ChemWiki - User contributions [en]

MRD:cat3718MRD

2020-05-11T17:45:00Z

Cat3718: /* Molecular reaction dynamics */

== Molecular reaction dynamics ==
'''
'''Potential energy surface diagram - The transition state:'''

The transition state on an energy surface diagram can be mathematically defined by ∂V('''ri''')/∂'''ri'''=0 which is the maximum point on the minimum energy path between the reactants and products. Which differentiates itself form local minima as local minima are the point on the diagram where the gradient=0 as is the transition state, but the transition state is the maximum point on the minimum energy path where the gradient=0.

[[File:Surface_Plot1cat3718.png| Inter-nuclear distance vs time plot]]

The transition state position rts estimated at 88 pm and can be seen on the distance vs time plot below at 20 fs where AB and BC paths cross. AB then goes into a vibration state whereas BC also has translation energy as shown by the distance increasing after the cross over.

'''Trajectory: Dynamic vs Mep'''

[[File:Surface_Plot2cat3718.png| Dynamic run trajectory]] [[File:Surface_Plot3cat3718.png| MEP run trajectory]]

As seen above in the dynamic surface plot above the path ends with vibration energy when compared to the mep calculation on the right there is clearly no vibration in the reaction path. For inter-nuclear distance vs time, r1 oscillates between 70-78 pm whereas once r2 gets to about 100 pm it just increases linearly as C moves away from AB with constant velocity. For momenta vs time once the nuclei have separated for the dynaimc calculation AB oscillates between 1-3.5 g.mol-1.pm.fs-1 and C levels out at 5 g.mol-1.pm.fs-1 for the mep calculation there is no change in momentum so a flat line is observed. As for the distance vs time for the mep calculation AB stays constant at 75 pm, C moves away and starts to plateau. If initial conditions are swapped for final conditons for the calculation above the distance vs time graph is flipped horizontally and the momenta vs time is flipped vertically.

{| class="wikitable"
!
{| class="wikitable"
!p1/ g.mol-1.pm.fs-1
|}
!p2/ g.mol-1.pm.fs-1
!Etot
!Reactive?
!Description of the dynamics
!Illustration of the trajector
|-
|<nowiki>-2.56</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-414.280</nowiki>
|Yes
|First diatomic AB not vibrating then collision occurs and reaction is successful BC moves away from A whilst vibrating as a new diatomic molecule.
|[[File:Surface_Plot6cat3718.png|Surface_Plot6cat3718.png|200x200px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-4.1</nowiki>
|<nowiki>-420.077</nowiki>
|No
|Collision unsuccessful C moves towards vibrating AB then is repelled and moves away, AB continues to vibrate.
|[[File:Surface_Plot7cat3718.png| |200x200px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-413.977</nowiki>
|Yes
|Collision successful C moves towards AB with greater momentum than the situation above overcomes repulsion and collides successfully making a new diatomic BC which then moves away from A whilst vibrating and A also moves away from BC constant velocity(velocity oscillates between two values but constant if vibrating motion of BC ignored).
|[[File:Surface_Plot8cat3718.png| |200x200px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.1</nowiki>
|<nowiki>-357.277</nowiki>
|No
|Initially successful with BC forms briefly starts vibrating, then B bonds back to A to form AB again so two transition states occur, as can be seen in the surface diagram the path crosses over itself.
|[[File:Surface_Plot9cat3718.png| |200x200px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.6</nowiki>
|<nowiki>-349.477</nowiki>
|Yes
|Successful reaction similar to reaction above in that B bonds to C then back to A except this time bonds back to C forming BC which then moves away from A whilst vibrating. Three crosses in paths on inter-nuclear distance vs time plot these crosses can be seen in the path on the surface plot to the right.
|[[File:Surface_Plot10cat3718.png| |200x200px]]
|}
From the table above it can be concluded that p2 has to be high enough to overcome p1 and that there can be recrossing on barrier for transition state. All calcultions above were at r1=74 pm and r2=200 pm on dynamic type of calculation.

'''Transition state theory vs experimental value:'''

So transition state theory states that based on the reactants and structure of the transition state that the rate of a reaction can be found. TS theory forbids recrossing of products over the transition state, in the penultimate experiment in the table this recrossing occurs showing experimentally transition state theory is not always followed and can be flawed .

'''F-H-H System:'''

For F + H2 this reaction is exothermic as can be seen in the dip in energy in the surface plot below as the BC distance decreases until it starts to fluctuate between two values when HF is bonded. The reaction path after the reaction takes place shows large oscillations due to the HF vibrations being larger as F is heavier.

[[File:Surface_Plot12cat3718.png| ]]

For HF + H the reaction is endothermic as can be seen that as the bond length of BC decreases as HB and HC get closer that the energy in the surface diagram below increases so energy comes into the system for the reaction to occur hence endothermic.

[[File:Surface_Plot11cat3718.png| ]]

The transition state for the reaction occurs at approximately 75pm for distance AB and 145pm for BC for F + H2 and for HF + H is approximately 100 pm for BC and AB. The activation energy is at 436 KJ mol-1 for F + H2 for HF + H the activation energy was 400 KJ mol-1.

'''Reaction dynamics''' :

The release of reaction energy could be found using conservation of momentum as will be the same before and after any lost can be accounted by a chnage in energy as the mass will stay constant. For reactions varying with F+H2 varying pHH for values >5.6, between -5 to -5.5, 0-1, 1.8, -2.1 all had successful reactions so not dependent on a minimum or maximum value for p(up to 6.1 tested). For 0.2 pHH and -1.6 for pHF no reaction occurred. For the reverse reaction if the HF bond is given 1.9 g.mol-1.pm.fs-1 and the incoming H atom with -4 g.mol-1.pm.fs-1 then the reaction does not occur as the activation energy barrier has not been passed these were the minimum values for p found which gave no reaction.

The higher the translational energy for the incoming atom the more likely the reaction is to occur if the transition state the highest point on the minimum reaction path is where the reaction takes place so if the vibrational energy is too high there can be too much repulsion for the incoming atom to react with the vibrating molecule. So if the transition state is closer to the reactants then it will resemble the reactants more in this case the vibrating HF molecule and incoming H atom and if closer to the products then the transition state will resemble that. So if closer to reactants depends more on the vibrational modes and if closer to products in a later transition state will depend more on the translational mode.

.

MRD:cat3718MRD

2020-05-09T14:41:48Z

Cat3718:

== Molecular reaction dynamics ==
'''
'''Potential energy surface diagram - The transition state:'''

The transition state on an energy surface diagram can be mathematically defined by ∂V('''ri''')/∂'''ri'''=0 which is the maximum point on the minimum energy path between the reactants and products. Which differentiates itself form local minima as local minima are the point on the diagram where the gradient=0 as is the transition state, but the transition state is the maximum point on the minimum energy path where the gradient=0.

[[File:Surface_Plot1cat3718.png| Inter-nuclear distance vs time plot]]

The transition state position rts estimated at 88 pm and can be seen on the distance vs time plot below at 20 fs where AB and BC paths cross. AB then goes into a vibration state whereas BC also has translation energy as shown by the distance increasing after the cross over.

'''Trajectory: Dynamic vs Mep'''

[[File:Surface_Plot2cat3718.png| Dynamic run trajectory]] [[File:Surface_Plot3cat3718.png| MEP run trajectory]]

As seen above in the dynamic surface plot above the path ends with vibration energy when compared to the mep calculation on the right there is clearly no vibration in the reaction path. For inter-nuclear distance vs time, r1 oscillates between 70-78 pm whereas once r2 gets to about 100 pm it just increases linearly as C moves away from AB with constant velocity. For momenta vs time once the nuclei have separated for the dynaimc calculation AB oscillates between 1-3.5 g.mol-1.pm.fs-1 and C levels out at 5 g.mol-1.pm.fs-1 for the mep calculation there is no change in momentum so a flat line is observed. As for the distance vs time for the mep calculation AB stays constant at 75 pm, C moves away and starts to plateau. If initial conditions are swapped for final conditons for the calculation above the distance vs time graph is flipped horizontally and the momenta vs time is flipped vertically.

{| class="wikitable"
!
{| class="wikitable"
!p1/ g.mol-1.pm.fs-1
|}
!p2/ g.mol-1.pm.fs-1
!Etot
!Reactive?
!Description of the dynamics
!Illustration of the trajector
|-
|<nowiki>-2.56</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-414.280</nowiki>
|Yes
|First diatomic AB not vibrating then collision occurs and reaction is successful BC moves away from A whilst vibrating as a new diatomic molecule.
|[[File:Surface_Plot6cat3718.png|Surface_Plot6cat3718.png|200x200px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-4.1</nowiki>
|<nowiki>-420.077</nowiki>
|No
|Collision unsuccessful C moves towards vibrating AB then is repelled and moves away, AB continues to vibrate.
|[[File:Surface_Plot7cat3718.png| |200x200px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-413.977</nowiki>
|Yes
|Collision successful C moves towards AB with greater momentum than the situation above overcomes repulsion and collides successfully making a new diatomic BC which then moves away from A whilst vibrating and A also moves away from BC constant velocity(velocity oscillates between two values but constant if vibrating motion of BC ignored).
|[[File:Surface_Plot8cat3718.png| |200x200px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.1</nowiki>
|<nowiki>-357.277</nowiki>
|No
|Initially successful with BC forms briefly starts vibrating, then B bonds back to A to form AB again so two transition states occur, as can be seen in the surface diagram the path crosses over itself.
|[[File:Surface_Plot9cat3718.png| |200x200px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.6</nowiki>
|<nowiki>-349.477</nowiki>
|Yes
|Successful reaction similar to reaction above in that B bonds to C then back to A except this time bonds back to C forming BC which then moves away from A whilst vibrating. Three crosses in paths on inter-nuclear distance vs time plot these crosses can be seen in the path on the surface plot to the right.
|[[File:Surface_Plot10cat3718.png| |200x200px]]
|}
From the table above it can be concluded that p2 has to be high enough to overcome p1 and that there can be recrossing on barrier for transition state. All calcultions above were at r1=74 pm and r2=200 pm on dynamic type of calculation.

'''Transition state theory vs experimental value:'''

So transition state theory states that based on the reactants and structure of the transition state that the rate of a reaction can be found. TS theory forbids recrossing of products over the transition state, in the penultimate experiment in the table this recrossing occurs showing experimentally transition state theory is not always followed and can be flawed .

'''F-H-H System:'''

For F + H2 this reaction is exothermic as can be seen in the dip in enthalpy in the surface plot below as the BC distance decreases until it starts to fluctuate between two values when HF is bonded. The reaction path after the reaction takes place shows large oscillations due to the HF vibrations being larger as F is heavier.

[[File:Surface_Plot12cat3718.png| ]]

For HF + H the reaction is endothermic as can be seen that as the bond length of BC decreases as HB and HC get closer that the enthalpy in the surface diagram below increases so energy comes into the system for the reaction to occur hence endothermic.

[[File:Surface_Plot11cat3718.png| ]]

MRD:cat3718MRD

2020-05-09T14:29:50Z

Cat3718:

== Molecular reaction dynamics ==
'''
'''Potential energy surface diagram - The transition state:'''

The transition state on an energy surface diagram can be mathematically defined by ∂V('''ri''')/∂'''ri'''=0 which is the maximum point on the minimum energy path between the reactants and products. Which differentiates itself form local minima as local minima are the point on the diagram where the gradient=0 as is the transition state, but the transition state is the maximum point on the minimum energy path where the gradient=0.

[[File:Surface_Plot1cat3718.png| Inter-nuclear distance vs time plot]]

The transition state position rts estimated at 88 pm and can be seen on the distance vs time plot below at 20 fs where AB and BC paths cross. AB then goes into a vibration state whereas BC also has translation energy as shown by the distance increasing after the cross over.

'''Trajectory: Dynamic vs Mep'''

[[File:Surface_Plot2cat3718.png| Dynamic run trajectory]] [[File:Surface_Plot3cat3718.png| MEP run trajectory]]

As seen above in the dynamic surface plot above the path ends with vibration energy when compared to the mep calculation on the right there is clearly no vibration in the reaction path. For inter-nuclear distance vs time, r1 oscillates between 70-78 pm whereas once r2 gets to about 100 pm it just increases linearly as C moves away from AB with constant velocity. For momenta vs time once the nuclei have separated for the dynaimc calculation AB oscillates between 1-3.5 g.mol-1.pm.fs-1 and C levels out at 5 g.mol-1.pm.fs-1 for the mep calculation there is no change in momentum so a flat line is observed. As for the distance vs time for the mep calculation AB stays constant at 75 pm, C moves away and starts to plateau. If initial conditions are swapped for final conditons for the calculation above the distance vs time graph is flipped horizontally and the momenta vs time is flipped vertically.

{| class="wikitable"
!
{| class="wikitable"
!p1/ g.mol-1.pm.fs-1
|}
!p2/ g.mol-1.pm.fs-1
!Etot
!Reactive?
!Description of the dynamics
!Illustration of the trajector
|-
|<nowiki>-2.56</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-414.280</nowiki>
|Yes
|First diatomic AB not vibrating then collision occurs and reaction is successful BC moves away from A whilst vibrating as a new diatomic molecule.
|[[File:Surface_Plot6cat3718.png|Surface_Plot6cat3718.png|200x200px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-4.1</nowiki>
|<nowiki>-420.077</nowiki>
|No
|Collision unsuccessful C moves towards vibrating AB then is repelled and moves away, AB continues to vibrate.
|[[File:Surface_Plot7cat3718.png| |200x200px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-413.977</nowiki>
|Yes
|Collision successful C moves towards AB with greater momentum than the situation above overcomes repulsion and collides successfully making a new diatomic BC which then moves away from A whilst vibrating and A also moves away from BC constant velocity(velocity oscillates between two values but constant if vibrating motion of BC ignored).
|[[File:Surface_Plot8cat3718.png| |200x200px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.1</nowiki>
|<nowiki>-357.277</nowiki>
|No
|Initially successful with BC forms briefly starts vibrating, then B bonds back to A to form AB again so two transition states occur, as can be seen in the surface diagram the path crosses over itself.
|[[File:Surface_Plot9cat3718.png| |200x200px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.6</nowiki>
|<nowiki>-349.477</nowiki>
|Yes
|Successful reaction similar to reaction above in that B bonds to C then back to A except this time bonds back to C forming BC which then moves away from A whilst vibrating. Three crosses in paths on inter-nuclear distance vs time plot these crosses can be seen in the path on the surface plot to the right.
|[[File:Surface_Plot10cat3718.png| |200x200px]]
|}
From the table above it can be concluded that p2 has to be high enough to overcome p1 and that there can be recrossing on barrier for transition state. All calcultions above were at r1=74 pm and r2=200 pm on dynamic type of calculation.

'''Transition state theory vs experimental value:'''

So transition state theory states that based on the reactants and structure of the transition state that the rate of a reaction can be found. TS theory forbids recrossing of products over the transition state, in the penultimate experiment in the table this recrossing occurs showing experimentally transition state theory is not always followed and can be flawed .

'''F-H-H System:'''

For F + H2 ===> HF + H this reaction is exothermic as can be seen in the dip in enthalpy in the surface plot below as the BC distance decreases until it starts to fluctuate between two values when HF is bonded. The reaction path after the reaction takes place shows large oscillations due to the HF vibrations being larger as F is heavier.
[[File:Surface_Plot12cat3718.png| ]]

[[File:Surface_Plot11cat3718.png| ]]

File:Surface Plot12cat3718.png

2020-05-09T14:29:43Z

Cat3718:

File:Surface Plot11cat3718.png

2020-05-09T14:29:26Z

Cat3718:

MRD:cat3718MRD

2019-03-15T10:44:30Z

Cat3718:

===NH3===
'''Molecule:''' Ammonia

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -56.55776873 au

'''RMS Gradient:''' 0.00000485 au

'''Point Group:''' C3v

'''Optimised bond distance:''' 1.04 Å

'''Optimised bond angle:''' 106°

<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>
<script>frame 1.16</script>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718_NH3_OPTF.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718_NH3_OPTF.LOG| here]]

[[File:Cat3718-vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 1090 || 1694 || 1694 || 3641 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image''' || [[File:Cat3718-vib1.png|150px]] || [[File:Cat3718-vib2.png|150px]] || [[File:Cat3718-vib3.png|150px]] || [[File:Cat3718-vib4.png|150px]] || [[File:Cat3718-vib5.png|150px]] || [[File:Cat3718-vib6.png|150px]]
|-
| '''Vibrational mode type:''' || Bending (Umbrella) ||Bending || Bending || Highly Symmetric Stretch || Stretch || Stretch
|}

'''Expected modes of vibration:'''(3x4)-6=6

'''Degenerate modes:''' 1694&1694(cm-1), and 3590&3590(cm-1)

'''Spectrum bands:''' 4

'''Charges'''
[[File:Cat3718 nh3 charge.png|400px]]

Expected charges would be negative on nitrogen and positive on hydrogen as nitrogen is more electronegative than hydrogen
so the electrons are pulled towards the nitrogen as greater effective nuclear charge.

===H2===
'''Molecule:''' Hydrogen

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -1.17853936 au

'''RMS Gradient:''' -0.00000017 au

'''Point Group:''' D∞h

'''Optimised bond distance:''' 0.74 Å

'''Optimised bond angle:''' -

<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>
<script>frame 1.6</script>
<title>H2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Cat3718-h2-optf 3.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:Cat3718-h2-optf 3.LOG| here]]

[[File:Cat3718-h2vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 4466
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-h2vib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

=== Charge distribution H2 ===

[[File:Cat3718-h2-charge.png|300px]]

Both atoms of equal electronegativity so no charge, perfectly covalent.

===N2===
'''Molecule:''' Nitrogen

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -109.52412868 au

'''RMS Gradient:''' 0.00000077 au

'''Point Group:''' D∞h

'''Optimised bond distance:''' 1.11 Å

<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 0.000001 0.001200 YES

</pre>

<jmol><jmolApplet>
<script>frame 1.6</script>
<title>N2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718-N2-OPTF 2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718-N2-OPTF 2.LOG| here]]

[[File:Cat3718-n2vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-n2vib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

=== Charge distribution N2 ===

[[File:Cat3718-n2-charge.png|300px]]

Both atoms of equal electronegativity so no charge, perfectly covalent.

===Mono-metallic TM complex that coordinating N2===

[[File:Cat3718-TMimage.png|300px]]

TM complex that coordinates N2 - https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BALWUG&DatabaseToSearch=Published

.<ref name="TM Complex" />

This Mono-metallic TM complex that coordinates N2 (name:μ2-Dinitrogen)-bis(dicarbonyl-bis(trimethylphosphite)-iron) has the unique identifier BALWUG and has a bond length of 1.13Å which is longer than the optimised bond length of 1.11Å. This could be because the iron surrounding the nitrogen withdraws electron density as it is a transition metal, so this will weaken the bond and therefore lengthen it. Or that in the computer programme when optimised it is in the gaseous state whereas it may not be when calculated otherwise which could effect the bond length.

===Energy of reaction of NH3===

E(NH3)= -56.5577687 au

2*E(NH3)= -113.11554 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.53562 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579 au (-146.47848 kj mol-1)

The energy change is negative and the ammonia product has lower energy than it's gaseous reactants so ammonia is therefore more stable than it's gaseous products.

===CO===

'''Molecule:''' Carbon Monoxide

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' --113.30945314 au

'''RMS Gradient:''' 0.00001828 au

'''Point Group:''' C∞v

'''Optimised bond distance:''' 1.14 Å

<pre>
Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000018 0.001200 YES
</pre>

<jmol><jmolApplet>
<script>frame 1.11</script>
<title>CO</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718-CO-OPTF-2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718-CO-OPTF-2.LOG| here]]

[[File:Cat3718-covibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 2209
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-covib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

=== Charge distribution ===

[[File:Cat3718-cocharge.png|300px]]

As oxygen is more electronegative than carbon the electrons in the covalent bond will be closer to the oxygen, which is why the charge diagram agrees with what the charges should be. Negative on the oxygen and positive on the carbon.
=== Molecular orbitals ===

[[File:Cat3718-columo (2).png|300px]]

This is the LUMO, lowest unoccupied molecular orbital, energy -0.02177 au, this is an anti-bonding orbital.

[[File:Cat3718-cohomo.png|300px]]

This is the HOMO, highest occupied molecular orbital, energy -0.37145 considerably lower in energy than the LUMO, this HOMO is a bonding orbital. The HOMO-LUMO gap determines the strength of interactions this energy gap for CO is -0.34968 au.

[[File:Cat3718-copidegen.png|300px]]

This is a pi orbital of which there are two, both degenerate with an energy of -0.46743 au both bonding orbitals.

[[File:Cat3718-copidegen-2.png|300px]]

This is the other pi orbital, of the same energy -0.46743 au there are 2 electrons in each pi orbital they are both filled.

[[File:Cat3718-loworb.png|300px]]

This is the lowest lying filled orbital with a significantly lower energy of -19.25805 au. This is so much lower in energy as is formed from the 2s atomic orbitals which are much lower lying and more tightly held to the nucleus. They are not very involved in bonding at all as you can see.

===O2===
'''Molecule:''' Oxygen

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -150.25742434 au

'''RMS Gradient:''' 0.00007502 au

'''Point Group:''' D∞h

'''Optimised bond distance:''' 1.22 Å

<pre>

Item Value Threshold Converged?
Maximum Force 0.000130 0.000450 YES
RMS Force 0.000130 0.000300 YES
Maximum Displacement 0.000080 0.001800 YES
RMS Displacement 0.000113 0.001200 YES

</pre>

<jmol><jmolApplet>
<script>frame 1.10</script>
<title>O2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718-O2-OPTF.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718-O2-OPTF.LOG| here]]

[[File:Cat3718-o2vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 1643
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-o2vib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

=== Charge distribution ===

[[File:Cat3718-o2-charge.png|300px]]

Both atoms of equal electronegativity so no charge, perfectly covalent.

<references>
<ref name="TM Complex">H.Berke, W.Bankhardt, G.Huttner, J.von Seyerl, L.Zsolnai, Chemische Berichte, 1981, 114, 2754, DOI: 10.1002/cber.19811140809
.</ref>
</references>

File:Cat3718-n2-charge.png

2019-03-15T10:43:21Z

Cat3718:

2019-03-15T10:30:42Z

Cat3718:

Rep:Mod:WSX4567

2019-03-15T10:29:06Z

Cat3718:

===NH3===
'''Molecule:''' Ammonia

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -56.55776873 au

'''RMS Gradient:''' 0.00000485 au

'''Point Group:''' C3v

'''Optimised bond distance:''' 1.04 Å

'''Optimised bond angle:''' 106

<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>
<script>frame 1.16</script>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718_NH3_OPTF.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718_NH3_OPTF.LOG| here]]

[[File:Cat3718-vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 1090 || 1694 || 1694 || 3641 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image''' || [[File:Cat3718-vib1.png|150px]] || [[File:Cat3718-vib2.png|150px]] || [[File:Cat3718-vib3.png|150px]] || [[File:Cat3718-vib4.png|150px]] || [[File:Cat3718-vib5.png|150px]] || [[File:Cat3718-vib6.png|150px]]
|-
| '''Vibrational mode type:''' || Bending (Umbrella) ||Bending || Bending || Highly Symmetric Stretch || Stretch || Stretch
|}

'''Expected modes of vibration:'''(3x4)-6=6

'''Degenerate modes:''' 1694&1694(cm-1), and 3590&3590(cm-1)

'''Spectrum bands:''' 4

'''Charges'''
[[File:Cat3718 nh3 charge.png|400px]]

Expected charges would be negative on nitrogen and positive on hydrogen as nitrogen is more electronegative than hydrogen
so the electrons are pulled towards the nitrogen as greater effective nuclear charge.

===H2===
'''Molecule:''' Hydrogen

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -1.17853936 au

'''RMS Gradient:''' -0.00000017 au

'''Point Group:''' D∞h

'''Optimised bond distance:''' 0.74 Å

'''Optimised bond angle:''' -

<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>
<script>frame 1.6</script>
<title>H2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Cat3718-h2-optf 3.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:Cat3718-h2-optf 3.LOG| here]]

[[File:Cat3718-h2vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 4466
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-h2vib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

===N2===
'''Molecule:''' Nitrogen

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -109.52412868 au

'''RMS Gradient:''' 0.00000077 au

'''Point Group:''' D∞h

'''Optimised bond distance:''' 1.11 Å

<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 0.000001 0.001200 YES

</pre>

<jmol><jmolApplet>
<script>frame 1.6</script>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718-N2-OPTF 2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718-N2-OPTF 2.LOG| here]]

[[File:Cat3718-n2vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-n2vib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

===Mono-metallic TM complex that coordinating N2===

[[File:Cat3718-TMimage.png|300px]]

TM complex that coordinates N2 - https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BALWUG&DatabaseToSearch=Published

.<ref name="TM Complex" />

This Mono-metallic TM complex that coordinates N2 (name:μ2-Dinitrogen)-bis(dicarbonyl-bis(trimethylphosphite)-iron) has the unique identifier BALWUG and has a bond length of 1.13Å which is longer than the optimised bond length of 1.11Å. This could be because the iron surrounding the nitrogen withdraws electron density as it is a transition metal, so this will weaken the bond and therefore lengthen it. Or that in the computer programme when optimised it is in the gaseous state whereas it may not be when calculated otherwise which could effect the bond length.

===Energy of reaction of NH3===

E(NH3)= -56.5577687 au

2*E(NH3)= -113.11554 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.53562 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579 au (-146.47848 kj mol-1)

The energy change is negative and the ammonia product has lower energy than it's gaseous reactants so ammonia is therefore more stable than it's gaseous products.

===CO===

'''Molecule:''' Carbon Monoxide

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' --113.30945314 au

'''RMS Gradient:''' 0.00001828 au

'''Point Group:''' C∞v

'''Optimised bond distance:''' 1.14 Å

<pre>
Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000018 0.001200 YES
</pre>

<jmol><jmolApplet>
<script>frame 1.11</script>
<title>CO</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718-CO-OPTF-2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718-CO-OPTF-2.LOG| here]]

[[File:Cat3718-covibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 2209
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-covib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

=== Charge distribution ===

[[File:Cat3718-cocharge.png|300px]]

As oxygen is more electronegative than carbon the electrons in the covalent bond will be closer to the oxygen, which is why the charge diagram agrees with what the charges should be. Negative on the oxygen and positive on the carbon.
=== Molecular orbitals ===

[[File:Cat3718-columo (2).png|300px]]

This is the LUMO, lowest unoccupied molecular orbital, energy -0.02177 au, this is an anti-bonding orbital.

[[File:Cat3718-cohomo.png|300px]]

This is the HOMO, highest occupied molecular orbital, energy -0.37145 considerably lower in energy than the LUMO, this HOMO is a bonding orbital. The HOMO-LUMO gap determines the strength of interactions this energy gap for CO is -0.34968 au.

[[File:Cat3718-copidegen.png|300px]]

This is a pi orbital of which there are two, both degenerate with an energy of -0.46743 au both bonding orbitals.

[[File:Cat3718-copidegen-2.png|300px]]

This is the other pi orbital, of the same energy -0.46743 au there are 2 electrons in each pi orbital they are both filled.

[[File:Cat3718-loworb.png|300px]]

This is the lowest lying filled orbital with a significantly lower energy of -19.25805 au. This is so much lower in energy as is formed from the 2s atomic orbitals which are much lower lying and more tightly held to the nucleus. They are not very involved in bonding at all as you can see.

===O2===
'''Molecule:''' Oxygen

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -150.25742434 au

'''RMS Gradient:''' 0.00007502 au

'''Point Group:''' D∞h

'''Optimised bond distance:''' 1.22 Å



Item Value Threshold Converged?
Maximum Force 0.000130 0.000450 YES
RMS Force 0.000130 0.000300 YES
Maximum Displacement 0.000080 0.001800 YES
RMS Displacement 0.000113 0.001200 YES



<jmol><jmolApplet>
<script>frame 1.11</script>
<title>CO</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718-CO-OPTF-2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718-CO-OPTF-2.LOG| here]]

[[File:Cat3718-o2vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 2209
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-o2vib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

=== Charge distribution ===

[[File:Cat3718-o2-charge.png|300px]]

Both atoms of equal electronegativity so no charge, perfectly covalent.

<references>
<ref name="TM Complex">H.Berke, W.Bankhardt, G.Huttner, J.von Seyerl, L.Zsolnai, Chemische Berichte, 1981, 114, 2754, DOI: 10.1002/cber.19811140809
.</ref>
</references>

File:Cat3718-o2-charge.png

2019-03-15T10:27:10Z

Cat3718:

File:Cat3718-o2vibtable.png

2019-03-15T10:26:36Z

Cat3718:

2019-03-15T09:24:41Z

Cat3718:

===NH3===
'''Molecule:''' Ammonia

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -56.55776873 au

'''RMS Gradient:''' 0.00000485 au

'''Point Group:''' C3v

'''Optimised bond distance:''' 1.04 Å

'''Optimised bond angle:''' 106

<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>
<script>frame 1.16</script>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718_NH3_OPTF.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718_NH3_OPTF.LOG| here]]

[[File:Cat3718-vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 1090 || 1694 || 1694 || 3641 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 14 || 14 || 1 || 0 || 0
|-
| '''Image''' || [[File:Cat3718-vib1.png|150px]] || [[File:Cat3718-vib2.png|150px]] || [[File:Cat3718-vib3.png|150px]] || [[File:Cat3718-vib4.png|150px]] || [[File:Cat3718-vib5.png|150px]] || [[File:Cat3718-vib6.png|150px]]
|-
| '''Vibrational mode type:''' || Bending (Umbrella) ||Bending || Bending || Highly Symmetric Stretch || Stretch || Stretch
|}

'''Expected modes of vibration:'''(3x4)-6=6

'''Degenerate modes:''' 1694&1694(cm-1), and 3590&3590(cm-1)

'''Spectrum bands:''' 4

'''Charges'''
[[File:Cat3718 nh3 charge.png|400px]]

Expected charges would be negative on nitrogen and positive on hydrogen as nitrogen is more electronegative than hydrogen
so the electrons are pulled towards the nitrogen as greater effective nuclear charge.

===H2===
'''Molecule:''' Hydrogen

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -1.17853936 au

'''RMS Gradient:''' -0.00000017 au

'''Point Group:''' D∞h

'''Optimised bond distance:''' 0.74 Å

'''Optimised bond angle:''' -

<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>
<script>frame 1.16</script>
<title>H2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Cat3718-h2-optf 3.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:Cat3718-h2-optf 3.LOG| here]]

[[File:Cat3718-h2vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 4466
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-h2vib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

===N2===
'''Molecule:''' Nitrogen

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' -109.52412868 au

'''RMS Gradient:''' 0.00000077 au

'''Point Group:''' D∞h

'''Optimised bond distance:''' 1.11 Å

<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 0.000001 0.001200 YES

</pre>

<jmol><jmolApplet>
<script>frame 1.16</script>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718-N2-OPTF 2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718-N2-OPTF 2.LOG| here]]

[[File:Cat3718-n2vibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 2457
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-n2vib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

===Mono-metallic TM complex that coordinating N2===

[[File:Cat3718-TMimage.png|300px]]

[[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=BALWUG&DatabaseToSearch=Published| Mono-metallic TM complex that coordinates N2]].<ref name="TM Complex" />

This Mono-metallic TM complex that coordinates N2 (name:μ2-Dinitrogen)-bis(dicarbonyl-bis(trimethylphosphite)-iron) has the unique identifier BALWUG and has a bond length of 1.13Å which is longer than the optimised bond length of 1.11Å. This could be because the iron surrounding the nitrogen withdraws electron density as it is a transition metal, so this will weaken the bond and therefore lengthen it. Or that in the computer programme when optimised it is in the gaseous state whereas it may not be when calculated otherwise which could effect the bond length.

===Energy of reaction of NH3===

E(NH3)= -56.5577687 au

2*E(NH3)= -113.11554 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.53562 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579 au (-146.47848 kj mol-1)

The energy change is negative and the ammonia product has lower energy than it's gaseous reactants so ammonia is therefore more stable than it's gaseous products.

===CO===

'''Molecule:''' Carbon Monoxide

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(d.p.)

'''Final energy:''' --113.30945314 au

'''RMS Gradient:''' 0.00001828 au

'''Point Group:''' D∞h

'''Optimised bond distance:''' 1.14 Å

<pre>
Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000018 0.001200 YES
</pre>

<jmol><jmolApplet>
<script>frame 1.11</script>
<title>CO</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CAT3718-CO-OPTF-2.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:CAT3718-CO-OPTF-2.LOG| here]]

[[File:File:Cat3718-covibtable.png|300px]]

[[File:Cat3718-covibtable.png|300px]]

{| class="wikitable" border="1"
|+ '''Display Vibrations'''
|-
| '''Wavenumber''' cm-1|| 2209
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:Cat3718-covib.png|150px]]
|-
| '''Vibrational mode type:''' || Symmetrical stretch
|}

=== Charge distribution ===

[[File:Cat3718-cocharge.png|300px]]

As oxygen is more electronegative than carbon the electrons in the covalent bond will be closer to the oxygen, which is why the charge diagram agrees with what the charges should be. Negative on the oxygen and positive on the carbon.
=== Molecular orbitals ===

[[File:Cat3718-columo (2).png|300px]]

This is the LUMO, lowest unoccupied molecular orbital, energy -0.02177 au, this is an anti-bonding orbital.

[[File:Cat3718-cohomo.png|300px]]

This is the HOMO, highest occupied molecular orbital, energy -0.37145 considerably lower in energy than the LUMO, this HOMO is a bonding orbital. The HOMO-LUMO gap determines the strength of interactions this energy gap for CO is -0.34968 au.

[[File:Cat3718-copidegen.png|300px]]

This is a pi orbital of which there are two, both degenerate with an energy of -0.46743 au both bonding orbitals.

[[File:Cat3718-copidegen-2.png|300px]]

This is the other pi orbital, of the same energy -0.46743 au there are 2 electrons in each pi orbital they are both filled.

[[File:Cat3718-loworb.png|300px]]

This is the lowest lying filled orbital with a significantly lower energy of -19.25805 au. This is so much lower in energy as is formed from the 2s atomic orbitals which are much lower lying and more tightly held to the nucleus. They are not very involved in bonding at all as you can see.

<references>
<ref name="TM Complex">H.Berke, W.Bankhardt, G.Huttner, J.von Seyerl, L.Zsolnai, Chemische Berichte, 1981, 114, 2754, DOI: 10.1002/cber.19811140809
.</ref>
</references>