ChemWiki - User contributions [en]

MRD:scm4918

2020-05-22T23:00:23Z

Scm4918: /* Transition State Theory */

== EXERCISE 1: H + H2 system ==
==== Transition state ====
[[File:Surface_Plot_scm4918.png|thumb|frame|right|Potential energy surface plot (transition state shown with red dot)]]
The mathematical definition for a transition state on a potential energy surface diagram is: δV/δr1 = δV/δr2 = 0, where V is the chemical potential and r1/2 the distances between the atoms. Furthermore, as this definition applies to all local minima, to distinguish the transition state from the rest, the following term must be less than 0: fxx(x0,y0)fyy(x0,y0)−f2xy(x0,y0), where x & y are the interatomic distances (r1/2) and (x0,y0) the coordinates of the saddle point.
The transition state is shown in the diagram with a red dot. This is along the calculated dynamic trajectory shown by the black line.

==== Locating the transition state ====
[[File:Surface_Plot1_scm4918.png|thumb|frame|right| Internuclear distance plot when R = 90.8 pm]]
[[File:Surface_Plot2_scm4918.png|thumb|frame|right|Internuclear distance plot when R = 92.0 pm]]
The best estimate for the transition state was found at r1=2 = 90.8 pm. By keeping the momentum at zero and the two distances equal a range of values from 85 pm to 110 pm were tested. The internuclear distance against time was plotted and at 90.8 pm the graph obtained showed 2 straight lines. Since the lines are straight the interatomic distances are constant and there is no more oscillation. Hence, the transition state has been reached.

==== Minimum energy path and calculated trajectory ====
The mep (minimum energy pathway) is the lowest energy trajectory taken by a group of atoms that are rearranging themselves between two different stable configurations. At every point the velocities are reset to 0. The difference between this and the previously calculated dynamic trajectory is that as can be seen from the internuclear distances vs time graphs there are no oscillations in the mep graph. This can be explained by the fact that for mep the motion starts at the transition state and the entire path flows downhill along the lowest energy where the momentum is always reset to zero and hence the effects of inertia neglected.

==== Reactive and unreactive trajectories ====

{| class="wikitable" border=1
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot (kJ.mol-1) !! Reactive? !! Description of the dynamics !! Illustration of the trajectory (internuclear distances against time)
|-
| -2.56 || -5.1 || -414.28 || Yes || H2 molecule moves towards HC. As it reaches the transition point HB binds to HC while oscillating and HA moves back || [[File:tfig1_scm4918.png|200px]]
|-
| -3.1 || -4.1 || -420.08 || No || H2 molecule moves towards HC. while osculating. Not enough energy to overcome TS barrier so the molecule goes back away from HC. ||[[File:tfig2_scm4918.png|200px]]
|-
| -3.1 || -5.1 || -413.98 || Yes || HC moves towards the H2 molecule with slight vibrations. There is enough energy for the molecule to form. HB binds to HC while oscillating and HA moves back. ||[[File:tfig3_scm4918.png|200px]]
|-
| -5.1 || -10.1 || -357.27 || No || HC slowly approaches the molecule again with few oscilations. HB-HC bond starts to form as the transition state is crossed and the newly formed molecule has strong vibrational energy. This causes the bond to break again and pass the TS to form approach the HA molecule and reform the initial bond.||[[File:tfig4_scm4918.png|200px]]
|-
| -5.1 || -10.6 || -349.48 || Yes || In this case the TS is crossed three times. This causes the products to form then break to form the reactant molecule and then form again to end up with the products. ||[[File:tfig5_scm4918.png|200px]]
|}

From the table above it becomes apparent that not all reactants that have enough kinetic energy to cross the TS barrier lead to a complete reaction since there is a possibility for the barrier to be crossed again.

==== Transition State Theory ====
The transition state theory does not allow for quantum mechanical phenomena and hence some of the reactions that are predicted not to occur by this theory would happen due to quantum tunneling. Another issue is the reaction is only allowed to pass through the lowest energy transition point which over predicts the frequency of reactions compared to what is found experimentally.

MRD:scm4918

2020-05-22T22:58:10Z

Scm4918:

MRD:scm4918

2020-05-22T22:52:14Z

Scm4918: /* Reactive and unreactive trajectories */

MRD:scm4918

2020-05-22T22:50:04Z

Scm4918:

File:Surface Plot2 scm4918.png

2020-05-22T22:47:50Z

Scm4918:

File:Surface Plot1 scm4918.png

2020-05-22T22:47:33Z

Scm4918:

MRD:scm4918

2020-05-22T22:45:17Z

Scm4918: /* Reactive and unreactive trajectories */

== EXERCISE 1: H + H2 system ==
==== Transition state ====
[[File:Surface_Plot_scm4918.png|thumb|frame|right|Potential energy surface plot (transition state shown with red dot)]]
The mathematical definition for a transition state on a potential energy surface diagram is: δV/δr1 = δV/δr2 = 0, where V is the chemical potential and r1/2 the distances between the atoms. Furthermore, as this definition applies to all local minima, to distinguish the transition state from the rest, the following term must be less than 0: fxx(x0,y0)fyy(x0,y0)−f2xy(x0,y0), where x & y are the interatomic distances (r1/2) and (x0,y0) the coordinates of the saddle point.
The transition state is shown in the diagram with a red dot. This is along the calculated dynamic trajectory shown by the black line.

==== Locating the transition state ====
The best estimate for the transition state was found at r1=2 = 90.8 pm. By keeping the momentum at zero and the two distances equal a range of values from 85 pm to 110 pm were tested. The internuclear distance against time was plotted and at 90.8 pm the graph obtained showed 2 straight lines. Since the lines are straight the interatomic distances are constant and there is no more oscillation. Hence, the transition state has been reached.

==== Minimum energy path and calculated trajectory ====
The mep (minimum energy pathway) is the lowest energy trajectory taken by a group of atoms that are rearranging themselves between two different stable configurations. At every point the velocities are reset to 0. The difference between this and the previously calculated dynamic trajectory is that as can be seen from the internuclear distances vs time graphs there are no oscillations in the mep graph. This can be explained by the fact that for mep the motion starts at the transition state and the entire path flows downhill along the lowest energy where the momentum is always reset to zero and hence the effects of inertia neglected.

==== Reactive and unreactive trajectories ====

{| class="wikitable" border=1
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot (kJ.mol-1) !! Reactive? !! Description of the dynamics !! Illustration of the trajectory (internuclear distances against time)
|-
| -2.56 || -5.1 || -414.28 || Yes || H2 molecule moves towards HC. As it reaches the transition point HB binds to HC while oscillating and HA moves back || [[File:tfig1_scm4918.png|200px]]
|-
| -3.1 || -4.1 || -420.08 || No || H2 molecule moves towards HC. while osculating. Not enough energy to overcome TS barrier so the molecule goes back away from HC. ||[[File:tfig2_scm4918.png|200px]]
|-
| -3.1 || -5.1 || -413.98 || Yes || HC moves towards the H2 molecule with slight vibrations. There is enough energy for the molecule to form. HB binds to HC while oscillating and HA moves back. ||[[File:tfig3_scm4918.png|200px]]
|-
| -5.1 || -10.1 || -357.27 || No || HC slowly approaches the molecule again with few oscilations. HB-HC bond starts to form as the transition state is crossed and the newly formed molecule has strong vibrational energy. This causes the bond to break again and pass the TS to form approach the HA molecule and reform the initial bond.||[[File:tfig4_scm4918.png|200px]]
|-
| -5.1 || -10.6 || -349.48 || Yes || In this case the TS is crossed three times. This causes the products to form then break to form the reactant molecule and then form again to end up with the products. ||[[File:tfig5_scm4918.png|200px]]
|}

MRD:scm4918

2020-05-22T22:21:36Z

Scm4918: /* Reactive and unreactive trajectories */

== EXERCISE 1: H + H2 system ==
==== Transition state ====
[[File:Surface_Plot_scm4918.png|thumb|frame|right|Potential energy surface plot (transition state shown with red dot)]]
The mathematical definition for a transition state on a potential energy surface diagram is: δV/δr1 = δV/δr2 = 0, where V is the chemical potential and r1/2 the distances between the atoms. Furthermore, as this definition applies to all local minima, to distinguish the transition state from the rest, the following term must be less than 0: fxx(x0,y0)fyy(x0,y0)−f2xy(x0,y0), where x & y are the interatomic distances (r1/2) and (x0,y0) the coordinates of the saddle point.
The transition state is shown in the diagram with a red dot. This is along the calculated dynamic trajectory shown by the black line.

==== Locating the transition state ====
The best estimate for the transition state was found at r1=2 = 90.8 pm. By keeping the momentum at zero and the two distances equal a range of values from 85 pm to 110 pm were tested. The internuclear distance against time was plotted and at 90.8 pm the graph obtained showed 2 straight lines. Since the lines are straight the interatomic distances are constant and there is no more oscillation. Hence, the transition state has been reached.

==== Minimum energy path and calculated trajectory ====
The mep (minimum energy pathway) is the lowest energy trajectory taken by a group of atoms that are rearranging themselves between two different stable configurations. At every point the velocities are reset to 0. The difference between this and the previously calculated dynamic trajectory is that as can be seen from the internuclear distances vs time graphs there are no oscillations in the mep graph. This can be explained by the fact that for mep the motion starts at the transition state and the entire path flows downhill along the lowest energy where the momentum is always reset to zero and hence the effects of inertia neglected.

==== Reactive and unreactive trajectories ====

{| class="wikitable" border=1
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot (kJ.mol-1) !! Reactive? !! Description of the dynamics !! Illustration of the trajectory (internuclear distances against time)
|-
| -2.56 || -5.1 || -414.28 || Yes || Little oscillations throughout the reaction. C approaches the molecule, bonds to B as A drifts away. The new diatomic is oscillating and distances itself from A.|| [[File:tfig1_scm4918.png|200px]]
|-
| -3.1 || -4.1 || -420.08 || No || Light oscillations in the diatomic A-B. rBC decreases, then increases with no collision between the atoms. ||[[File:tfig2_scm4918.png|200px]]
|-
| -3.1 || -5.1 || -413.98 || Yes || Little oscillations. C approaches the molecule, bonds to B as A drifts away. The new diatomic is oscillating and distances itself from A ||[[File:tfig3_scm4918.png|200px]]
|-
| -5.1 || -10.1 || -357.27 || No || Strong oscillations. C approaches the diatomic, bonds with B, A distances itself slightly then reverts to its initial position, forms a new bond with B as C drifts away in the opposite direction||[[File:tfig4_scm4918.png|200px]]
|-
| -5.1 || -10.6 || -349.48 || Yes || Strong oscillations. C approaches the diatomic, bons with B. A distances itself then nears B to form the TS (AB=BC) again, then drifts away as B-C oscillates ||[[File:tfig5_scm4918.png|200px]]
|}

File:Tfig5 scm4918.png

2020-05-22T22:20:08Z

Scm4918:

File:Tfig4 scm4918.png

2020-05-22T22:19:07Z

Scm4918:

File:Tfig3 scm4918.png

2020-05-22T22:18:20Z

Scm4918:

File:Tfig2 scm4918.png

2020-05-22T22:17:24Z

Scm4918:

File:Tfig1 scm4918.png

2020-05-22T22:16:38Z

Scm4918:

MRD:scm4918

2020-05-22T22:02:09Z

Scm4918: /* Reactive and unreactive trajectories */

== EXERCISE 1: H + H2 system ==
==== Transition state ====
[[File:Surface_Plot_scm4918.png|thumb|frame|right|Potential energy surface plot (transition state shown with red dot)]]
The mathematical definition for a transition state on a potential energy surface diagram is: δV/δr1 = δV/δr2 = 0, where V is the chemical potential and r1/2 the distances between the atoms. Furthermore, as this definition applies to all local minima, to distinguish the transition state from the rest, the following term must be less than 0: fxx(x0,y0)fyy(x0,y0)−f2xy(x0,y0), where x & y are the interatomic distances (r1/2) and (x0,y0) the coordinates of the saddle point.
The transition state is shown in the diagram with a red dot. This is along the calculated dynamic trajectory shown by the black line.

==== Locating the transition state ====
The best estimate for the transition state was found at r1=2 = 90.8 pm. By keeping the momentum at zero and the two distances equal a range of values from 85 pm to 110 pm were tested. The internuclear distance against time was plotted and at 90.8 pm the graph obtained showed 2 straight lines. Since the lines are straight the interatomic distances are constant and there is no more oscillation. Hence, the transition state has been reached.

==== Minimum energy path and calculated trajectory ====
The mep (minimum energy pathway) is the lowest energy trajectory taken by a group of atoms that are rearranging themselves between two different stable configurations. At every point the velocities are reset to 0. The difference between this and the previously calculated dynamic trajectory is that as can be seen from the internuclear distances vs time graphs there are no oscillations in the mep graph. This can be explained by the fact that for mep the motion starts at the transition state and the entire path flows downhill along the lowest energy where the momentum is always reset to zero and hence the effects of inertia neglected.

==== Reactive and unreactive trajectories ====

{| class="wikitable" border=1
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot (kJ.mol-1) !! Reactive? !! Description of the dynamics !! Illustration of the trajectory (internuclear distances against time)
|-
| -2.56 || -5.1 || -414.28 || Yes || Little oscillations throughout the reaction. C approaches the molecule, bonds to B as A drifts away. The new diatomic is oscillating and distances itself from A.|| [[File:Fzm18-tablefig1.png|200px]]
|-
| -3.1 || -4.1 || -420.08 || No || Light oscillations in the diatomic A-B. rBC decreases, then increases with no collision between the atoms. ||[[File:Fzm18-tablefig2.png|200px]]
|-
| -3.1 || -5.1 || -413.98 || Yes || Little oscillations. C approaches the molecule, bonds to B as A drifts away. The new diatomic is oscillating and distances itself from A ||[[File:Fzm18-tablefig3.png|200px]]
|-
| -5.1 || -10.1 || -357.27 || No || Strong oscillations. C approaches the diatomic, bonds with B, A distances itself slightly then reverts to its initial position, forms a new bond with B as C drifts away in the opposite direction||[[File:Fzm18-tablefig4.png|200px]]
|-
| -5.1 || -10.6 || -349.48 || Yes || Strong oscillations. C approaches the diatomic, bons with B. A distances itself then nears B to form the TS (AB=BC) again, then drifts away as B-C oscillates ||[[File:Fzm18-tablefig5.png|200px]]
|}

MRD:scm4918

2020-05-22T22:00:33Z

Scm4918: /* Reactive and unreactive trajectories */

== EXERCISE 1: H + H2 system ==
==== Transition state ====
[[File:Surface_Plot_scm4918.png|thumb|frame|right|Potential energy surface plot (transition state shown with red dot)]]
The mathematical definition for a transition state on a potential energy surface diagram is: δV/δr1 = δV/δr2 = 0, where V is the chemical potential and r1/2 the distances between the atoms. Furthermore, as this definition applies to all local minima, to distinguish the transition state from the rest, the following term must be less than 0: fxx(x0,y0)fyy(x0,y0)−f2xy(x0,y0), where x & y are the interatomic distances (r1/2) and (x0,y0) the coordinates of the saddle point.
The transition state is shown in the diagram with a red dot. This is along the calculated dynamic trajectory shown by the black line.

==== Locating the transition state ====
The best estimate for the transition state was found at r1=2 = 90.8 pm. By keeping the momentum at zero and the two distances equal a range of values from 85 pm to 110 pm were tested. The internuclear distance against time was plotted and at 90.8 pm the graph obtained showed 2 straight lines. Since the lines are straight the interatomic distances are constant and there is no more oscillation. Hence, the transition state has been reached.

==== Minimum energy path and calculated trajectory ====
The mep (minimum energy pathway) is the lowest energy trajectory taken by a group of atoms that are rearranging themselves between two different stable configurations. At every point the velocities are reset to 0. The difference between this and the previously calculated dynamic trajectory is that as can be seen from the internuclear distances vs time graphs there are no oscillations in the mep graph. This can be explained by the fact that for mep the motion starts at the transition state and the entire path flows downhill along the lowest energy where the momentum is always reset to zero and hence the effects of inertia neglected.

==== Reactive and unreactive trajectories ====

{| class="wikitable" border=1
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot (kJ.mol-1) !! Reactive? !! Description of the dynamics !! Illustration of the trajectory (internuclear distances against time)
|-
| -2.56 || -5.1 || -414.28 || Yes || Little oscillations throughout the reaction. C approaches the molecule, bonds to B as A drifts away. The new diatomic is oscillating and distances itself from A.|| [[File:Fzm18-tablefig1.png|200px]]
|-
| -3.1 || -4.1 || -420.08 || No || Light oscillations in the diatomic A-B. rBC decreases, then increases with no collision between the atoms. {{fontcolor1|red|There is no ''reaction'', but is there no ''collision''? Think about what 'collision' means - there must be some kind of repulsion, which is clearly present. [[User:Fdp18|Fdp18]] ([[User talk:Fdp18|talk]]) 09:11, 9 May 2020 (BST)}} ||[[File:Fzm18-tablefig2.png|200px]]
|-
| -3.1 || -5.1 || -413.98 || Yes || Little oscillations. C approaches the molecule, bonds to B as A drifts away. The new diatomic is oscillating and distances itself from A ||[[File:Fzm18-tablefig3.png|200px]]
|-
| -5.1 || -10.1 || -357.27 || No || Strong oscillations. C approaches the diatomic, bonds with B, A distances itself slightly then reverts to its initial position, forms a new bond with B as C drifts away in the opposite direction||[[File:Fzm18-tablefig4.png|200px]]
|-
| -5.1 || -10.6 || -349.48 || Yes || Strong oscillations. C approaches the diatomic, bons with B. A distances itself then nears B to form the TS (AB=BC) again, then drifts away as B-C oscillates {{fontcolor1|red|Just a little picky side note for your understanding: The atoms don't need to pass '''the''' TS (as in the mathematical TS, which is just one single point. Actually, because it is just a point, they will never pass it exactly.) [[User:Fdp18|Fdp18]] ([[User talk:Fdp18|talk]]) 09:16, 9 May 2020 (BST)}} ||[[File:Fzm18-tablefig5.png|200px]]
|}

MRD:scm4918

2020-05-22T21:25:54Z

Scm4918: /* EXERCISE 1: H + H2 system */

MRD:scm4918

2020-05-22T17:01:24Z

Scm4918: /* Transition state */

MRD:scm4918

2020-05-22T17:00:37Z

Scm4918: /* Transition state */

== EXERCISE 1: H + H2 system ==
==== Transition state ====
The mathematical definition for a transition state on a potential energy surface diagram is: δV/δr1 = δV/δr2 = 0, where V is the chemical potential and r1/2 the distances between the atoms. Furthermore, as this definition applies to all local minima, to distinguish the transition state from the rest, the following term must be less than 0: fxx(x0,y0)fyy(x0,y0)−f2xy(x0,y0), where x & y are the interatomic distances (r1/2) and (x0,y0) the coordinates of the saddle point.
[[File:Surface_Plot_scm4918.png|thumb|frame|right|Potential energy surface plot (transition state shown with red dot)]]
The transition state is shown in the diagram with a red dot. This is along the reaction path (minimum energy path) shown by the black line.

MRD:scm4918

2020-05-22T16:51:19Z

Scm4918:

File:Surface Plot scm4918.png

2020-05-22T16:45:34Z

Scm4918:

MRD:scm4918

2020-05-22T16:43:48Z

Scm4918: /* Transition state */

MRD:scm4918

2020-05-22T12:15:40Z

Scm4918:

== EXERCISE 1: H + H2 system ==
==== Transition state ====
The mathematical definition for a transition state is: δV/δr1 = δV/δr2 = 0, where V is the chemical potential and r1/2 the distances between the atoms. Furthermore, as this definition applies to all local minima, to distinguish the transition state from the rest, the following term must be less than 0: fxx(x0,y0)fyy(x0,y0)−f2xy(x0,y0), where x & y are the interatomic distances (r1/2) and

MRD:scm4918

2020-05-22T12:11:51Z

Scm4918: Created page with "== EXERCISE 1: H + H2 system == ==== Transition state ==== The mathematical definition for a transition state is: δV/δr1 = δV/δr2 = 0, where V is the chemical..."

== EXERCISE 1: H + H2 system ==
==== Transition state ====
The mathematical definition for a transition state is: δV/δr1 = δV/δr2 = 0, where V is the chemical potential and r1/2 the distances between the atoms. Furthermore, as this definition applies to all local minima, to distinguish the transition state from the rest, the following term must be less than 0: fxx(x0,y0)*fyy(x0,y0)−f2xy(x0,y0), where x & y are the interatomic distances (r1/2) and

Rep:Mod:scm4918

2019-03-15T17:17:56Z

Scm4918: /* Mono-metallic TM Complex */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that The 2 electrons in the H2 bond must be diffused between 3 atoms and therefore lead to a weaker, more dispersed bond. Another reason is that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.

===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of carbon monoxide you would expect to see one band since the single stretching vibration produces a change in dipole moment.

===Atomic Charges===
The charge on the O-atom was found to be -0.506 and 0.506 on the C-atom. This matches the expectation since Oxygen is a more electronegative atom than Carbon and therefore draws electron density towards itself resulting in a relative negative charge.

===Molecular Orbitals===
{| class="wikitable" border="1"
|+ Molecular Orbitals of CO
! MO number
|4
|5
|7
|8
|10
|-
! energy /a.u.
| -0.57004
| -0.46742
| -0.37145
| -0.02178
|0.26241
|-
! image
|[[File:Scm4918_co_mo4.png|200px]]
|[[File:Scm4918_co_mo5.png|200px]]
|[[File:Scm4918_co_mo7.png|200px]]
|[[File:Scm4918_co_mo8.png|200px]]
|[[File:Scm4918_co_mo10.png|200px]]
|}
The 4th MO arises from the antibonding overlap of the 2sAOs.
The 5th MO arises from the bonding overlap of two pAOs oriented perpendicular to the bond.
The 7th MO arises from the bonding overlap of two pAOs oriented along the bond, this is the '''HOMO'''.
The 8th MO arises from the antibonding overlap of two pAOs oriented perpendicular to the bond, this is the '''LUMO'''.
The 10th MO arises from the antibonding overlap of two pAOs oriented along the bond (this orbital is also unoccupied).

A good reason for this molecules stability is the fact that only the bonding pAO based MOs are occupied.

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T07:02:22Z

Scm4918: /* Molecular Orbitals */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of carbon monoxide you would expect to see one band since the single stretching vibration produces a change in dipole moment.

===Atomic Charges===
The charge on the O-atom was found to be -0.506 and 0.506 on the C-atom. This matches the expectation since Oxygen is a more electronegative atom than Carbon and therefore draws electron density towards itself resulting in a relative negative charge.

===Molecular Orbitals===
{| class="wikitable" border="1"
|+ Molecular Orbitals of CO
! MO number
|4
|5
|7
|8
|10
|-
! energy /a.u.
| -0.57004
| -0.46742
| -0.37145
| -0.02178
|0.26241
|-
! image
|[[File:Scm4918_co_mo4.png|200px]]
|[[File:Scm4918_co_mo5.png|200px]]
|[[File:Scm4918_co_mo7.png|200px]]
|[[File:Scm4918_co_mo8.png|200px]]
|[[File:Scm4918_co_mo10.png|200px]]
|}
The 4th MO arises from the antibonding overlap of the 2sAOs.
The 5th MO arises from the bonding overlap of two pAOs oriented perpendicular to the bond.
The 7th MO arises from the bonding overlap of two pAOs oriented along the bond, this is the '''HOMO'''.
The 8th MO arises from the antibonding overlap of two pAOs oriented perpendicular to the bond, this is the '''LUMO'''.
The 10th MO arises from the antibonding overlap of two pAOs oriented along the bond (this orbital is also unoccupied).

A good reason for this molecules stability is the fact that only the bonding pAO based MOs are occupied.

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T06:39:02Z

Scm4918: /* Molecular Orbitals */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of carbon monoxide you would expect to see one band since the single stretching vibration produces a change in dipole moment.

===Atomic Charges===
The charge on the O-atom was found to be -0.506 and 0.506 on the C-atom. This matches the expectation since Oxygen is a more electronegative atom than Carbon and therefore draws electron density towards itself resulting in a relative negative charge.

===Molecular Orbitals===
{| class="wikitable" border="1"
|+ Molecular Orbitals of CO
! MO number
|4
|5
|7
|8
|10
|-
! energy /a.u.
| -0.57004
| -0.46742
| -0.37145
| -0.02178
|0.26241
|-
! image
|[[File:Scm4918_co_mo4.png|200px]]
|[[File:Scm4918_co_mo5.png|200px]]
|[[File:Scm4918_co_mo7.png|200px]]
|[[File:Scm4918_co_mo8.png|200px]]
|[[File:Scm4918_co_mo10.png|200px]]
|}

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T06:35:48Z

Scm4918: /* Molecular Orbitals */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of carbon monoxide you would expect to see one band since the single stretching vibration produces a change in dipole moment.

===Atomic Charges===
The charge on the O-atom was found to be -0.506 and 0.506 on the C-atom. This matches the expectation since Oxygen is a more electronegative atom than Carbon and therefore draws electron density towards itself resulting in a relative negative charge.

===Molecular Orbitals===
{| class="wikitable" border="1"
|+ Molecular Orbitals of CO
! MO number
|4
|5
|7
|8
|10
|-
! energy /a.u.
|-0.57004
|-0.46742
|-0.37145
|-0.02178
|0.26241
|-
! image
|[[File:Scm4918_co_mo4_-_Copy.png|200px]]
|[[File:Scm4918_co_mo5.tif|200px]]
|[[File:Scm4918_co_vib10000.png|200px]]
|[[File:Scm4918_co_vib10000.png|200px]]
|[[File:Scm4918_co_vib10000.png|200px]]
|}

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

File:Scm4918 co mo10.png

2019-03-15T06:35:36Z

Scm4918:

File:Scm4918 co mo8.png

2019-03-15T06:35:24Z

Scm4918:

File:Scm4918 co mo7.png

2019-03-15T06:35:11Z

Scm4918: Scm4918 uploaded a new version of File:Scm4918 co mo7.png

File:Scm4918 co mo7.png

2019-03-15T06:34:59Z

Scm4918:

File:Scm4918 co mo5.png

2019-03-15T06:34:50Z

Scm4918:

File:Scm4918 co mo4.png

2019-03-15T06:32:58Z

Scm4918:

File:Scm4918 co mo4.tif

2019-03-15T06:26:06Z

Scm4918:

Rep:Mod:scm4918

2019-03-15T06:25:36Z

Scm4918: /* Molecular Orbitals */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of carbon monoxide you would expect to see one band since the single stretching vibration produces a change in dipole moment.

===Atomic Charges===
The charge on the O-atom was found to be -0.506 and 0.506 on the C-atom. This matches the expectation since Oxygen is a more electronegative atom than Carbon and therefore draws electron density towards itself resulting in a relative negative charge.

===Molecular Orbitals===
{| class="wikitable" border="1"
|+ Molecular Orbitals of CO
! MO number
|4
|5
|7
|8
|10
|-
! energy /a.u.
|-0.57004
|-0.46742
|-0.37145
|-0.02178
|0.26241
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|[[File:Scm4918_co_vib10000.png|200px]]
|[[File:Scm4918_co_vib10000.png|200px]]
|[[File:Scm4918_co_vib10000.png|200px]]
|[[File:Scm4918_co_vib10000.png|200px]]
|}

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T06:18:53Z

Scm4918: /* CO molecule */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of carbon monoxide you would expect to see one band since the single stretching vibration produces a change in dipole moment.

===Atomic Charges===
The charge on the O-atom was found to be -0.506 and 0.506 on the C-atom. This matches the expectation since Oxygen is a more electronegative atom than Carbon and therefore draws electron density towards itself resulting in a relative negative charge.

===Molecular Orbitals===
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T05:41:42Z

Scm4918: /* Atomic Charges */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of carbon monoxide you would expect to see one band since the single stretching vibration produces a change in dipole moment.

===Atomic Charges===
The charge on the O-atom was found to be -0.506 and 0.506 on the C-atom. This matches the expectation since Oxygen is a more electronegative atom than Carbon and therefore draws electron density towards itself resulting in a relative negative charge.

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T05:39:14Z

Scm4918: /* Frequancy Analysis */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of carbon monoxide you would expect to see one band since the single stretching vibration produces a change in dipole moment.

===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T05:37:52Z

Scm4918: /* Frequancy Analysis */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of P4
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.

===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T05:37:16Z

Scm4918: /* CO molecule */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -113.30945314 a.u.

RMS gradient: 0.00000433 a.u.

Point group: D∞v

C-O bond distance = 1.13794 Å

C-O bond angle = 180 °
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000007 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000004 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>Carbon Monoxide Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_CO_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_CO_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_co_display_vibrations.PNG|frame|left|Display vibrations window for optimised CO molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of CO
! symmetry
|SG
|-
! wavenumber /cm-1
|2209
|-
! intensity /arbitrary units
|68
|-
! image
|[[File:Scm4918_co_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.
===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T05:32:06Z

Scm4918: /* N2 molecule */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==CO molecule==
'''Choice Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.
===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T05:30:02Z

Scm4918:

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.
===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

File:Scm4918 co display vibrations.PNG

2019-03-15T05:27:52Z

Scm4918:

File:Scm4918 h2 display vibrations.PNG

2019-03-15T05:27:29Z

Scm4918: Scm4918 uploaded a new version of File:Scm4918 h2 display vibrations.PNG

File:Scm4918 co vib10000.png

2019-03-15T05:27:11Z

Scm4918:

File:SCM4918 CO OPTF POP.LOG

2019-03-15T05:26:58Z

Scm4918:

Rep:Mod:scm4918

2019-03-15T05:03:08Z

Scm4918:

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.
==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The three modes at wavenumber 367 cm-1 and the three at 464 cm-1 are degenerate. In an experimental spectrum white phosphorous you would expect to see 1 band since the three IR-active vibrations are degenerate.
===Atomic Charges===
There is no charge on any P-atom. This matches the expectation since they all have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

Rep:Mod:scm4918

2019-03-15T04:52:32Z

Scm4918: /* P4 molecule */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 3 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.
==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 6 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

Rep:Mod:scm4918

2019-03-15T04:50:44Z

Scm4918: /* P4 molecule */

==NH3 molecule==
===Molecule Information===
<nowiki> </nowiki>
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

Point group: C3v

N-H bond distance = 1.01798 Å

H-N-H bond angle = 105.74115 °
===Optimisation===
<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
</pre>

<jmol><jmolApplet>
<title>Ammonia Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918 PHUNT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918 PHUNT NH3 OPTF POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_nh3_display_vibrations.PNG|frame|left|Display vibrations window for optimised NH3 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|A1||E||E||A1||E||E
|-
! wavenumber /cm-1
|1090||1694||1694||3461||3590||3590
|-
! intensity /arbitrary units
|145||14||14||1||0||0
|-
! image
|[[File:Scm4918_nh3_vib10000.png|200px]]
|[[File:Scm4918_nh3_vib20000.png|200px]]
|[[File:Scm4918_nh3_vib30000.png|200px]]
|[[File:Scm4918_nh3_vib40000.png|200px]]
|[[File:Scm4918_nh3_vib50000.png|200px]]
|[[File:Scm4918_nh3_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 3 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

==N2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -109.52412868 a.u.

RMS gradient: 0.00000060 a.u.

Point group: D∞h

N-N bond distance = 1.10550 Å

N-N bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Nitrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_N2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_N2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_n2_display_vibrations.PNG|frame|left|Display vibrations window for optimised N2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of N2
! symmetry
|SGG
|-
! wavenumber /cm-1
|2457
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_n2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous nitrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.
===Atomic Charges===
There is no charge on either N-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==H2 molecule==
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1.17853936 a.u.

RMS gradient: 0.00000017 a.u.

Point group: D∞h

H-H bond distance = 0.74279 Å

H-H bond angle = 180 °
===Optimisation===
<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><jmolApplet>
<title>Hydrogen Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_H2_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_H2_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_h2_display_vibrations.PNG|frame|left|Display vibrations window for optimised H2 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of H2
! symmetry
|SGG
|-
! wavenumber /cm-1
|4466
|-
! intensity /arbitrary units
|0
|-
! image
|[[File:Scm4918_h2_vib10000.png|200px]]
|}
 
From the 3N-5 rule for linear molecules we would expect this molecule to have 1 mode. The mode shown in the table is a stretching vibration. In an experimental spectrum of gaseous hydrogen you would expect to see zero bands since the single stretching vibration does not produce a change in dipole moment.

===Atomic Charges===
There is no charge on either H-atom. This matches the expectation since they both have the same electronegativity and therefore the charge is equally distributed throughout the molecule.

==Structure and Reactivity==
===Mono-metallic TM Complex===
A search for mono-metallic TM complexes that coordinate H2 was ran in ConQuest software. The H-H bond length was defined as an identifier and one of the resulting molecules was selected. The unique identifier for the complex is: [[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=HIHVIE&DatabaseToSearch=Published HIHVIE]] and the obtained '''H-H bond length=1.050Å'''. This is bigger than the value previously computed: '''H-H bond length=0.74279Å'''. This difference could arise from the fact that there are 6 ligands bound to the central metal complex. Therefore, one would expect an octahedral structure that requires a greater H-Ru-H angle and therefore pull the H-H bond further apart. However, the angles deviated from the regular octahedral ones since the 6 ligands are different and some much bigger than the H-atoms. These bigger ligands would have a repulsive effect on the H-H bond and reduce it. The rigidity of the H-H bond would also prvent it from reaching a 90° H-Ru-H angle that is expected from a octahedral complex.
===Haber-Bosch process===
E(NH3) = -56.5577687 a.u.

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

E(N2) = -109.5241287 a.u.

E(H2) = -1.1785394 a.u.

3*E(H2) = -3.5356181 a.u.

ΔE=2*E(NH3)-[E(N2)+3*E(H2)] = -146.5 kJ/mol

From this result we can conclude that the ammonia product is more stable.
==P4 molecule==
'''Extra Molecule'''
===Molecule Information===
Calculation method: RB3LYP

Basis set: 6-31G(d,p)

Final energy: -1365.44182877 a.u.

RMS gradient: 0.00002517 a.u.

Point group: Td

P-P bond distance = 2.21771 Å

P-P-P bond angle = 60°
===Optimisation===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000101 0.001800 YES
RMS Displacement 0.000076 0.001200 YES
</pre>

<jmol><jmolApplet>
<title>White Phosphorus Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SCM4918_P4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:SCM4918_P4_OPTF_POP.LOG| here]]
===Frequancy Analysis===
[[File:Scm4918_p4_display_vibrations.PNG|frame|left|Display vibrations window for optimised P4 molecule.]]
{| class="wikitable" border="1"
|+ Frequency Analysis of NH3
! symmetry
|E||E||T2||T2||T2||A1
|-
! wavenumber /cm-1
|367||367||464||464||464||607
|-
! intensity /arbitrary units
|0||0||2||2||2||0
|-
! image
|[[File:Scm4918_p4_vib10000.png|200px]]
|[[File:Scm4918_p4_vib20000.png|200px]]
|[[File:Scm4918_p4_vib30000.png|200px]]
|[[File:Scm4918_p4_vib40000.png|200px]]
|[[File:Scm4918_p4_vib50000.png|200px]]
|[[File:Scm4918_p4_vib60000.png|200px]]
|}
From the 3N-6 rule for non-linear molecules we would expect this molecule to have 3 modes. The two modes at wavenumber 1694 cm-1 and the ones at 3590 cm-1 are degenerate. The first three modes in the table are bending vibrations, the last three are bond stretching vibrations. The "umbrella" mode is the first one in the table at 1090 cm-1. In an experimental spectrum of gaseous ammonia you would expect to see 3 bands.
===Atomic Charges===
The charge on the N-atom was found to be -1.125 and 0.375 on the H-atom. This matches the expectation since Nitrogen is a more electronegative atom than Hydrogen and therefore draws electron density towards itself resulting in a relative negative charge. On each Hydrogen atom you would expect a third of the charge on the Nitrogen since there are three atoms all donating the same amount of electron density.

File:Scm4918 p4 vib60000.png

2019-03-15T04:47:42Z

Scm4918: