View source for Rep:Mod:YX8818

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


=== Summary information ===

{| class="wikitable" border="1"
|-
|molecule name || NH<sub>3</sub>
|-
| N-H bond distance || 1.018
|-
| H-N-H bond angle || 105.7
|-
| Calculation method || RB3LYP
|-
| Basis set || 6-31G(D,P)
|-
| Final energy E(RB3LYP) in atomic units (au)||-56.5577687 a.u.
|-
|the point group || C<sub>3v</sub> 
|}

===  "Item" section in the log file ===
<pre>
         Item               Value     Threshold  Converged?
 Maximum Force            0.000004     0.000450     YES
 RMS     Force            0.000004     0.000300     YES
 Maximum Displacement     0.000070     0.001800     YES
 RMS     Displacement     0.000033     0.001200     YES
</pre>

=== JMol of structure ===

<jmol><jmolApplet>
  <script>frame x.y</script>
  <title> Ammonia molecule </title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>YX8818_NH3_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:YX8818_NH3_OPTIMISATION.LOG|thumb|A Gaussview image of an optimised NH3 molecule.]]

=== Snap shot of the display vibrations ===

[[File:vibration list capture.png]]

=== Table of vibrations and intensities ===

{| class="wikitable" border="1"
|+ '''summary'''
|-
| '''wavenumber  '''  cm<sup>-1      || 1090 || 1694|| 1694 || 3461 || 3590 || 3590
|-
| '''symmetry'''                     || A1   ||  E  || E    ||  A1  || E    || E
|-
| '''intensity'''in arbitrary units  || 145  || 14  || 14   ||  1   || 0.3  || 0.3
|-
| '''image'''                        ||[[File:vibration screenshot_yxx8818_1090.png|150px]]|| [[File:vibration screenshot_yxx8818_1694.png|150px]]|| [[File:vibration screenshot_yxx8818_1694_1.png|150px]] || [[File:vibration screenshot_yxx8818_3461.png|150px]] || [[File:vibration screenshot_yxx8818_3590.png|150px]] || [[File:vibration screenshot_yxx8818_3590_1.png|150px]]
|}





{| class="wikitable" border="1"
|-
| how many modes do you expect from the 3N-6 rule? || 6
|-
| which modes are degenerate ? || The two bending modes at 1694 cm<sup>-1</sup> are degnerate,   and the two stretching modes at 3590 cm<sup>-1</sup> are degenerate.
|-
| which modes are "bending" vibrations and which are "bond stretch" vibrations? || The to vibrations at 1090 and the one 1694 cm<sup>-1</sup> are bending vibrations.
The vibrations at 3461 and two vibrations at 3590 cm<sup>-1</sup>  are stretching vibrations. 
|-
| which mode is highly symmetric? || The modes at 1090 and 3461 cm<sup>-1</sup>  are highly symmetric.
|-
| one mode is known as the "umbrella" mode, which one is this?|| The mode at 1090 cm<sup>-1</sup>   is known as the embrella mode.
|-
| how many bands would you expect to see in an experimental spectrum of gaseous ammonia? || 2 bands are expected.
|}

=== NBO charges === 
{| class="wikitable" border="1"
|-
|N-atom || -1.125
|-
|H-atoms|| 0.375
|}

A negative charge is expected for N because is more electronegative than H, hence it draws the electron density away from H. Hence H is expected to have a positive charge.

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

=== Summary information ===

{| class="wikitable" border="1"
|-
|molecule name || Nitrogen  (N<sub>2</sub>)
|-
| N-N bond distance || 1.106
|-
| Calculation method || RB3LYP
|-
| Basis set || 6-31G(d,p)
|-
| Final energy E(RB3LYP) in atomic units (au)||-109.52412868 a.u.
|-
|the point group || D<sub>∞h</sub> 
|}

===  "Item" section in the 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
</pre>

=== JMol of structure ===

<jmol><jmolApplet>
  <script>frame x.y</script>
  <title>Nitrogen molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>YX8818_N2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:YX8818_N2_OPTIMISATION.LOG|thumb|A Gaussview image of an optimised NH3 molecule.]]

=== Snap shot of the display vibrations ===

[[File:Yx8818 n2 vibration capture.PNG]]

=== Table of vibrations and intensities ===
{| class="wikitable" border="1"
|-
| '''wavenumber  '''  cm<sup>-1      || 2457
|-
| '''symmetry'''                     || SGG
|-
| '''intensity''' in arbitrary units  || 0
|-
| '''image'''                        ||[[File:Yx8818 n2 optimisation vibration.png|150px]]
|}

=== NBO charges ===
{| class="wikitable" border="1"
|-
|N-atom || 0.000
|}

== H<sub>2</sub> molecule ==
=== summary information ===
{| class="wikitable" border="1"
|-
|molecule name || Hydrogen (H<sub>2</sub>)
|-
| H-H bond distance || 0.743
|-
| Calculation method || RB3LYP
|-
| Basis set || 6-31G(d,p)
|-
| Final energy E(RB3LYP) in atomic units (au)||-1.1785394 a.u.
|-
|the point group || D<sub>∞h</sub> 
|}

===  "Item" section in the 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
</pre>

=== JMol of structure ===

<jmol><jmolApplet>
  <script>frame x.y</script>
  <title>Hydrogen molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>YX8818 H2 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:YX8818 H2 OPTIMISATION.LOG|thumb|A Gaussview image of an optimised NH3 molecule.]]

=== Snap shot of the display vibrations ===

[[File:Yx8818 h2 optimisation capture.PNG]]

=== Table of vibrations and intensities ===

{| class="wikitable" border="1"
|-
| '''wavenumber  '''  cm<sup>-1      || 4466
|-
| '''symmetry'''                     || SGG
|-
| '''intensity''' in arbitrary units  || 0
|-
| '''image'''                        ||[[File:Yx8818 h2 optimisation.png|150px]]
|}

=== NBO charges ===
{| class="wikitable" border="1"
|-
|H-atom || 0.000
|}

== Mono-metallic TM complex ==

unique identifier = BARTOF

N-N bond distance =1.112

<jmol><jmolApplet>
  <script>frame x.y</script>
  <title>(dinitrogen)-(2,6-bis(1-(2,6-diisopropylphenylimino)propyl)pyridine)-iron</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>Yx8818 BARTOF.mol2</uploadedFileContents>
</jmolApplet></jmol>

[[File:Yx8818 BARTOF.mol2|thumb|A Gaussview image of an optimised NH3 molecule ]]


The N-N bond distance in the TM-complex is longer than that from the N<sub>2</sub> (1.106). This maybe be due to the MOs on Nitrogen constructively interact with the orbitals on the TM-metal. This draws away electron density away from the N-N bonds, thus weakening the bond and makes the bond length longer.

== The Haber-Bosch process ==

{| class="wikitable" border="1"
|-                     
|  '''Energy '''  ||'''Values ''' in atomic units || '''Values ''' in kJ/mol
|-
| E(NH<sub>3</sub>)=      || -56.5577687 || -148492.4 
|-
| 2*E(NH<sub>3</sub>)=    || -113.1155375 || -296984.8
|-
| E(N<sub>2</sub>)=       ||-109.5241287 || -287555.6
|-
| E(H<sub>2</sub>)=        ||-1.1785394 || -3094.3
|-                     
|  3*E(H<sub>2</sub>)=     ||-3.5356181 || -9282.8
|-                     
|   ΔE=2*E(NH<sub>3</sub>)-[E(N<sub>2</sub>)+3*E(H<sub>2</sub>)]=  ||-0.0557907 || -146.5

|}

Energy for converting hydrogen and nitrogen gas into ammonia gas:

ΔE=2*E(NH<sub>3</sub>)-[E(N<sub>2</sub>)]+3*E(H<sub>2</sub>)= -0.0557907 au = -146.5 kJ/mol.

As the reaction is exothermic, enegry is given out during the reaction to form NH<sub>3</sub>. Hence, NH<sub>3</sub> gas is the more stable than the gaseous reactants.

== Project molecule : SiH<sub>4</sub> molecule ==

=== Summary information ===

{| class="wikitable" border="1"
|-
|molecule name || SiH<sub>4</sub>
|-
| Si-H bond distance || 1.485
|-
| H-Si-H bond angle || 109.5
|-
| Calculation method || RB3LYP
|-
| Basis set || 6-31G(D,P)
|-
| Final energy E(RB3LYP) in atomic units (au)||-291.8880276 a.u.
|-
|the point group || T<sub>d</sub> 
|}

===  "Item" section in the 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     0.000000     0.001200     YES

</pre>


=== JMol of structure ===

<jmol><jmolApplet>
  <script>frame x.y</script>
  <title> Silane molecule </title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>YX8818 SIH4 OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File:YX8818 SIH4 OPTIMISATION.LOG|thumb|A Gaussview image of an optimised NH3 molecule.]]

=== Snap shot of the display vibrations ===

[[File:Yx8818 sih4 vibration capture.PNG]]

=== Table of vibrations and intensities ===

{| class="wikitable" border="1"
|+ '''summary'''
|-
| '''wavenumber  '''  cm<sup>-1      || 919|| 919|| 919 || 978 || 978 || 2244 || 2255 || 2255 || 2255
|-
| '''symmetry'''                     || T2   || T2  ||  T2  ||  E  || E    || A1 || T2|| T2|| T2
|-
| '''intensity'''in arbitrary units  || 136 || 136 || 136  ||  0  || 0  || 0 || 143 ||143 || 143
|-
| '''image'''                        ||[[File:Yx8818 sih4 optimised vib 919 1.png|150px]]|| [[File:Yx8818 sih4 optimised vib 919 2.png|150px]]|| [[File:Yx8818 sih4 optimised vib 919 3.png|150px]] || [[File:Yx8818 sih4 optimised vib 978 1.png|150px]] || [[File: Yx8818 sih4 optimised vib 978 2.png|150px]] || [[File:Yx8818 sih4 optimised vib 2244.png|150px]] ||[[File:Yx8818 sih4 optimised vib 2255 1.png|150px]] ||[[File:Yx8818 sih4 optimised vib 2255 2.png|150px]] ||[[File:Yx8818 sih4 optimised vib 2255 3.png|150px]]
|}




{| class="wikitable" border="1"
|-
| how many modes do you expect from the 3N-6 rule? || 9
|-
| which modes are degenerate ? || The three vibrational modes at 919 cm <sup>-1</sup> are degnerate. 
The two vibrational modes at 978 cm<sup>-1</sup> are degnerate.

The three vibrational modes at 2255 cm <sup>-1</sup> are degnerate.
|-
| which modes are "bending" vibrations and which are "bond stretch" vibrations? || The three modes at 919 cm <sup>-1</sup> and the two modes at 978 cm<sup>-1</sup> are bending.
  The one mode at 2244 cm <sup>-1</sup> and the three modes at 2255 cm<sup>-1</sup> are bending.
|-
| how many bands would you expect to see in an experimental spectrum? || 2 bands are expected.
|}

=== NBO charges === 
{| class="wikitable" border="1"
|-
|Si-atom || 0.629
|-
|H-atoms|| -0.157
|}

Write a sentence saying what charge (positive or negative) you would expect for N and H and why


== MOs of SiH<sub>4</sub> molecule ==

=== MO1: HOMO ===
[[File:Yx8818 sih4 mo 9 HOMO.png|300px]]

{| class="wikitable" border="1"
|-
|Type of MO || Bonding MOs
|-
|Energy of MO in au || -0.35184
|-
|What AOs contribute to the MO || 3p <sub>x</sub> AO of Si atom and the 1S, 2S AOs of H atoms.
|-
|Is the MO deep in energy, in the HOMO/LUMO region or high in energy? || In the HOMO/LUMO region
|-
|Is the MO occupied or unoccupied? || Occupied.
|-
|Which mode is highly symmetric? || Highly symmetric.
|}

=== MO2: LUMO ===
[[File:Yx8818 sih4 mo 10 LUMO.png|300px]]

{| class="wikitable" border="1"
|-
|Type of MO || Anti-bonding MOs
|-
|Energy of MO in au || -0.05053
|-
|What AOs contribute to the MO || 3p <sub>x</sub> and 4p <sub>x</sub> AOs of Si atom and the 2S AOs of two H atoms.
|-
|Is the MO deep in energy, in the HOMO/LUMO region or high in energy? || In the HOMO/LUMO region
|-
|Is the MO occupied or unoccupied? || unoccupied.
|-
|Which mode is highly symmetric? || Highly symmetric.
|}

=== MO3 ===
[[File:Yx8818 sih4 mo 6.png|300px]]

{| class="wikitable" border="1"
|-
| Type of MO || Bonding MOs
|-
|Energy of MO in au || -0.54726
|-
|What AOs contribute to the MO ||3s (58.2 %) and 4s (13.6 %) AOs of the Si atom and the 1s AOs on the four H<sub>2</sub> atoms (13.0 % each). 
|-
| Is the MO deep in energy, in the HOMO/LUMO region or high in energy?|| high in energy
|-
|Is the MO occupied or unoccupied? || Occupied.
|-
|Which mode is highly symmetric? || Highly symmetric.
|}

=== MO4 ===
[[File:Yx8818 sih4 mo 3.png|300px]]

{| class="wikitable" border="1"
|-
| Type of MO || Non-bonding MOs
|-
|Energy of MO in au || -0.35184
|-
| what AOs contribute to the MO || 2p <sub>x</sub> AO of Si atom.
|-
| Is the MO deep in energy, in the HOMO/LUMO region or high in energy?|| Deep in energy.
|-
|Is the MO occupied or unoccupied? || Occupied.
|-
|Which mode is highly symmetric? || Highly symmetric.
|}

=== MO5 ===
[[File:Yx8818 sih4 mo 2.png|300px]]

{| class="wikitable" border="1"
|-
| Type of MO || Non-bonding MOs
|-
|Energy of MO in au || -0.35184
|-
| What AOs contribute to the MO ||2s AO of Si atom
|-
|Is the MO deep in energy, in the HOMO/LUMO region or high in energy? || Deep in energy.
|-
|Is the MO occupied or unoccupied? || Occupied.
|}

=Independence=

All calculated molecular vibrations for NH<sub>3</sub>, N<sub>2</sub>,H<sub>2</sub>, and SiH<sub>4</sub> are checked against literature values:

The values calculated are close to but not exactly equal to the literature values. This is probably because the calculations in Gaussian was undertaken in pure gaseous phase without the consideration of external envirnoment such as nearby electric and gravitational fields.

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

====Table of experimental vibrations and intensities <ref name="nh3vib" />==== 

{| class="wikitable" border="1"
|+ '''summary'''
|-
| '''wavenumber  '''  cm<sup>-1      || 3337|| 950|| 3444   || 1627
|-
| '''symmetry'''                     || A1   ||  A1 || E    || E 
|-
| '''intensity'''in arbitrary units  || 7.1  || 138.0  || 4.3   ||  28.2 
|}

==== Table of calculated vibrations and intensities ====
{| class="wikitable" border="1"
|+ '''summary'''
|-
| '''wavenumber  '''  cm<sup>-1      || 1090 || 1694|| 1694 || 3461 || 3590 || 3590
|-
| '''symmetry'''                     || A1   ||  E  || E    ||  A1  || E    || E
|-
| '''intensity'''in arbitrary units  || 145  || 14  || 14   ||  1   || 0.3  || 0.3
|}


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

==== Table of experimental vibrations and intensities <ref name="n2vib" />====
{| class="wikitable" border="1"
|-
| '''wavenumber  '''  cm<sup>-1      || 2359
|-
| '''symmetry'''                     || SGG
|-
| '''intensity''' in arbitrary units  || -
|}

==== Table of calculated vibrations and intensities ====
{| class="wikitable" border="1"
|-
| '''wavenumber  '''  cm<sup>-1      || 2457
|-
| '''symmetry'''                     || SGG
|-
| '''intensity''' in arbitrary units  || 0
|}

===H<sub>2</sub>===
==== Table of experimental vibrations and intensities<ref name="h2vib" />====
{| class="wikitable" border="1"
|-
| '''wavenumber  '''  cm<sup>-1      || 4401
|-
| '''symmetry'''                     || SGG
|-
| '''intensity''' in arbitrary units  || -
|}
==== Table of calculated vibrations and intensities ====

{| class="wikitable" border="1"
|-
| '''wavenumber  '''  cm<sup>-1      || 4466
|-
| '''symmetry'''                     || SGG
|-
| '''intensity''' in arbitrary units  || 0
|}


===SiH<sub>4</sub>===

==== Table of experimental vibrations and intensities<ref name="sih4vib" />====

{| class="wikitable" border="1"
|+ '''summary'''
|-
| '''wavenumber  '''  cm<sup>-1      || 2187|| 975|| 2191|| 914
|-
| '''symmetry'''                     ||A1  ||  E  || T2 || T2   
|-
| '''intensity'''in arbitrary units  || - || - || 282.0 ||  381.0
|}

==== Table of calculated vibrations and intensities ====

{| class="wikitable" border="1"
|+ '''summary'''
|-
| '''wavenumber  '''  cm<sup>-1      || 919|| 919|| 919 || 978 || 978 || 2244 || 2255 || 2255 || 2255
|-
| '''symmetry'''                     || T2   || T2  ||  T2  ||  E  || E    || A1 || T2|| T2|| T2
|-
| '''intensity'''in arbitrary units  || 136 || 136 || 136  ||  0  || 0  || 0 || 143 ||143 || 143
|-
|}

=References=

<references>
<ref name="nh3vib">Koops, T., Visser, T. & Smit, W. M. A. Measurement and interpretation of the absolute infrared intensities of NH3 and ND3. J. Mol. Struct. 96, 203–218 (1983).</ref>

<ref name="n2vib"> C. GRAHAM D. A. IMRIE R. E. RAAB, C. G. D. A. I. R. E. Measurement of the electric quadrupole moments of CO 2 , CO, N 2 , Cl 2 and BF 3. Mol. Phys. 93, 49–56 (1998).</ref> 

<ref name="h2vib">Irikura, K. K. Experimental Vibrational Zero-Point Energies: Diatomic Molecules. J. Phys. Chem. Ref. Data 36, 389–397 (2007).  </ref>

<ref name="sih4vib">Coats, A. M., McKean, D. C. & Steele, D. Infrared intensities of ν3 and ν4 in SiH4, GeH4 and SnH4. J. Mol. Struct. 320, 269–280 (1994).</ref> 
</references>


=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 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, you could have explained that the charges are 0 as the electronegativities are equal.
 
==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?  
 
NO - but you included the unique identifier.
 
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
 
Have you added information about MOs and charges on atoms?
 
You have done a good job of presenting this information, well done!
Probably this is a typo but you stated the modes at 2244cm-1 and 2255cm-1 to be bending vibrations. But these are stretching vibrations.
You should have used an electronegativity argument to explain the atomic charges.
Your MO analysis is very good!
 
== 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 - well done! However, the given reason for differences in computed and real IR spectra is not the predominant one. The main difference should arise from the fact that gaussian uses the model of a harmonic oscillator. In reality molecules behave like an anharmonic oscillator.

Do an extra calculation on another small molecule, or
Do some deeper analysis on your results so far


Overall you have done a really good job!