational mode of the H<sub>2</sub> molecule
!  !! Vibration 1
|-
| '''Wavenumber''' [cm-1] || 4466
|-
| '''Symmetry''' || SGG
|-
| ''' IR Intensity''' || 0
|-
| '''Image''' || [[File: DP3618 screenshot vibration1 h2.png|200 px]]
|-
|}

There are 3N-5 expected vibrational modes in a linear molecule. Since our molecule consists of 2 atoms, we would expect 1 vibrational mode to exist and that is confirmed by the quantum calculation.

The vibrational mode is the "stretching" type and is symmetric.

There is no change in dipole moment and the molecule shows no bands in the IR spectrum, this is also predicted by our calculation (IR Intensity = 0).

===Charge analysis===
This molecule consists of two identical atoms with same electronegativities. We expect a purely covalent bond with charge 0 on both atoms. This is exactly what we see from the results of the calculation.

[[File: DP3618 screenshot charges h2.png|300 px]]

==Structure and Reactivity==
===N<sub>2</sub> molecule in a mono-metallic complex===
An example of a mono-metallic TM complex coordinating an N<sub>2</sub> molecule.
Its crystal structure identifier is VEJROU. The structure was reported [https://onlinelibrary.wiley.com/doi/full/10.1002/ejic.201700569 here].

Structure of the complex:

[[File: DP3618 screenshot complex.png|300 px]]


N-N bond distance in this complex is 1.20 Å, which is longer than the calculated N-N distance in the gas phase (1.11 Å). Some electron density which was used purely for bonding between the two nitrogens in the gas phase is now used to bond one nitrogen to the transition metal. There is less electron density between the nitrogens now, the bonding is weaker and longer. Since end-on N<sub>2</sub> complexes are linear around the nitrogen, π backbonding can occur. In this case the d orbital of the metal atom can donate electron density into the π<sup>*</sup> orbital of the N<sub>2</sub>. The extend of this phenomena is dependent on the metal atom. If it is relatively electropositive, this effect is more significant, whereas in the case of more electronegative metals, such as Fe in our case, this is not so substantial.<ref name="backbonding" />

The values might also differ because of computational errors, these could be reduced by using a more accurate computational method. One should note, though, that there is also some error in the experimental data, due to instrumental or random errors.


===Energy of N<sub>2</sub>(g) + 3 H<sub>2</sub>(g) -> 2 NH<sub>3</sub>(g) reaction===
{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| E(NH<sub>3</sub>) || -56.55776873 a.u.
|-
| 2 * E(NH<sub>3</sub>) || -113.11553746 a.u.
|-
| E(N<sub>2</sub>) || -109.52412868 a.u.
|-
| E(H<sub>2</sub>) || -1.17853936 a.u.
|-
| 3 * E(H<sub>2</sub>) || -3.53561808 a.u.
|-
| ΔE = 2 * E(NH<sub>3</sub>) - [E(N<sub>2</sub>) + 3 * E(H<sub>2</sub>)] || -0.0557907 a.u.
|-
|}

In the gas phase, the product of the above reaction is more stable than the reactants by 146.5 kJ/mol.


==SF<sub>4</sub> molecule==

===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || SF<sub>4</sub>
|-
| File name || dp3618_sf4_optf_pop
|-
| File type || .log
|-
| Calculation Type || FREQ
|-
| Calculation Method || RB3LYP
|-
| Basis set || 6-31G(d,p)
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -797.45952418 a.u.
|-
| RMS Gradient Norm || 0.00016003 a.u.
|-
| Dipole Moment || 0.8894 Debye
|-
| Point group || C<sub>2v</sub>
|}

Labeled picture of the molecule:

[[File: DP3618 screenshot sf4label.png|300 px]]

S-F(2 or 5) bond length: 1.67 Å

S-F(3 or 4) bond length: 1.59 Å

F(3)-S-F(4) bond angle: 102°

F(2)-S-F(5) bond angle: 171°

"Item" table:
<pre>
         Item               Value     Threshold  Converged?
 Maximum Force            0.000245     0.000450     YES
 RMS     Force            0.000136     0.000300     YES
 Maximum Displacement     0.001150     0.001800     YES
 RMS     Displacement     0.000520     0.001200     YES
 Predicted change in Energy=-5.227194D-07
 Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.672          -DE/DX =    0.0002              !
 ! R2    R(1,3)                  1.5946         -DE/DX =   -0.0002              !
 ! R3    R(1,4)                  1.5946         -DE/DX =   -0.0002              !
 ! R4    R(1,5)                  1.672          -DE/DX =    0.0002              !
 ! A1    A(2,1,3)               87.3127         -DE/DX =    0.0                 !
 ! A2    A(2,1,4)               87.3127         -DE/DX =    0.0                 !
 ! A3    A(3,1,4)              101.9122         -DE/DX =    0.0001              !
 ! A4    A(3,1,5)               87.3127         -DE/DX =    0.0                 !
 ! A5    A(4,1,5)               87.3127         -DE/DX =    0.0                 !
 ! A6    L(2,1,5,3,-1)         174.6253         -DE/DX =    0.0001              !
 ! A7    L(2,1,5,3,-2)         186.6353         -DE/DX =   -0.0001              !
 ! D1    D(2,1,4,3)             86.6823         -DE/DX =    0.0                 !
 ! D2    D(3,1,5,4)           -102.0679         -DE/DX =   -0.0001              !
 --------------------------------------------------------------------------------
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad</pre>

<jmol><jmolApplet>
  <title>SF<sub>4</sub>molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>DP3618 SF4 OPTF POP.LOG</uploadedFileContents>
  <script>frame 1.18</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 SF4 OPTF POP.LOG| here]].

===Vibrational analysis===

[[File: DP3618 screenshot DisplayVibrations sf4.png]]


{| class="wikitable" border="1"
|+ Vibrational modes of the SF<sub>4</sub> molecule
!  !! Vibration 1 !! Vibration 2 !! Vibration 3 !! Vibration 4 !! Vibration 5 !! Vibration 6 !! Vibration 7 !! Vibration 8 !! Vibration 9
|-
| '''Wavenumber''' [cm-1] || 189 || 330 || 435 || 488 || 496 || 585 || 809 || 851 || 866
|-
| '''Symmetry''' || A1 || B1 || A2 || A1 || B2 || A1 || B2 || B1 || A1
|-
| '''IR Intensity''' || 0 || 10 || 0 || 20 || 2 || 3 || 509 || 150 || 101
|-
| '''Image''' || [[File: DP3618 screenshot vibration1 sf4.png|150 px]] || [[File: DP3618 screenshot vibration2 sf4.png|150 px]] || [[File: DP3618 screenshot vibration3 sf4.png|150 px]] || [[File: DP3618 screenshot vibration4 sf4.png|150 px]] || [[File: DP3618 screenshot vibration5 sf4.png|150 px]] || [[File: DP3618 screenshot vibration6 sf4.png|150 px]]  || [[File: DP3618 screenshot vibration7 sf4.png|150 px]]  || [[File: DP3618 screenshot vibration8 sf4.png|150 px]]
 || [[File: DP3618 screenshot vibration9 sf4.png|150 px]]
|-
|}


There are 3N-6 expected vibrational modes in a non-linear molecule. Since our molecule consists of 5 atoms, we would expect 9 vibrational modes to exist. There are two vibrational modes with an expected IR intensity of 0 and there are no degenerate vibrational modes, so we would expect to see 7 peaks in an IR spectrum.


===Charge analysis===
This molecule consists of two types of atoms. Fluorine is more electronegative than sulphur, so we expect it to have slight negative charge. The charges on the two types of F atoms will probably be slightly different because of different bond lengths. This is exactly what we see from the results of the calculation.

Charge on sulphur is 1.983, charge on the closer two fluorines (3 and 4 in the above labelled picture) is -0.455 and on the two further apart (2 and 5) it is -0.537.

[[File: DP3618 screenshot charges sf4.png|300 px]]

===Molecular orbital analysis===
'''MO 2'''

[[File: DP3618 screenshot MO2 sf4.png|300 px]]

As can be concluded by looking at the visualisation of the orbital, the F atom s orbitals most likely contribute most to this molecular orbital (MO). This can be checked by inspecting the Molecular Orbital Coefficients in the .log file of the calculation. For this MO, the contribution of the S s atomic orbitals (AOs) is negligible, just as we would expect. Simmilarly, the other two F atom AOs do not contribute much towards this MO. The two 1s orbitals from two F atoms contribute most towards this MO, which is reflected in the size and shape of the orbital. This MO is very deep in energy and is therefore not involved in bonding.


'''MO 7'''

[[File: DP3618 screenshot MO7 sf4.png|300 px]]

This orbital mostly has contributions from the sulphur AOs. It is almost entirely a 2p<sub>x</sub> orbital, with very minor contribution from the other orbitals. It is also deep in energy, therefore it is a non-bonding orbital.


'''MO 10'''

[[File: DP3618 screenshot MO10 sf4.png|300 px]]

This orbital is very interesting because it has relatively equal contributions from all atoms in the molecule. Another thing we notice when looking at the MO Coefficients is that this MO is almost entirely composed of 2s and 3s orbitals of all atoms. It is a bonding orbital.


'''MO 18'''

[[File: DP3618 screenshot MO18 sf4.png|300 px]]

This MO has practically zero contribution from the s AOs. It is an antibonding orbital of the 2p and 3p fluorine AOs. Antibonding can also be noted by looking at the visualisation. There are 2 nodal planes going through the bonds.


'''MO 22'''

[[File: DP3618 screenshot MO22 sf4.png|300 px]]

A MO composed of many AOs, mostly 2p and 3p AO of the fluorines and also 3p and 4pz AOs from the sulphur atom. This is a bonding orbital.


'''MO 26'''

[[File: DP3618 screenshot MO26 sf4.png|300 px]]

Another very diverse MO, with substantial amount of anti-bonding character. It has many contributions from s and p orbitals of all atoms in the molecule. This MO is important because it is the highest occupied molecular orbital (HOMO).


'''MO 27'''

[[File: DP3618 screenshot MO27 sf4.png|300 px]]

This is another anti-bonding orbital with many contributions from different AOs. It is the lowest unoccupied molecular orbital (LUMO) of this molecule. Since this is the lowest-lying MO, any electrons donated to this molecule will first occupy this orbital.


There is a gap in the MO energies between the 9th and the 10th. All MOs up to the 9th have energy lower than -6 a.u. These are non-bonding orbitals, which could also be concluded by looking at the visualisation of the orbitals since all of these are very localised to individual atoms. The 10th MO, on the other hand, is spread out over the whole molecule and has an energy value of -1.3 a.u. This orbital is therefore the lowest bonding orbital.

==Independent work==
===Comparison of our results with other studies===
An interesting study was carried out by Hay on the electronic structures of different sulphur compounds, including SF<sub>4</sub>, which was studied here.<ref name="calcstudy" /> That study took a different approach than ours, but the results are rather similar. The MO energies for example, are consistently slightly lower in our case, but all the trends coincide. There is a ~65 a.u. difference between the lowest and the second lowest orbital. These are followed by two pairs of degenerate orbitals. There is another substantial energy gap between the 5th and the 6th orbital. These similarities continue throughout the MOs.

Another study performed by Oberhammer et al. focused on the structure of chalcogen tetrahalides in the gas phase.<ref name="structurestudy" /> Their bond length results are in great agreement with our findings. The S-F bond lengths were 1.67 Å and 1.59 Å in our case and ~1.65 Å and ~1.55 Å in their. There was, however a difference in bond angles. Whilst ours were 102° and 171°, theirs were 87.5° and 101.5°. This is definitely something that should be further explored in the future.


===Using different computational  methods===
NH<sub>3</sub>, N<sub>2</sub> and H<sub>2</sub> were also optimised using a different calculation method to explore what effect a different computational method would have on the outcome of the optimisation. The RCCSD-FC calculation method was suggested by a demonstator. There are very few differences between the two optimisations, probably owing to the simplicity of the molecules studied.

'''NH<sub>3</sub> molecule'''
The energy of the optimised structure was slightly higher in this second case at -56.39854662 a.u. The dipole was slightly higher, being 1.8637 D here. The N-H bond distance was 1.01 Å, which is slightly shorter than in the case of the RB3LYP calculation method. The H-N-H bond angle was the same at 106°. Vibrational frequencies were consistently higher by 40-80 cm<sup>-1</sup>. The full .log file can be viewed [[Media:DP3618 NH3CCSD OPTF POP.LOG| here]].

'''N<sub>2</sub> molecule'''
In this case the energy of the second optimised structure was slightly higher at -109.25579376 a.u. N-N bond distance was the same as in the initial calculation. The vibrational frequency was slightly lower with 2411 cm<sup>-1</sup>. The full .log file can be viewed [[Media:DP3618 N2CCSD OPTF POP.LOG| here]].

'''H<sub>2</sub> molecule'''
Again, the energy of the optimised structure was slightly higher in the additional calculation, this time being -1.16515738 a.u. Bond length was the same, but the vibrational frequency was slightly higher: 4504 cm<sup>-1</sup>. The full .log file can be viewed [[Media:DP3618 H2CCSD OPTF POP.LOG| here]].

It is evident from the paragraphs above that the two methods used are very similar. They can therefore be used interchangeably in systems similar to the ones studied here. Perhaps the molecules used were not complex enough to invoke greater discrepancies in the results obtained.

===CO molecule===

===Optimisation===

{| class="wikitable" border="1"

! colspan="2" style="text-align: center;"|Optimisation data
|-
| Molecule || CO
|-
| File name || dp3618_co_optf_pop
|-
| File type || .log
|-
| Calculation Type || FREQ
|-
| Calculation Method || RB3LYP
|-
| Basis set || 6-31G(d,p)
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -113.30945314 a.u.
|-
| RMS Gradient Norm || 0.00001828 a.u.
|-
| Dipole Moment || 0.0599 Debye
|-
| Point group || C<sub>∞v</sub>
|}

C-O bond length: 1.14 Å

"Item" table:
<pre>
         Item               Value     Threshold  Converged?
 Maximum Force            0.000032     0.000450     YES
 RMS     Force            0.000032     0.000300     YES
 Maximum Displacement     0.000011     0.001800     YES
 RMS     Displacement     0.000018     0.001200     YES
 Predicted change in Energy=-3.956716D-10
 Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.1379         -DE/DX =    0.0                 !
 --------------------------------------------------------------------------------
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad</pre>

<jmol><jmolApplet>
  <title>CO molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>DP3618 CO OPTF POP.LOG</uploadedFileContents>
  <script>frame 1.10</script>
</jmolApplet></jmol>

The full optimisation .log file can be viewed [[Media:DP3618 CO OPTF POP.LOG| here]].

===Vibrational analysis===


{| class="wikitable" border="1"
|+ Vibrational mode of the H<sub>2</sub> molecule
!  !! Vibration 1
|-
| '''Wavenumber''' [cm-1] || 2209
|-
| '''Symmetry''' || SG
|-
| ''' IR Intensity''' || 68
|-
| '''Image''' || [[File: DP3618 screenshot vibration1 co.png|200 px]]
|-
|}


===Charge analysis===
This molecule consists of two atoms with different electronegativities. We expect a dipole moment and two charges of opposite signs on carbon and oxygen. This is exactly what we see from the results of the calculation.

[[File: DP3618 screenshot charges co.png|300 px]]


==References==
<references>
<ref name="vibrations">Harwood, L. M., Claridge, T. D. W. (Eds.). (1997). Introduction to Organic Spectroscopy (pp.22-33). New York, Oxford University Press Inc.</ref>
<ref name="backbonding">Holland PL. Metal-dioxygen and metal-dinitrogen complexes: where are the electrons?. Dalton Trans. 2010;39(23):5415-25.</ref>
<ref name="calcstudy">Jeffrey Hay, P. (1977). Generalized valence bond studies of the electronic structure of SF2, SF4, and SF6. 99. 1003-1012.</ref>
<ref name="structurestudy">Oberhammer H., Shlykov S. A., Gas phase structures of chalcogen tetrahalides MX4 with M=S, Se, Te and X=F, Cl, Br, I. Dalton Trans. 2010; 39: 2838-2841.</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 0.5/1 ==

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, overall very good however captions should always describe the item - captioning all of your jmols "molecule" is not helpful for the reader!

==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

== 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 4/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, overall very good effort with your explanations, well done. There are a couple of errors in your MO analysis, for example MO 18 is actually a bonding orbital of the F4 fragment (non bonding between S and F). The bonding interactions are through space between adjacent F atoms. There are nodal planes but these are along bonds, nodal planes indicating antibonding interactions are usually across the bonds.

== 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 did extra calculations, analysis and comparison to the literature, well done!