View source for Rep:Mod:lc2.25.19


== Molecular Modelling 2 ==
Molecules examined in this workshop: NO<sub>3</sub>, H<sub>2</sub>, N<sub>2</sub>, PF<sub>5</sub>, 

=== NH<sub>3</sub> ===
Calculation method: B3LYP

basis set: 6-31G(d.p)

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C<sub>3v</sub>

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
!  !! Item !! Value !! Threshold !! Converge? 
|-
| 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
|}

Log File: [[File:CD1618NH3result.LOG | Log File]]

[[File:Cd1618 pic.PNG]]

{| class="wikitable" border="1"
|+ Optimisation Table
! Mode !! 1 !! 2 !! 3 !! 4 !! 5 !! 6
|-
| symmetry || A1 || E || E || A1 || E || E
|-
| Frequencies || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| IR Inten || 145 || 14 ||  14 || 1 || 0 || 0
|}

<jmol><jmolApplet>
  <title>NH3</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>CD1618NH3result.LOG</uploadedFileContents>
</jmolApplet></jmol>

Charge distribution:  N: -1.125  H: 0.375

Questions

1. 3*4-6=6 so 6 modes

2. two pairs of vibration modes with frequency 1694 and 3590

3. Bond stretch: 3461cm-1 3590cm-1 3590cm-1 Bending 1090cm-1 1694cm-1 1694cm-1

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

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

Calculation method: B3LYP

basis set: 6-31G(d.p)

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

{| class="wikitable" border="1"
|+ Optimisation Table
!  !! Item !! Value !! Threshold !! Converge? 
|-
| Maximum || Force || 0.000066 || 0.000450 || YES
|-
| RMS || Force || 0.000066 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000087 || 0.001800 || YES
|-
| RMS || Displacement || 0.000123 || 0.001200 || YES
|}

Log File: [[File:CD1618H2OUTPUT.LOG | Log File]]

[[File:Cd1618H2 pic.PNG]]

{| class="wikitable" border="1"
|+ Optimisation Table
! Mode !! 1
|-
| symmetry || SGG
|-
| Frequencies || 4464
|-
| IR Inten || 0
|}

<jmol><jmolApplet>
  <title>H2</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>CD1618H2OUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å


[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=CILXAX&DatabaseToSearch=Published | Complex Structure]]

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

Calculation method: B3LYP

basis set: 6-31G(d.p)

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

{| class="wikitable" border="1"
|+ Optimisation Table
!  !! Item !! Value !! Threshold !! Converge? 
|-
| Maximum || Force || 0.000006 || 0.000450 || YES
|-
| RMS || Force || 0.000006 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000002 || 0.001800 || YES
|-
| RMS || Displacement || 0.000003 || 0.001200 || YES
|}

Log File: [[File:CD1618N2OUTPUT.LOG | Log File]]

[[File:Cd1618N2pic.PNG]]

{| class="wikitable" border="1"
|+ Optimisation Table
! Mode !! 1
|-
| symmetry || SGG
|-
| Frequencies || 2457
|-
| IR Inten || 0
|}

<jmol><jmolApplet>
  <title>N2</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>CD16118N2OUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=1553733&DatabaseToSearch=Published | Complex Structure]]

In the complex, the bond length of N<sub>2</sub> and H<sub>2</sub> is longer than the calculated value. Theoretically, when forming a dative bond, the electron from the metal is feed into the LUMO of the ligand molecule, so the bond order of ligand molecule decreases and the anti-bonding character increases. Thus a longer and weaker bond is observed.

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

2*E(NH3)= -113.1155375 a.u.

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

3*E(H2)= -3.53561805 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -146.4785616 kJ/Mol

The ammonia product is more stable.

=== PF<sub>5</sub> ===

Calculation method: B3LYP

basis set: 6-31G(d.p)

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D<sub>3</sub>h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

{| class="wikitable" border="1"
|+ Optimisation Table
!  !! Item !! Value !! Threshold !! Converge? 
|-
| Maximum || Force || 0.000299 || 0.000450 || YES
|-
| RMS || Force || 0.000090 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000868 || 0.001800 || YES
|-
| RMS || Displacement || 0.000269 || 0.001200 || YES
|}

Log File: [[File:CD1618PF5INPUT.LOG | Log File]]

[[File:Cd1618PF5pic.PNG]]

{| class="wikitable" border="1"
|+ Optimisation Table
! Mode !! 1 || 2 || 3 || 4 || 5 || 6 || 7 || 8 || 9 || 10 || 11 || 12
|-
| symmetry || E' || E" || E" ||  E" || E' || E' || A2" || A1' || A1' || A2" || E' || E'
|-
| Frequencies || 172 || 172 || 478 || 478 || 503 || 503 || 544 || 669 || 784 || 997 || 1020 || 1020
|-
| IR Inten || 0 || 0 || 0 || 0 || 38 || 38 || 47 || 0 || 0 || 363 || 248 || 248
|}

<jmol><jmolApplet>
  <title>PF5</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>CD1618PF5INPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

Charge on F: -0.578

Charge on P: 2.748

MO

Axial F-P-F is z axis in the disciession below

[[File:CD1618MO25.png|350px]]

-0.47310 a.u.

Three 2p orbitals from equatorial F atoms, there is three nodal planes and each orbital is out of phase with the orbital next to it.

[[File:Cd1618mo26.png|350px]]

-0.45487 a.u.

Three 2pz orbitals from equatorial F atoms art in phase and two axial 2pz orbitals are out of phase with each other and equatorial orbitals.

[[File:Cd1618mo28.png|350px]]

-0.43685 a.u.

Three 2p orbitals from equatorial F atoms are interacting, but the electron density is mainly on the axial F atoms,and these 2p orbitals are in phase with each other. 

[[File:Cd1618mo29.png|350px]]

-0.41452 a.u.

This MO has a nodal plane going across the P-F bond and all the 2p orbitals from the other F atoms are out of phase.

[[File:Cd1618mo30.png|350px]]

-0.41452 a.u.

A pair of 2pz orbitals from equatorial F atoms art in phase but out of phase with the last one and two axial 2pz orbitals are out of phase with each other and equatorial orbitals. This is the HOMO

[[File:Cd1618mo31.png|350px]]

0.00039 a.u.

The 4s orbial of central P is out of phase with each of the 2p orbital from F atoms.
THis is the LUMO

=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 0.5/1 ==

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?

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?

You didn't answer the question asking you to explain what you would expect the charge distribution to be in ammonia. Your answer to question 6 doesn't explain why there are only 2 modes - there are two sets of degenerate vibrations which would give 4 peaks, but 2 of these are too low in intensity to be visible experimentally.

== 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 - good explanation, well done.

==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, you should have reported to 1 d.p. maximum.

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?

YES - however you could have explained the charges in terms of the relative electronegativity of the elements. Your MO descriptions are good but lacking in detail.

== 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