ChemWiki - User contributions [en]

MRD:01533219

2020-05-22T18:49:27Z

Vi4018:

=='''Molecular Reaction Dynamics'''==

=== H + H2 System ===

==== Dynamics from the transition state region ====

'''1. On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?''' ''

Mathematically, a transition state is a maximum point on the plot i.e. the first derivative of energy with the respect to position is zero and the second derivative is negative. Because it's second derivative is negative it can be distinguished from a local minimum as the local minimum will have a positive second derivative.

'''2. Report your best estimate of the transition state position (rts) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.''' ''

Transition state occurs when r1=r2. Due to the nature of the transition state explained above, if one starts a trajectory at the transition state, with both momentums being equal to zero (p1=p2=0), it will remain there and never fall off. There is also no vibrational motion. Using Internuclear Distance vs Time plot (figure 1) it was estimated that rts is about 90.8 pm.

[[File:01533219-Transition state H+H2.png|thumb|Figure 1: Internuclear vs. Time plot for H + H2 | centre]]

'''3. Comment on how the mep and the trajectory you just calculated differ.''' ''
Reaction path when r1=rts+1 and r2=rts can be plotted using two ways: MEP or Dynamic Method. In the calculation of the MEP velocities are reset to zero each step which results in a shorter path compared to dynamic method. Also unlike MEP, the dynamic method takes into the account the oscillations of the molecule.

[[File:01533219-H_Dynamics.png|thumb|Figure 2: Contour plot using Dynamics | centre]]
[[File:01533219-H_MEP.png|thumb|Figure 3: Contour plot using MEP | centre]]

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

For the initial positions r1 = 74 pm and r2 = 200 pm, trajectories with the following momenta were run.

{| class="wikitable" border=1
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || Yes || Reaction pathway goes through the transition state and exits through the products channel. || [[File:MRD01533219-first.png|400px|]]
|-
| -3.1 || -4.1 || -433.787 || No || Reaction does not proceed as the energy barrier is not crossed due to reactants not possesing enough energy. || [[File:MRD01533219-second.png|400px|]]
|-
| -3.1 || -5.1 || -413.977 || Yes || Reaction pathway goes through the transition state and exits through the products channel. || [[File:MRD01533219-third.png|400px|]]
|-
| -5.1 || -10.1 || -357.277 || No || Reactants have enough energy to proceed through the energy barrier. However, reactants are then reformed due to barrier recrossing.|| [[File:MRD01533219-fourth.png|400px|]]
|-
| -5.1 || -10.6 || -349.477 || Yes || Reaction pathway crosses the transition state multiple times and then exits through the products channel. || [[File:MRD01533219-fifth.png|400px|]]
|}

From this table we can conclude that it is not enough for the system to just have enough energy to cross the energy barrier, due to the possibility of barrier recrossing. Vibrational modes must also be considered.

'''1. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?'''

Main assumption of TST is that once the transition state is crossed, reactants cannot reform1. However from reaction 4 in the table above we can see that it is experimentally possible. This would lead to the overestimation of the reaction rate by TST compared to the actual reaction rate.

=== F-H-H System ===

==== PES inspection ====

'''1. By inspecting the potential energy surfaces, classify the F + H2 and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved?'''

F+H2 is an exothermic reaction while H + HF is an endothermic reaction. This can be seen in figure 4. This shows that the H-F bond is lower in energy and therefore stronger than the H-H bond.

[[File:01533219-H_F_Surface Plot.png|thumb|Figure 4: Surface plot of F + H2 reaction | centre]]

'''2. Locate the approximate position of the transition state.'''

Hammond's postulate states that the transition state resembles either reactants or the products, whichever it is closer in energy2. Because F+H2 is an exothermic, transition state will be closer in energy to F+H2 (reactants) and therefore resemble it, meaning that the distances should be similar to the ones present in F+H2 system. By trial and error and setting momentums to zero, the approximate position of the transition state was found to be at rFH=181 pm and rHH=74.5 pm. This can be confirmed by the Internuclear Distances vs Time plot on which there are no oscillations of the lines.

[[File:01533219-H_F_Internuclear.png|thumb|Figure 5: Internuclear Distances vs Time plot for F + H2/ H + HF transition state | centre]]

'''3. Report the activation energy for both reactions.'''

The energy of the transition state = -433.981 kJ/mol

''' F+H2 '''

rHF was set to 1000 pm and rHH was set to 74.5 pm. The energy of this state is -435.057 kJ/mol. Therefore the activation energy is:
-433.981 + 435.057 = 1.076 kJ/mol
This is a relatively small activation energy which is expected as this reaction is exothermic so the transition state is similar energetically to the starting material.

''' H + HF '''

rHF was set to 91 pm and rHH was now set to 1000 pm. The energy of this state is -560.404 kJ/mol. Therefore the activation energy is:
-433.981 + 560.404 = 126.43 kJ/mol
This higher than for F+H2 reaction as expected as H + HF endothermic and the transition state will resemble products energetically rather than the reactants.

==== Reaction Dynamics ====

'''1. In light of the fact that energy is conserved, discuss the mechanism of release of the reaction energy. Explain how this could be confirmed experimentally.'''

Initial parameters:

rFH = 170 pm, pFH=-0.5 g.mol-1.pm.fs-1

rHH = 75 pm, pFH=0 g.mol-1.pm.fs-1

From the figure 6 it can be seen that the total energy is conserved while kinetic and potential energies are constantly interchanging. From this figure, it can also be seen that H-F bond has greater oscillations than the H-H bond. Therefore it can be suggested that the energy released (exothermic reaction) is used to make H-F bond oscillate. To confirm this experimentally IR spectroscopy can be employed to measure the difference in the vibrational energy of the reactants compared to the products.

[[File:01533219-Conservation_Of_Energy.png|thumb|Figure 6: Internuclear Distances vs Time plot for F + H2/ H + HF transition state | centre]]

'''2. Discuss how the distribution of energy between different modes (translation and vibration) affect the efficiency of the reaction, and how this is influenced by the position of the transition state.'''

Polanyi's empirical rules3 lead to the fact that the initial states with high translational energy promote reactions with an early transition state (exothermic) while the initial states with high vibrational energy promote reactions with late transition state (endothermic). Therefore it is more efficient for H + HF to have higher vibrational energy rather than the translational energy and for F + H2 it is better to have higher translational energy.

=== References ===

1. Atkins, P., De Paula, J. and Keeler, J., n.d. Atkins' Physical Chemistry. 11th ed. New York: Oxford University Press, p.792.

2. Clayden, J., 2004. Organic Chemistry. 2nd ed. New York: Oxford University Press, p.989.

3. Guo, H. and Liu, K., 2016. Control of chemical reactivity by transition-state and beyond. Chemical Science, 7(7), pp.3992-4003.

File:01533219-Conservation Of Energy.png

2020-05-22T18:30:18Z

Vi4018:

File:01533219-H F Internuclear.png

2020-05-22T18:26:32Z

Vi4018:

File:01533219-H F Surface Plot.png

2020-05-22T18:22:20Z

Vi4018:

File:01533219-H MEP.png

2020-05-22T18:18:46Z

Vi4018:

File:01533219-H Dynamics.png

2020-05-22T18:18:24Z

Vi4018:

File:01533219-Transition state H+H2.png

2020-05-22T18:13:59Z

Vi4018:

File:MRD01533219-fifth.png

2020-05-22T14:42:19Z

Vi4018:

File:MRD01533219-fourth.png

2020-05-22T14:42:07Z

Vi4018:

File:MRD01533219-third.png

2020-05-22T14:41:19Z

Vi4018:

File:MRD01533219-second.png

2020-05-22T14:40:54Z

Vi4018:

MRD:01533219

2020-05-21T19:08:06Z

Vi4018:

=='''Molecular Reaction Dynamics'''==

=== H + H2===

==== Dynamics from the transition state region ====

'''1. On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?''' ''

Mathematically, a transition state is a maximum point on the plot i.e. the first derivative of energy with the respect to position is zero and the second derivative is negative. Because it's second derivative is negative it can be distinguished from a local minimum as the local minimum will have a positive second derivative.

'''2. Report your best estimate of the transition state position (rts) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.''' ''

Transition state occurs when r1=r2. Due to the nature of the transition state explained above, if one starts a trajectory at the transition state, with both momentums being equal to zero (p1=p2=0), it will remain there and never fall off. There is also no vibrational motion. Using Internuclear Distance vs Time plot it was estimated that rts is about 90.8 pm

'''3. Comment on how the mep and the trajectory you just calculated differ.''' ''
Reaction path when r1=rts+1 and r2=rts can be plotted using two ways: MEP or Dynamic Method. In the calculation of the MEP velocities are reset to zero each step which results in a shorter path compared to dynamic method. Also unlike MEP, the dynamic method takes into the account the oscillations of the molecule.

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

For the initial positions r1 = 74 pm and r2 = 200 pm, trajectories with the following momenta were run.

{| class="wikitable" border=1
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || Yes || Reaction pathway goes through the transition state and exits through the products channel. || [[File:MRD01533219-first.png|400px|]]
|-
| -3.1 || -4.1 || -433.787 || No || Reaction does not proceed as the energy barrier is not crossed due to reactants not possesing enough energy. ||
|-
| -3.1 || -5.1 || -413.977 || Yes || Reaction pathway goes through the transition state and exits through the products channel. ||
|-
| -5.1 || -10.1 || -357.277 || No || Reactants have enough energy to proceed through the energy barrier. However, reactants are then reformed due to barrier recrossing.||
|-
| -5.1 || -10.6 || -349.477 || Yes || Reaction pathway crosses the transition state multiple times and then exits through the products channel. ||
|}

From this table we can conclude that it is not enough for the system to just have enough energy to cross the energy barrier, due to the possibility of barrier recrossing. Vibrational modes must also be considered.

'''1. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?'''

Main assumption of TST is that once the transition state is crossed, reactants cannot reform. However from reaction 4 in the table above we can see that it is experimentally possible. This would lead to the overestimation of the reaction rate by TST compared to the actual reaction rate.

File:MRD01533219-first.png

2020-05-21T19:05:16Z

Vi4018:

MRD:01533219

2020-05-21T18:50:23Z

Vi4018:

=='''Molecular Reaction Dynamics'''==

=== H + H2===

==== Dynamics from the transition state region ====

'''1. On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?''' ''

Mathematically, a transition state is a maximum point on the plot i.e. the first derivative of energy with the respect to position is zero and the second derivative is negative. Because it's second derivative is negative it can be distinguished from a local minimum as the local minimum will have a positive second derivative.

'''2. Report your best estimate of the transition state position (rts) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.''' ''

Transition state occurs when r1=r2. Due to the nature of the transition state explained above, if one starts a trajectory at the transition state, with both momentums being equal to zero (p1=p2=0), it will remain there and never fall off. There is also no vibrational motion. Using Internuclear Distance vs Time plot it was estimated that rts is about 90.8 pm

'''3. Comment on how the mep and the trajectory you just calculated differ.''' ''
Reaction path when r1=rts+1 and r2=rts can be plotted using two ways: MEP or Dynamic Method. In the calculation of the MEP velocities are reset to zero each step which results in a shorter path compared to dynamic method. Also unlike MEP, the dynamic method takes into the account the oscillations of the molecule.

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

For the initial positions r1 = 74 pm and r2 = 200 pm, trajectories with the following momenta were run.

{| class="wikitable" border=1
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || Yes || Reaction pathway goes through the transition state and exits through the products channel. ||
|-
| -3.1 || -4.1 || -433.787 || No || Reaction does not proceed as the energy barrier is not crossed due to reactants not possesing enough energy. ||
|-
| -3.1 || -5.1 || -413.977 || Yes || Reaction pathway goes through the transition state and exits through the products channel. ||
|-
| -5.1 || -10.1 || -357.277 || No || Reactants have enough energy to proceed through the energy barrier. However, reactants are then reformed due to barrier recrossing.||
|-
| -5.1 || -10.6 || -349.477 || Yes || Reaction pathway crosses the transition state multiple times and then exits through the products channel. ||
|}

From this table we can conclude that it is not enough for the system to just have enough energy to cross the energy barrier, due to the possibility of barrier recrossing. Vibrational modes must also be considered.

'''1. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?'''

Main assumption of TST is that once the transition state is crossed, reactants cannot reform. However from reaction 4 in the table above we can see that it is experimentally possible. This would lead to the overestimation of the reaction rate by TST compared to the actual reaction rate.

MRD:01533219

2020-05-21T18:24:12Z

Vi4018:

=='''Molecular Reaction Dynamics'''==

=== H + H2===

==== Dynamics from the transition state region ====

'''1. On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?''' ''

Mathematically, a transition state is a maximum point on the plot i.e. the first derivative of energy with the respect to position is zero and the second derivative is negative. Because it's second derivative is negative it can be distinguished from a local minimum as the local minimum will have a positive second derivative.

'''2. Report your best estimate of the transition state position (rts) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.''' ''

Transition state occurs when r1=r2. Due to the nature of the transition state explained above, if one starts a trajectory at the transition state, with both momentums being equal to zero (p1=p2=0), it will remain there and never fall off. There is also no vibrational motion. Using Internuclear Distance vs Time plot it was estimated that rts is about 90.8 pm

'''3. Comment on how the mep and the trajectory you just calculated differ.''' ''
Reaction path when r1=rts+1 and r2=rts can be plotted using two ways: MEP or Dynamic Method. In the calculation of the MEP velocities are reset to zero each step which results in a shorter path compared to dynamic method. Also unlike MEP, the dynamic method takes into the account the oscillations of the molecule.

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

For the initial positions r1 = 74 pm and r2 = 200 pm, trajectories with the following momenta were run.

{| class="wikitable" border=1
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || Yes || Reaction pathway goes through the transition state and exits through the products channel. ||
|-
| -3.1 || -4.1 || -433.787 || No || Reaction does not proceed as the energy barrier is not crossed due to reactants not possesing enough energy. ||
|-
| -3.1 || -5.1 || -413.977 || Yes || Reaction pathway goes through the transition state and exits through the products channel. ||
|-
| -5.1 || -10.1 || -357.277 || No || Reactants have enough energy to proceed through the energy barrier. However, reactants are then reformed due to barrier recrossing.||
|-
| -5.1 || -10.6 || -349.477 || Yes || Reaction pathway crosses the transition state multiple times and then exits through the products channel. ||
|}

MRD:01533219

2020-05-21T17:27:27Z

Vi4018: Created page with "=='''Molecular Reaction Dynamics'''== === H + H2=== ==== Dynamics from the transition state region ==== '''1. On a potential energy surface diagram, how is the t..."

Rep:MOD:VI4018

2019-02-22T14:09:49Z

Vi4018:

== '''Molecular Modelling Lab''' ==
=== '''NH3 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_NH3_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: C3v

Final energy: -56.55776873 au

RMS gradient: 0.00000485 au

Bond length: 1.01798 Å

Bond angle: 105.741°

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986273D-10
Optimization completed.
</pre>

[[File:VI_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_NH3_Vibrations.PNG]]

{| class="wikitable" border="1"
| '''wavenumber''' cm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 13.6 || 13.6 || 1.06 || 0.271 || 0.271
|-
| '''Image''' || [[File:VI_vibration_1090.PNG|200px]] || [[File:VI_vibration_1964(1).PNG|200px]] || [[File:VI_vibration_1964(2).PNG|200px]] || [[File:VI_vibration_3461.PNG|200px]] || [[File:VI_vibration_3490(1).PNG|200px]] || [[File:VI_vibration_3490(2).PNG|200px]]
|}

From The 3N-6 rule 6 modes are expected because there are 4 atoms in the ammonia molecule. There are 2 modes with the wavenumber of 1694 cm-1 and 2 modes with the wavenumber of 3590 cm-1. This means they are degenerate. Vibrations at 1090 and 1694 cm-1 are bending while vibrations at 3461 and 3590 cm-1 are stretching. Vibrations at 1090 and 3461 cm-1 have A1 symmetry and are highly symmetrical. Vibration at 1090 also is commonly known as the "umbrella" mode. In the IR spectrum, there are 4 peaks present, with 2 of them being clearly visible.

[[File:VI_IR_Spectrum.PNG|800px]]

==== Charge ====

[[File:VI_Charge.PNG|300px]]

Nitrogen is more electronegative atom than hydrogen. It will have more electron density around it and therefore will be negatively charged while hydrogen atoms will be positively charged. Overall ammonia molecule is neutral so individual charges on the atoms must cancel out and they do give an overall charge of 0.

=== '''N2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> N2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_N2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞h

Final energy: -109.52412868 au

RMS gradient: 0.00000060 au

Bond length: 1.10550 Å

Bond angle: 180°

[[File:VI_n2_Item.PNG]]

[[File:VI_n2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_n2_vibrations.PNG]]

{| class="wikitable" border="1"
| '''Wavenumber''' cm-1 || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_n2_vibration_2457.PNG|200px]]
|}

N2 is a linear molecule so 3N-5 expression is used to determine the number of vibrational modes available to the molecule. N2 has two atoms so it has one vibrational mode available to it. This mode is a stretching vibration which doesn't lead to the change in dipole in a molecule so it is IR inactive.

==== Charge ====

[[File:VI_n2_charge.PNG]]

N2 consists of the atoms of the same element with the same electronegativity, therefore, there is no partial charge on any of the atoms. The overall charge of the molecule is 0.

=== '''H2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> H2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_H2_OPTF_POP.LOG </uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_H2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞h

Final energy: -1.17853936 au

RMS gradient: 0.00000017 au

Bond length: 0.74279 Å

Bond angle: 180°

[[File:VI_h2_item.PNG]]

[[File:VI_h2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_h2_vibrations.PNG]]

{| class="wikitable" border="1"
| '''Wavenumber''' cm-1 || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_h2_vibration_4466.PNG|200px]]
|}

H2 is a linear molecule so 3N-5 expression is used to determine the number of vibrational modes available to the molecule. H2 has two atoms so the number of vibrational modes is 1. It is a stretching vibration which doesn't lead to the change in the dipole mode so it is IR inactive.

==== Charge ====

[[File:VI_h2_charge.PNG]]

H2 consists of the same atoms with the same electronegativity so there are no partial charges on any of the atoms. The overall charge of the molecule is 0.

=== '''Transition Metal Complex''' ===

==== Structure ====

Unique Identifier: VEJSOV

Link: https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VEJSOV&DatabaseToSearch=Published

[[File:VI_Complex_diagram.PNG]] [[File:VI_Complex.PNG|400px]]

==== Bond length between Nitrogens ====

Bond length: 1.1165 Å

Bond length between nitrogens in the transition metal complex is longer than in the nitrogen molecule because one of the nitrogens donates the lone pair to the transition metal. This makes it positively charged and the electrons in the triple bond move towards it. This decreases the electron density between the nitrogens and therefore lowers the length of the bond.

=== '''Energy of Haber-Bosch process''' ===

==== Calculation ====

N2 + 3H2 -> 2NH3

E(NH3)= -56.55776873 au

2*E(NH3)= -113.11553746 au

E(N2)= -109.52412868 au

E(H2)= -1.17853936

3*E(H2)= -3.53561808

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au

1 kJ/mol = 0.00038 au

Therefore ΔE = -146.5 kJ/mol

The negative sign indicates that the reaction is exothermic and that the product is more stable than the reactants.

=== '''SH2 Molecule''' ===
==== Optimisation ====

[[Media:VI_SH2_OPTF_POP.LOG | LOG file]]

<jmol><jmolApplet>
<title> SH2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_SH2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C2v

Final energy: -399.39162414 au

RMS gradient: 0.00012068 au

Bond length: 1.34737 Å

Bond angle: 92.681°

[[File:VI_sh2_item.PNG]]

[[File:VI_sh2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_sh2_vibrations.PNG]]

{| class="wikitable" border="1"
| '''Wavenumber''' cm-1 || 1224 || 2692 || 2712
|-
| '''Symmetry''' || A1 || A1 || B2
|-
| '''Intensity''' arbitrary units || 4.92 || 6.73 || 8.62
|-
| '''Image''' || [[File:VI_sh2_vibration_1224.PNG|200px]] || [[File:VI_sh2_vibration_2692.PNG|200px]] || [[File:VI_sh2_vibration_2712.PNG|200px]]
|
|}

[[File:VI_sh2_spectrum.PNG|800px]]

SH2 is a non-linear molecule so to predict the number of vibrational modes 3N-6. There are three atoms in the molecule so three vibrational modes are expected. As can be seen from the IR spectrum they are all IR active as they lead to a change of dipole in the molecule.

==== Charge ====

[[File:VI_sh2_charge.PNG]]

Sulphur is more electronegative than hydrogens, therefore, has a partial negative charge and hydrogens have a partial positive charge. The overall charge of the molecule is 0 and the sum partial charges of each atom adds up to 0.

==== Molecular Orbitals ====

{| class="wikitable" border="1"
| [[File:VI_sh2_mo_s_bonding.PNG]] || [[File:VI_sh2_mo_lone_pair.PNG|300px]] || [[File:VI_sh2_mo_LUMO.PNG|300px]] || [[File:VI_sh2_mo_p_and_s.PNG|300px]] || [[File:VI_sh2_mo_hybridised.PNG|300px]]
|-
| This a bonding orbital between sulphur's 3s orbital and both hydrogen's 1s orbitals. A molecular orbital is occupied and has an energy value of -0.74654 au. || This is a HOMO of the hydrogen sulfide. The lone pair of the 3p orbital on the sulphur is responsible for it and the orbital has an energy value of -0.26181 au. HOMO plays an important part in the reactions because in a lot of the reactions a HOMO of one molecule interacts with the LUMO of another. || This is the LUMO of the hydrogen sulfide. It is an antibonding orbital formed by an overlap of a 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of 0.02126 au. LUMO plays a big role in the reaction as that's where usually the electron pair from the nucleophile goes to break the existing bond. || This is a bonding orbital formed by an overlap between 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.44963 au. || This is a bonding orbital formed by an overlap of the mixing of the 3p and 2s orbitals on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.36725 au.
|}

Rep:MOD:VI4018

2019-02-22T14:06:26Z

Vi4018:

== '''Molecular Modelling Lab''' ==
=== '''NH3 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_NH3_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: C3v

Final energy: -56.55776873 au

RMS gradient: 0.00000485 au

Bond length: 1.01798 Å

Bond angle: 105.741°

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986273D-10
Optimization completed.
</pre>

[[File:VI_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_NH3_Vibrations.PNG]]

{| class="wikitable" border="1"
| '''wavenumber''' cm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 13.6 || 13.6 || 1.06 || 0.271 || 0.271
|-
| '''Image''' || [[File:VI_vibration_1090.PNG|200px]] || [[File:VI_vibration_1964(1).PNG|200px]] || [[File:VI_vibration_1964(2).PNG|200px]] || [[File:VI_vibration_3461.PNG|200px]] || [[File:VI_vibration_3490(1).PNG|200px]] || [[File:VI_vibration_3490(2).PNG|200px]]
|}

From The 3N-6 rule 6 modes are expected because there are 4 atoms in the ammonia molecule. There are 2 modes with the wavenumber of 1694 cm-1 and 2 modes with the wavenumber of 3590 cm-1. This means they are degenerate. Vibrations at 1090 and 1694 cm-1 are bending while vibrations at 3461 and 3590 cm-1 are stretching. Vibrations at 1090 and 3461 cm-1 have A1 symmetry and are highly symmetrical. Vibration at 1090 also is commonly known as the "umbrella" mode. In the IR spectrum there are 4 peaks present, with 2 of them being clearly visible.

[[File:VI_IR_Spectrum.PNG|800px]]

==== Charge ====

[[File:VI_Charge.PNG|300px]]

Nitrogen is more electronegative atom than hydrogen. It will have more electron density around it and therefore will be negatively charged while hydrogen atoms will ve positevly charged. Overall ammonia molecule is neutral so individual charges on the atoms must cancel out and they do give an overall charge of 0.

=== '''N2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> N2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_N2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞h

Final energy: -109.52412868 au

RMS gradient: 0.00000060 au

Bond length: 1.10550 Å

Bond angle: 180°

[[File:VI_n2_Item.PNG]]

[[File:VI_n2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_n2_vibrations.PNG]]

{| class="wikitable" border="1"
| '''Wavenumber''' cm-1 || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_n2_vibration_2457.PNG|200px]]
|}

N2 is a linear molecule so 3N-5 expression is used to determine the number of vibrational modes available to the molecule. N2 has two atoms so it has one vibrational mode available to it. This mode is a stretching vibration which doesn't lead to the change in dipole in a molecule so it is IR inactive.

==== Charge ====

[[File:VI_n2_charge.PNG]]

N2 consists of the atoms of the same element with the same electronegativity, therefore, there is no partial charge on any of the atoms. The overall charge of the molecule is 0.

=== '''H2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> H2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_H2_OPTF_POP.LOG </uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_H2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞h

Final energy: -1.17853936 au

RMS gradient: 0.00000017 au

Bond length: 0.74279 Å

Bond angle: 180°

[[File:VI_h2_item.PNG]]

[[File:VI_h2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_h2_vibrations.PNG]]

{| class="wikitable" border="1"
| '''Wavenumber''' cm-1 || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_h2_vibration_4466.PNG|200px]]
|}

H2 is a linear molecule so 3N-5 expression is used to determine the number of vibrational modes available to the molecule. H2 has two atoms so the number of vibrational modes is 1. It is a strecthing vibration which doesn't lead to the change in the dipole mode so it is IR inactive.

==== Charge ====

[[File:VI_h2_charge.PNG]]

H2 consists of the same atoms with the same electronegativity so there are no partial charges on any of the atoms. The overall charge of the molecule is 0.

=== '''Transition Metal Complex''' ===

==== Structure ====

Unique Identifier: VEJSOV

Link: https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VEJSOV&DatabaseToSearch=Published

[[File:VI_Complex_diagram.PNG]] [[File:VI_Complex.PNG|400px]]

==== Bond length between Nitrogens ====

Bond length: 1.1165 Å

Bond length between nitrogens in the transition metal complex is longer than in the nitrogen molecule because one of the nitrogens donates the lone pair to the transition metal. This makes it positively charged and the electrons in the triple bond move towards it. This decreases the electron density between the nitrogens and therefore lowers the length of the bond.

=== '''Energy of Haber-Bosch process''' ===

==== Calculation ====

N2 + 3H2 -> 2NH3

E(NH3)= -56.55776873 au

2*E(NH3)= -113.11553746 au

E(N2)= -109.52412868 au

E(H2)= -1.17853936

3*E(H2)= -3.53561808

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au

1 kJ/mol = 0.00038 au

Therefore ΔE = -146.5 kJ/mol

The negative sign indicates that the reaction is exothermic and that the product is more stable than the reactants.

=== '''SH2 Molecule''' ===
==== Optimisation ====

[[Media:VI_SH2_OPTF_POP.LOG | LOG file]]

<jmol><jmolApplet>
<title> SH2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_SH2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C2v

Final energy: -399.39162414 au

RMS gradient: 0.00012068 au

Bond length: 1.34737 Å

Bond angle: 92.681°

[[File:VI_sh2_item.PNG]]

[[File:VI_sh2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_sh2_vibrations.PNG]]

{| class="wikitable" border="1"
| '''Wavenumber''' cm-1 || 1224 || 2692 || 2712
|-
| '''Symmetry''' || A1 || A1 || B2
|-
| '''Intensity''' arbitrary units || 4.92 || 6.73 || 8.62
|-
| '''Image''' || [[File:VI_sh2_vibration_1224.PNG|200px]] || [[File:VI_sh2_vibration_2692.PNG|200px]] || [[File:VI_sh2_vibration_2712.PNG|200px]]
|
|}

[[File:VI_sh2_spectrum.PNG|800px]]

SH2 is a non-linear molecule so to predict the number of vibrational modes 3N-6. There are three atoms in the molecule so three vibrational modes are expected. As can be seen from the IR spectrum they are all IR active as they lead to a change of dipole in the molecule.

==== Charge ====

[[File:VI_sh2_charge.PNG]]

Sulphur is more electronegative than hydrogens, therefore, has a partial negative charge and hydrogens have a partial positive charge. The overall charge of the molecule is 0 and the sum partial charges of the each atom adds up to 0.

==== Molecular Orbitals ====

{| class="wikitable" border="1"
| [[File:VI_sh2_mo_s_bonding.PNG]] || [[File:VI_sh2_mo_lone_pair.PNG|300px]] || [[File:VI_sh2_mo_LUMO.PNG|300px]] || [[File:VI_sh2_mo_p_and_s.PNG|300px]] || [[File:VI_sh2_mo_hybridised.PNG|300px]]
|-
| This a bonding orbital between sulphur's 3s orbital and both hydrogen's 1s orbitals. Molecular orbital is occupied and has an energy value of -0.74654 au. || This is a HOMO of the hydrogen sulfide. The lone pair of the 3p orbital on the sulphur is responsible for it and the orbital has an energy value of -0.26181 au. HOMO plays an important part in the reactions because in a lot of the reactions a HOMO of one molecule interacts with the LUMO of another. || This is the LUMO of the hydrogen sulfide. It is an antibonding orbital formed by an overlap of a 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of 0.02126 au. LUMO plays a big role in the reaction as that's where usually the electron pair from the nucleophile goes to break the existing bond. || This is a bonding orbital formed by an overlap between 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.44963 au. || This is a bonding orbital formed by an overlap of the mixing of the 3p and 2s orbitals on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.36725 au.
|}

Rep:MOD:VI4018

2019-02-22T14:01:46Z

Vi4018:

== '''Molecular Modelling Lab''' ==
=== '''NH3 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_NH3_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: C3v

Final energy: -56.55776873 au

RMS gradient: 0.00000485 au

Bond length: 1.01798 Å

Bond angle: 105.741°

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986273D-10
Optimization completed.
</pre>

[[File:VI_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_NH3_Vibrations.PNG]]

{| class="wikitable" border="1"
| '''wavenumber''' cm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 13.6 || 13.6 || 1.06 || 0.271 || 0.271
|-
| '''Image''' || [[File:VI_vibration_1090.PNG|200px]] || [[File:VI_vibration_1964(1).PNG|200px]] || [[File:VI_vibration_1964(2).PNG|200px]] || [[File:VI_vibration_3461.PNG|200px]] || [[File:VI_vibration_3490(1).PNG|200px]] || [[File:VI_vibration_3490(2).PNG|200px]]
|}

From The 3N-6 rule 6 modes are expected because there are 4 atoms in the ammonia molecule. There are 2 modes with the wavenumber of 1694 cm-1 and 2 modes with the wavenumber of 3590 cm-1. This means they are degenerate. Vibrations at 1090 and 1694 cm-1 are bending while vibrations at 3461 and 3590 cm-1 are stretching. Vibrations at 1090 and 3461 cm-1 have A1 symmetry and are highly symmetrical. Vibration at 1090 also is commonly known as the "umbrella" mode. In the IR spectrum there are 4 peaks present, with 2 of them being clearly visible.

[[File:VI_IR_Spectrum.PNG|800px]]

==== Charge ====

[[File:VI_Charge.PNG|300px]]

Nitrogen is more electronegative atom than hydrogen. It will have more electron density around it and therefore will be negatively charged while hydrogen atoms will ve positevly charged. Overall ammonia molecule is neutral so individual charges on the atoms must cancel out and they do give an overall charge of 0.

=== '''N2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> N2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_N2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -109.52412868 au

RMS gradient: 0.00000060 au

Bond length: 1.10550 Å

Bond angle: 180°

[[File:VI_n2_Item.PNG]]

[[File:VI_n2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_n2_vibrations.PNG]]

{| class="wikitable" border="1"
| '''Wavenumber''' cm-1 || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_n2_vibration_2457.PNG|200px]]
|}

N2 is a linear molecule so 3N-5 expression is used to determine the number of vibrational modes available to the molecule. N2 has two atoms so it has one vibrational mode available to it. This mode is a stretching vibration which doesn't lead to the change in dipole in a molecule so it is IR inactive.

==== Charge ====

[[File:VI_n2_charge.PNG]]

N2 consists of the atoms of the same element with the same electronegativity, therefore, there is no partial charge on any of the atoms. The overall charge of the molecule is 0.

=== '''H2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> H2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_H2_OPTF_POP.LOG </uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_H2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -1.17853936 au

RMS gradient: 0.00000017 au

Bond length: 0.74279 Å

Bond angle: 180°

[[File:VI_h2_item.PNG]]

[[File:VI_h2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_h2_vibrations.PNG]]

{| class="wikitable" border="1"
| '''Wavenumber''' cm-1 || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_h2_vibration_4466.PNG|200px]]
|}

H2 is a linear molecule so 3N-5 expression is used to determine the number of vibrational modes available to the molecule. H2 has two atoms so the number of vibrational modes is 1. It is a strecthing vibration which doesn't lead to the change in the dipole mode so it is IR inactive.

==== Charge ====

[[File:VI_h2_charge.PNG]]

H2 consists of the same atoms with the same electronegativity so there are no partial charges on any of the atoms. The overall charge of the molecule is 0.

=== '''Transition Metal Complex''' ===

==== Structure ====

Unique Identifier: VEJSOV

Link: https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VEJSOV&DatabaseToSearch=Published

[[File:VI_Complex_diagram.PNG]] [[File:VI_Complex.PNG|400px]]

==== Bond length between Nitrogens ====

Bond length: 1.1165 Å

Bond length between nitrogens in the transition metal complex is longer than in the nitrogen molecule because one of the nitrogens donates the lone pair to the transition metal. This makes it positively charged and the electrons in the triple bond move towards it. This decreases the electron density between the nitrogens and therefore lowers the length of the bond.

=== '''Energy of Haber-Bosch process''' ===

==== Calculation ====

N2 + 3H2 -> 2NH3

E(NH3)= -56.55776873 au

2*E(NH3)= -113.11553746 au

E(N2)= -109.52412868 au

E(H2)= -1.17853936

3*E(H2)= -3.53561808

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au

1 kJ/mol = 0.00038 au

Therefore ΔE = -146.5 kJ/mol

The negative sign indicates that the reaction is exothermic and that the product is more stable than the reactants.

=== '''SH2 Molecule''' ===
==== Optimisation ====

[[Media:VI_SH2_OPTF_POP.LOG | LOG file]]

<jmol><jmolApplet>
<title> SH2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_SH2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C2v

Final energy: -399.39162414 au

RMS gradient: 0.00012068 au

Bond length: 1.34737 Å

Bond angle: 92.681°

[[File:VI_sh2_item.PNG]]

[[File:VI_sh2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_sh2_vibrations.PNG]]

{| class="wikitable" border="1"
| '''Wavenumber''' cm-1 || 1224 || 2692 || 2712
|-
| '''Symmetry''' || A1 || A1 || B2
|-
| '''Intensity''' arbitrary units || 4.92 || 6.73 || 8.62
|-
| '''Image''' || [[File:VI_sh2_vibration_1224.PNG|200px]] || [[File:VI_sh2_vibration_2692.PNG|200px]] || [[File:VI_sh2_vibration_2712.PNG|200px]]
|
|}

[[File:VI_sh2_spectrum.PNG|800px]]

SH2 is a non-linear molecule so to predict the number of vibrational modes 3N-6. There are three atoms in the molecule so three vibrational modes are expected. As can be seen from the IR spectrum they are all IR active as they lead to a change of dipole in the molecule.

==== Charge ====

[[File:VI_sh2_charge.PNG]]

Sulphur is more electronegative than hydrogens, therefore, has a partial negative charge and hydrogens have a partial positive charge. The overall charge of the molecule is 0 and the sum partial charges of the each atom adds up to 0.

==== Molecular Orbitals ====

{| class="wikitable" border="1"
| [[File:VI_sh2_mo_s_bonding.PNG]] || [[File:VI_sh2_mo_lone_pair.PNG|300px]] || [[File:VI_sh2_mo_LUMO.PNG|300px]] || [[File:VI_sh2_mo_p_and_s.PNG|300px]] || [[File:VI_sh2_mo_hybridised.PNG|300px]]
|-
| This a bonding orbital between sulphur's 3s orbital and both hydrogen's 1s orbitals. Molecular orbital is occupied and has an energy value of -0.74654 au. || This is a HOMO of the hydrogen sulfide. The lone pair of the 3p orbital on the sulphur is responsible for it and the orbital has an energy value of -0.26181 au. HOMO plays an important part in the reactions because in a lot of the reactions a HOMO of one molecule interacts with the LUMO of another. || This is the LUMO of the hydrogen sulfide. It is an antibonding orbital formed by an overlap of a 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of 0.02126 au. LUMO plays a big role in the reaction as that's where usually the electron pair from the nucleophile goes to break the existing bond. || This is a bonding orbital formed by an overlap between 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.44963 au. || This is a bonding orbital formed by an overlap of the mixing of the 3p and 2s orbitals on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.36725 au.
|}

Rep:MOD:VI4018

2019-02-22T13:59:34Z

Vi4018:

== '''Molecular Modelling Lab''' ==
=== '''NH3 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_NH3_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: C3v

Final energy: -56.55776873 au

RMS gradient: 0.00000485 au

Bond length: 1.01798 Å

Bond angle: 105.741°

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986273D-10
Optimization completed.
</pre>

[[File:VI_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_NH3_Vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''wavenumber''' cm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 13.6 || 13.6 || 1.06 || 0.271 || 0.271
|-
| '''Image''' || [[File:VI_vibration_1090.PNG|200px]] || [[File:VI_vibration_1964(1).PNG|200px]] || [[File:VI_vibration_1964(2).PNG|200px]] || [[File:VI_vibration_3461.PNG|200px]] || [[File:VI_vibration_3490(1).PNG|200px]] || [[File:VI_vibration_3490(2).PNG|200px]]
|}

From The 3N-6 rule 6 modes are expected because there are 4 atoms in the ammonia molecule. There are 2 modes with the wavenumber of 1694 cm-1 and 2 modes with the wavenumber of 3590 cm-1. This means they are degenerate. Vibrations at 1090 and 1694 cm-1 are bending while vibrations at 3461 and 3590 cm-1 are stretching. Vibrations at 1090 and 3461 cm-1 have A1 symmetry and are highly symmetrical. Vibration at 1090 also is commonly known as the "umbrella" mode. In the IR spectrum there are 4 peaks present, with 2 of them being clearly visible.

[[File:VI_IR_Spectrum.PNG|800px]]

==== Charge ====

[[File:VI_Charge.PNG|300px]]

Nitrogen is more electronegative atom than hydrogen. It will have more electron density around it and therefore will be negatively charged while hydrogen atoms will ve positevly charged. Overall ammonia molecule is neutral so individual charges on the atoms must cancel out and they do give an overall charge of 0.

=== '''N2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> N2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_N2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -109.52412868 au

RMS gradient: 0.00000060 au

Bond length: 1.10550 Å

Bond angle: 180°

[[File:VI_n2_Item.PNG]]

[[File:VI_n2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_n2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_n2_vibration_2457.PNG|200px]]
|}

N2 is a linear molecule so 3N-5 expression is used to determine the number of vibrational modes available to the molecule. N2 has two atoms so it has one vibrational mode available to it. This mode is a stretching vibration which doesn't lead to the change in dipole in a molecule so it is IR inactive.

==== Charge ====

[[File:VI_n2_charge.PNG]]

N2 consists of the atoms of the same element with the same electronegativity, therefore, there is no partial charge on any of the atoms. The overall charge of the molecule is 0.

=== '''H2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> H2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_H2_OPTF_POP.LOG </uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_H2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -1.17853936 au

RMS gradient: 0.00000017 au

Bond length: 0.74279 Å

Bond angle: 180°

[[File:VI_h2_item.PNG]]

[[File:VI_h2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_h2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_h2_vibration_4466.PNG|200px]]
|}

H2 is a linear molecule so 3N-5 expression is used to determine the number of vibrational modes available to the molecule. H2 has two atoms so the number of vibrational modes is 1. It is a strecthing vibration which doesn't lead to the change in the dipole mode so it is IR inactive.

==== Charge ====

[[File:VI_h2_charge.PNG]]

H2 consists of the same atoms with the same electronegativity so there are no partial charges on any of the atoms. The overall charge of the molecule is 0.

=== '''Transition Metal Complex''' ===

==== Structure ====

Unique Identifier: VEJSOV

Link: https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VEJSOV&DatabaseToSearch=Published

[[File:VI_Complex_diagram.PNG]] [[File:VI_Complex.PNG|400px]]

==== Bond length between Nitrogens ====

Bond length: 1.1165 Å

Bond length between nitrogens in the transition metal complex is longer than in the nitrogen molecule because one of the nitrogens donates the lone pair to the transition metal. This makes it positively charged and the electrons in the triple bond move towards it. This decreases the electron density between the nitrogens and therefore lowers the length of the bond.

=== '''Energy of Haber-Bosch process''' ===

==== Calculation ====

N2 + 3H2 -> 2NH3

E(NH3)= -56.55776873 au

2*E(NH3)= -113.11553746 au

E(N2)= -109.52412868 au

E(H2)= -1.17853936

3*E(H2)= -3.53561808

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au

1 kJ/mol = 0.00038 au

Therefore ΔE = -146.5 kJ/mol

The negative sign indicates that the reaction is exothermic and that the product is more stable than the reactants.

=== '''SH2 Molecule''' ===
==== Optimisation ====

[[Media:VI_SH2_OPTF_POP.LOG | LOG file]]

<jmol><jmolApplet>
<title> SH2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_SH2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C2v

Final energy: -399.39162414 au

RMS gradient: 0.00012068 au

Bond length: 1.34737 Å

Bond angle: 92.681°

[[File:VI_sh2_item.PNG]]

[[File:VI_sh2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_sh2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 1224 || 2692 || 2712
|-
| '''Symmetry''' || A1 || A1 || B2
|-
| '''Intensity''' arbitrary units || 4.92 || 6.73 || 8.62
|-
| '''Image''' || [[File:VI_sh2_vibration_1224.PNG|200px]] || [[File:VI_sh2_vibration_2692.PNG|200px]] || [[File:VI_sh2_vibration_2712.PNG|200px]]
|
|}

[[File:VI_sh2_spectrum.PNG|800px]]

SH2 is a non-linear molecule so to predict the number of vibrational modes 3N-6. There are three atoms in the molecule so three vibrational modes are expected. As can be seen from the IR spectrum they are all IR active as they lead to a change of dipole in the molecule.

==== Charge ====

[[File:VI_sh2_charge.PNG]]

Sulphur is more electronegative than hydrogens, therefore, has a partial negative charge and hydrogens have a partial positive charge. The overall charge of the molecule is 0 and the sum partial charges of the each atom adds up to 0.

==== Molecular Orbitals ====

{| class="wikitable" border="1"
|+ caption
| [[File:VI_sh2_mo_s_bonding.PNG]] || [[File:VI_sh2_mo_lone_pair.PNG|300px]] || [[File:VI_sh2_mo_LUMO.PNG|300px]] || [[File:VI_sh2_mo_p_and_s.PNG|300px]] || [[File:VI_sh2_mo_hybridised.PNG|300px]]
|-
| This a bonding orbital between sulphur's 3s orbital and both hydrogen's 1s orbitals. Molecular orbital is occupied and has an energy value of -0.74654 au. || This is a HOMO of the hydrogen sulfide. The lone pair of the 3p orbital on the sulphur is responsible for it and the orbital has an energy value of -0.26181 au. HOMO plays an important part in the reactions because in a lot of the reactions a HOMO of one molecule interacts with the LUMO of another. || This is the LUMO of the hydrogen sulfide. It is an antibonding orbital formed by an overlap of a 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of 0.02126 au. LUMO plays a big role in the reaction as that's where usually the electron pair from the nucleophile goes to break the existing bond. || This is a bonding orbital formed by an overlap between 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.44963 au. || This is a bonding orbital formed by an overlap of the mixing of the 3p and 2s orbitals on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.36725 au.
|}

Rep:MOD:VI4018

2019-02-22T11:48:25Z

Vi4018:

== '''Molecular Modelling Lab''' ==
=== '''NH3 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_NH3_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: C3v

Final energy: -56.55776873 au

RMS gradient: 0.00000485 au

Bond length: 1.01798 Å

Bond angle: 105.741°

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986273D-10
Optimization completed.
</pre>

[[File:VI_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_NH3_Vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''wavenumber''' cm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 13.6 || 13.6 || 1.06 || 0.271 || 0.271
|-
| '''Image''' || [[File:VI_vibration_1090.PNG|200px]] || [[File:VI_vibration_1964(1).PNG|200px]] || [[File:VI_vibration_1964(2).PNG|200px]] || [[File:VI_vibration_3461.PNG|200px]] || [[File:VI_vibration_3490(1).PNG|200px]] || [[File:VI_vibration_3490(2).PNG|200px]]
|}

From The 3N-6 rule 6 modes are expected because there are 4 atoms in the ammonia molecule. There are 2 modes with the wavenumber of 1694 cm-1 and 2 modes with the wavenumber of 3590 cm-1. This means they are degenerate. Vibrations at 1090 and 1694 cm-1 are bending while vibrations at 3461 and 3590 cm-1 are stretching. Vibrations at 1090 and 3461 cm-1 have A1 symmetry and are highly symmetrical. Vibration at 1090 also is commonly known as the "umbrella" mode. In the IR spectrum there are 4 peaks present, with 2 of them being clearly visible.

[[File:VI_IR_Spectrum.PNG|800px]]

==== Charge ====

[[File:VI_Charge.PNG|300px]]

Nitrogen is more electronegative atom than hydrogen. It will have more electron density around it and therefore will be negatively charged while hydrogen atoms will ve positevly charged. Overall ammonia molecule is neutral so individual charges on the atoms must cancel out and they do give an overall charge of 0.

=== '''N2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> N2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_N2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -109.52412868 au

RMS gradient: 0.00000060 au

Bond length: 1.10550 Å

Bond angle: 180°

[[File:VI_n2_Item.PNG]]

[[File:VI_n2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_n2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_n2_vibration_2457.PNG|200px]]
|}

==== Charge ====

[[File:VI_n2_charge.PNG]]

=== '''H2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> H2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_H2_OPTF_POP.LOG </uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

[[Media:VI_H2_OPTF_POP.LOG | LOG file]]

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -1.17853936 au

RMS gradient: 0.00000017 au

Bond length: 0.74279 Å

Bond angle: 180°

[[File:VI_h2_item.PNG]]

[[File:VI_h2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_h2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_h2_vibration_4466.PNG|200px]]
|}

==== Charge ====

[[File:VI_h2_charge.PNG]]

=== '''Transition Metal Complex''' ===

==== Structure ====

Unique Identifier: VEJSOV

Link: https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=VEJSOV&DatabaseToSearch=Published

[[File:VI_Complex_diagram.PNG]] [[File:VI_Complex.PNG|400px]]

==== Bond length between Nitrogens ====

Bond length: 1.1165 Å

Bond length between nitrogens in the transition metal complex is longer than in the nitrogen molecule because one of the nitrogens donates the lone pair to the transition metal. This makes it positively charged and the electrons in the triple bond move towards it. This decrease the elctron density between the nitrogens and therefore lowers the length of the bond.

=== '''Energy of Haber-Bosch process''' ===

==== Calculation ====

N2 + 3H2 -> 2NH3

E(NH3)= -56.55776873 au

2*E(NH3)= -113.11553746 au

E(N2)= -109.52412868 au

E(H2)= -1.17853936

3*E(H2)= -3.53561808

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au

1 kJ/mol = 0.00038 au

Therefore ΔE = -146.5 kJ/mol

=== '''SH2 Molecule''' ===
==== Optimisation ====

[[Media:VI_SH2_OPTF_POP.LOG | LOG file]]

<jmol><jmolApplet>
<title> SH2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_SH2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C2v

Final energy: -399.39162414 au

RMS gradient: 0.00012068 au

Bond length: 1.34737 Å

Bond angle: 92.681°

[[File:VI_sh2_item.PNG]]

[[File:VI_sh2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_sh2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 1224 || 2692 || 2712
|-
| '''Symmetry''' || A1 || A1 || B2
|-
| '''Intensity''' arbitrary units || 4.92 || 6.73 || 8.62
|-
| '''Image''' || [[File:VI_sh2_vibration_1224.PNG|200px]] || [[File:VI_sh2_vibration_2692.PNG|200px]] || [[File:VI_sh2_vibration_2712.PNG|200px]]
|
|}

[[File:VI_sh2_spectrum.PNG|800px]]

==== Charge ====

[[File:VI_sh2_charge.PNG]]

==== Molecular Orbitals ====

[[File:VI_sh2_mo_s_bonding.PNG]] This a bonding orbital between sulphur's 3s orbital and both hydrogen's 1s orbitals. Molecular orbital is occupied and has an energy value of -0.74654 au.

[[File:VI_sh2_mo_lone_pair.PNG|300px]] This is a HOMO of the hydrogen sulfide. The lone pair of the 3p orbital on the sulphur is responsible for it and the orbital has an energy value of -0.26181 au.

[[File:VI_sh2_mo_LUMO.PNG|300px]] This is the LUMO of the hydrogen sulfide. It is an antibonding orbital formed by an overlap of a 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of 0.02126 au. LUMO plays a big role in the reaction as that's where usually the electron pair from the nucleophile goes to break the existing bond.

[[File:VI_sh2_mo_p_and_s.PNG|300px]] This is a bonding orbital formed by an overlap between 2p orbital on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.44963 au.

[[File:VI_sh2_mo_hybridised.PNG|300px]] This is a bonding orbital formed by an overlap of the mixing of the 3p and 2s orbitals on the sulphur and 1s orbital on each of the hydrogens. It has an energy value of -0.36725 au.

File:VI NH3 OPTF POP.LOG

2019-02-22T11:29:50Z

Vi4018: Vi4018 uploaded a new version of File:VI NH3 OPTF POP.LOG

File:VI sh2 mo hybridised.PNG

2019-02-22T11:13:13Z

Vi4018:

File:VI sh2 mo p and s.PNG

2019-02-22T11:03:10Z

Vi4018:

Rep:MOD:VI4018

2019-02-22T10:58:15Z

Vi4018:

== '''Project Molecule''' ==
=== '''NH3 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C3v

Final energy: -56.55776873 au

RMS gradient: 0.00000485 au

Bond length: 1.01798 Å

Bond angle: 105.741

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986273D-10
Optimization completed.
</pre>

[[File:VI_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_NH3_Vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''wavenumber''' cm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 13.6 || 13.6 || 1.06 || 0.271 || 0.271
|-
| '''Image''' || [[File:VI_vibration_1090.PNG|200px]] || [[File:VI_vibration_1964(1).PNG|200px]] || [[File:VI_vibration_1964(2).PNG|200px]] || [[File:VI_vibration_3461.PNG|200px]] || [[File:VI_vibration_3490(1).PNG|200px]] || [[File:VI_vibration_3490(2).PNG|200px]]
|}

From The 3N-6 rule 6 modes are expected because there are 4 atoms in the ammonia molecule. There are 2 modes with the wavenumber of 1694 cm-1 and 2 modes with the wavenumber of 3590 cm-1. This means they are degenerate. Vibrations at 1090 and 1694 cm-1 are bending while vibrations at 3461 and 3590 cm-1 are stretching. Vibrations at 1090 and 3461 cm-1 have A1 symmetry and are highly symmetrical. Vibration at 1090 also is commonly known as the "umbrella" mode. In the IR spectrum there are 4 peaks present, with 2 of them being clearly visible.

[[File:VI_IR_Spectrum.PNG|800px]]

==== Charge ====

[[File:VI_Charge.PNG|300px]]

Nitrogen is more electronegative atom than hydrogen. It will have more electron density around it and therefore will be negatively charged while hydrogen atoms will ve positevly charged. Overall ammonia molecule is neutral so individual charges on the atoms must cancel out and they do give an overall charge of 0.

=== '''N2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> N2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -109.52412868 au

RMS gradient: 0.00000060 au

Bond length: 1.10550 Å

Bond angle: 180

[[File:VI_n2_Item.PNG]]

[[File:VI_n2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_n2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_n2_vibration_2457.PNG|200px]]
|}

==== Charge ====

[[File:VI_n2_charge.PNG]]

=== '''H2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> H2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_H2_OPTF_POP.LOG </uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -1.17853936 au

RMS gradient: 0.00000017 au

Bond length: 0.74279 Å

Bond angle: 180

[[File:VI_h2_item.PNG]]

[[File:VI_h2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_h2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_h2_vibration_4466.PNG|200px]]
|}

==== Charge ====

[[File:VI_h2_charge.PNG]]

=== '''Transition Metal Complex''' ===

==== Structure ====

Unique Identifier: VEJSOV

[[File:VI_Complex_diagram.PNG]] [[File:VI_Complex.PNG|400px]]

==== Bond length between Nitrogens ====

Bond length: 1.1165 Å

Bond length between nitrogens in the transition metal complex is longer than in the nitrogen molecule because one of the nitrogens donates the lone pair to the transition metal. This makes it positively charged and the electrons in the triple bond move towards it. This decrease the elctron density between the nitrogens and therefore lowers the length of the bond.

=== '''Energy of Haber-Bosch process''' ===

==== Calculation ====

N2 + 3H2 -> 2NH3

E(NH3)= -56.55776873 au

2*E(NH3)= -113.11553746 au

E(N2)= -109.52412868 au

E(H2)= -1.17853936

3*E(H2)= -3.53561808

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au

1 kJ/mol = 0.00038 au

Therefore ΔE = -146.48 kJ/mol

=== '''SH2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> SH2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_SH2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C2v

Final energy: -399.39162414 au

RMS gradient: 0.00012068 au

Bond length: 1.34737 Å

Bond angle: 180

[[File:VI_sh2_item.PNG]]

[[File:VI_sh2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_sh2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 1224 || 2692 || 2712
|-
| '''Symmetry''' || A1 || A1 || B2
|-
| '''Intensity''' arbitrary units || 4.92 || 6.73 || 8.62
|-
| '''Image''' || [[File:VI_sh2_vibration_1224.PNG|200px]] || [[File:VI_sh2_vibration_2692.PNG|200px]] || [[File:VI_sh2_vibration_2712.PNG|200px]]
|
|}

[[File:VI_sh2_spectrum.PNG|800px]]

==== Charge ====

[[File:VI_sh2_charge.PNG]]

==== Molecular Orbitals ====

[[File:VI_sh2_mo_s_bonding.PNG]] This a bonding orbital between sulphur's 3s orbital and both hydrogen's 1s orbitals. Molecular orbital is occupied and has an energy value of -0.74654 au.

[[File:VI_sh2_mo_lone_pair.PNG]] This is a HOMO of the hydrogen sulfide. The lone pair of the 3p orbital on the sulphur is responsible for it and the orbital has an energy value of -0.26181 au.

[[File:VI_sh2_mo_LUMO.PNG]] This is the LUMO of the hydrogen sulfide. It is an antibonding orbital formed by an overlap of a 2p orbital on the sulphur and 1s orbital on each of the hydrogens.

File:VI sh2 mo LUMO.PNG

2019-02-22T10:44:56Z

Vi4018:

File:VI sh2 mo lone pair.PNG

2019-02-22T10:38:09Z

Vi4018:

File:VI sh2 mo s bonding.PNG

2019-02-22T10:12:12Z

Vi4018:

Rep:MOD:VI4018

2019-02-22T09:44:29Z

Vi4018:

== '''Project Molecule''' ==
=== '''NH3 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C3v

Final energy: -56.55776873 au

RMS gradient: 0.00000485 au

Bond length: 1.01798 Å

Bond angle: 105.741

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986273D-10
Optimization completed.
</pre>

[[File:VI_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_NH3_Vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''wavenumber''' cm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 13.6 || 13.6 || 1.06 || 0.271 || 0.271
|-
| '''Image''' || [[File:VI_vibration_1090.PNG|200px]] || [[File:VI_vibration_1964(1).PNG|200px]] || [[File:VI_vibration_1964(2).PNG|200px]] || [[File:VI_vibration_3461.PNG|200px]] || [[File:VI_vibration_3490(1).PNG|200px]] || [[File:VI_vibration_3490(2).PNG|200px]]
|}

From The 3N-6 rule 6 modes are expected because there are 4 atoms in the ammonia molecule. There are 2 modes with the wavenumber of 1694 cm-1 and 2 modes with the wavenumber of 3590 cm-1. This means they are degenerate. Vibrations at 1090 and 1694 cm-1 are bending while vibrations at 3461 and 3590 cm-1 are stretching. Vibrations at 1090 and 3461 cm-1 have A1 symmetry and are highly symmetrical. Vibration at 1090 also is commonly known as the "umbrella" mode. In the IR spectrum there are 4 peaks present, with 2 of them being clearly visible.

[[File:VI_IR_Spectrum.PNG|800px]]

==== Charge ====

[[File:VI_Charge.PNG|300px]]

Nitrogen is more electronegative atom than hydrogen. It will have more electron density around it and therefore will be negatively charged while hydrogen atoms will ve positevly charged. Overall ammonia molecule is neutral so individual charges on the atoms must cancel out and they do give an overall charge of 0.

=== '''N2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> N2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -109.52412868 au

RMS gradient: 0.00000060 au

Bond length: 1.10550 Å

Bond angle: 180

[[File:VI_n2_Item.PNG]]

[[File:VI_n2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_n2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_n2_vibration_2457.PNG|200px]]
|}

==== Charge ====

[[File:VI_n2_charge.PNG]]

=== '''H2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> H2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_H2_OPTF_POP.LOG </uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -1.17853936 au

RMS gradient: 0.00000017 au

Bond length: 0.74279 Å

Bond angle: 180

[[File:VI_h2_item.PNG]]

[[File:VI_h2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_h2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' arbitrary units || 0
|-
| '''Image''' || [[File:VI_h2_vibration_4466.PNG|200px]]
|}

==== Charge ====

[[File:VI_h2_charge.PNG]]

=== '''Transition Metal Complex''' ===

==== Structure ====

Unique Identifier: VEJSOV

[[File:VI_Complex_diagram.PNG]] [[File:VI_Complex.PNG|400px]]

==== Bond length between Nitrogens ====

Bond length: 1.1165 Å

=== '''Energy of Haber-Bosch process''' ===

N2 + 3H2 -> 2NH3

E(NH3)= -56.55776873 au

2*E(NH3)= -113.11553746 au

E(N2)= -109.52412868 au

E(H2)= -1.17853936

3*E(H2)= -3.53561808

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au

1 kJ/mol = 0.00038 au

Therefore ΔE = -146.48 kJ/mol

=== '''SH2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> SH2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_SH2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C2v

Final energy: -399.39162414 au

RMS gradient: 0.00012068 au

Bond length: 1.34737 Å

Bond angle: 180

[[File:VI_sh2_item.PNG]]

[[File:VI_sh2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_sh2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 1224 || 2692 || 2712
|-
| '''Symmetry''' || A1 || A1 || B2
|-
| '''Intensity''' arbitrary units || 4.92 || 6.73 || 8.62
|-
| '''Image''' || [[File:VI_sh2_vibration_1224.PNG|200px]] || [[File:VI_sh2_vibration_2692.PNG|200px]] || [[File:VI_sh2_vibration_2712.PNG|200px]]
|
|}

[[File:VI_sh2_spectrum.PNG|800px]]

==== Charge ====

[[File:VI_sh2_charge.PNG]]

File:VI sh2 charge.PNG

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Vi4018:

File:VI sh2 spectrum.PNG

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Vi4018:

File:VI sh2 vibration 1224.PNG

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Vi4018:

File:VI sh2 vibration 2692.PNG

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Vi4018:

File:VI sh2 vibration 2712.PNG

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Vi4018:

File:VI sh2 vibrations.PNG

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Vi4018:

File:VI sh2 Energy And Gradient.PNG

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Vi4018:

File:VI sh2 item.PNG

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Vi4018:

File:VI SH2 OPTF POP.LOG

2019-02-22T09:11:27Z

Vi4018: Vi4018 uploaded a new version of File:VI SH2 OPTF POP.LOG

Rep:MOD:VI4018

2019-02-21T20:32:26Z

Vi4018:

== '''Project Molecule''' ==
=== '''NH3 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: C3v

Final energy: -56.55776873 au

RMS gradient: 0.00000485 au

Bond length: 1.01798 Å

Bond angle: 105.741

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986273D-10
Optimization completed.
</pre>

[[File:VI_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_NH3_Vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''wavenumber''' cm-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590
|-
| '''Symmetry''' || A1 || E || E || A1 || E || E
|-
| '''Intensity''' arbitrary units || 145 || 13.6 || 13.6 || 1.06 || 0.271 || 0.271
|-
| '''Image''' || [[File:VI_vibration_1090.PNG|200px]] || [[File:VI_vibration_1964(1).PNG|200px]] || [[File:VI_vibration_1964(2).PNG|200px]] || [[File:VI_vibration_3461.PNG|200px]] || [[File:VI_vibration_3490(1).PNG|200px]] || [[File:VI_vibration_3490(2).PNG|200px]]
|}

From The 3N-6 rule 6 modes are expected because there are 4 atoms in the ammonia molecule. There are 2 modes with the wavenumber of 1694 cm-1 and 2 modes with the wavenumber of 3590 cm-1. This means they are degenerate. Vibrations at 1090 and 1694 cm-1 are bending while vibrations at 3461 and 3590 cm-1 are stretching. Vibrations at 1090 and 3461 cm-1 have A1 symmetry and are highly symmetrical. Vibration at 1090 also is commonly known as the "umbrella" mode. In the IR spectrum there are 4 peaks present, with 2 of them being clearly visible.

[[File:VI_IR_Spectrum.PNG|800px]]

==== Charge ====

[[File:VI_Charge.PNG|300px]]

Nitrogen is more electronegative atom than hydrogen. It will have more electron density around it and therefore will be negatively charged while hydrogen atoms will ve positevly charged. Overall ammonia molecule is neutral so individual charges on the atoms must cancel out and they do give an overall charge of 0.

=== '''N2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> N2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_N2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -109.52412868 au

RMS gradient: 0.00000060 au

Bond length: 1.10550 Å

Bond angle: 180

[[File:VI_n2_Item.PNG]]

[[File:VI_n2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_n2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 2457
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' || 0
|-
| '''Image''' || [[File:VI_n2_vibration_2457.PNG|200px]]
|}

==== Charge ====

[[File:VI_n2_charge.PNG]]

=== '''H2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> H2 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_H2_OPTF_POP.LOG </uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

Method: RB3LYP

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

Symmetry/Point group: D∞

Final energy: -1.17853936 au

RMS gradient: 0.00000017 au

Bond length: 0.74279 Å

Bond angle: 180

[[File:VI_h2_item.PNG]]

[[File:VI_h2_Energy_And_Gradient.PNG|800px]]

==== Vibrations ====

[[File:VI_h2_vibrations.PNG]]

{| class="wikitable" border="1"
|+ caption
| '''Wavenumber''' cm-1 || 4466
|-
| '''Symmetry''' || SGG
|-
| '''Intensity''' || 0
|-
| '''Image''' || [[File:VI_h2_vibration_4466.PNG|200px]]
|}

==== Charge ====

[[File:VI_h2_charge.PNG]]

=== '''Transition Metal Complex''' ===

==== Structure ====

Unique Identifier: VEJSOV

[[File:VI_Complex_diagram.PNG]] [[File:VI_Complex.PNG|400px]]

==== Bond length between Nitrogens ====

Bond length: 1.1165 Å

=== '''Energy of Haber-Bosch process''' ===

N2 + 3H2 -> 2NH3

E(NH3)= -56.55776873 au

2*E(NH3)= -113.11553746 au

E(N2)= -109.52412868 au

E(H2)= -1.17853936

3*E(H2)= -3.53561808

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au

1 kJ/mol = 0.00038 au

Therefore ΔE = -146.48 kJ/mol

=== '''SH2 Molecule''' ===
==== Optimisation ====

<jmol><jmolApplet>
<title> NH3 Molecule </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>VI_SH2_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.16</script>
</jmolApplet></jmol>

File:VI SH2 OPTF POP.LOG

2019-02-21T20:30:19Z

Vi4018: Vi4018 uploaded a new version of File:VI SH2 OPTF POP.LOG

File:VI SH2 OPTF POP.LOG

2019-02-21T20:21:31Z

Vi4018:

Rep:MOD:VI4018

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Vi4018:

File:VI Complex.PNG

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Vi4018:

File:VI Complex diagram.PNG

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Vi4018:

Rep:MOD:VI4018

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Vi4018:

File:VI h2 charge.PNG

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Vi4018:

File:VI h2 vibration 4466.PNG

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File:VI h2 vibrations.PNG

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File:VI h2 Energy And Gradient.PNG

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File:VI h2 item.PNG

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