ChemWiki - User contributions [en]

MRD:cd1618

2020-05-08T14:05:59Z

Cd1618: /* Questions and Answers */

== Questions and Answers ==

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?

A saddle point is a point on the potential surface that the slope in orthogonal directions are zero and is not a local minimum or maximum.
It can be identified by finding the first-order saddle point on potential energy surface.
To differentiate saddle point from a local minimum, second partial derivative test can be done. Taking two orthogonal curves on potential surface both orthogonal to z axis, if the product of the second derivatives of the is negative, then it is a saddle point. However for a local minimum, the product of second derivatives and the curvature are positive, which indicates the energy goes up in all directions.

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.

rts= 91 pm All atoms in this system are hydrogen atoms. In this case, a symmetric transition state is expected, the Internuclear Distances vs Time graph confirmed that the distances between AB and BC are the same.

[[File:TScd1618.png|250px]]

3.Comment on how the mep and the trajectory you just calculated differ.

Dynamic calculation makes trajectory vibrate more at the valley, because it considers the vibration of the bond.
Minimum energy path calculation resets momenta to zero in each step, so there is no bond vibration, the trajectory is more like a smooth curve.

4.Complete the table above by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?

{| class="wikitable" border="1"
|+ Reactive and unreactive trajectories
! 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 || Reactive || after TS, more bond vibration is observed || [[File:-2.56-5.1cd1618.png|150px]]
|-
| -3.1 || -4.1 || -420.077 || Unreactive || fail to reach TS || [[File:-3.1-4.1cd1618.png|150px]]
|-
| -3.1 || -5.1 || -413.977 || Reactive || a reactive trajectory with more vibrational energy || [[File:-3.1-5.1cd1618.png|150px]]
|-
| -5.1 || -10.1 || -357.277 || Unreactive || energy is too high, barrier recrossed || [[File:-5.1-10.1cd1618.png|150px]]
|-
| -5.1 || -10.6 || -349.477 || Reavtive || energy high enough to pass TS after recrossing || [[File:-5.1-10.6cd1618.png|150px]]
|}

Even with high enough energy, a trajectory is not always reactive. Right amount of energy is required for the reaction to happen. The system can go beyond the transition state and recross the energy barrier back to reactant.

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

TST will overestimate reaction rate, because it assumes any trajectory with kinetic energy higher than activation energy will be reactive, but from the simulation, it can be found that even with higher energy can recross the transition state and goes back to reactant. So experimentally, the rate will be lower than the estimated value.

6.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?

Exothermic for F + H2 and endo thermic for H + HF, this indicates that the bond strength for H-F is higher than H-H. So breaking a weak H-H bond to form a strong H-F bond will be exothermic and vice versa

[[File:PEScd1618.png|250px]]

7.Locate the approximate position of the transition state.

F-H distance 181 pm H-H distance 75 pm

8.Report the activation energy for both reactions.

-433.940 kJmol-1 for transition state
0.066 kJmol-1 for F + H2 It is very close to 0 and hard to determine.
125.367 kJmol-1 for H + HF

9.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.

The energy of bond forming is transferred to the vibration of F-H bond, shown in the Momenta vs Time diagram. The Momentum of F-H experienced a huge increase when the system goes over the transition state. In the experiment, this can be confirmed by infrared chemiluminiscence.
Also, the internal vibration will be converted to translational energy and transferred to the surrendering molecules.

10.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.

In the exothermic process examined here, F + H2, translational energy is more effective in overcoming the activation energy barrier. This can be confirmed by calculation, the total kinetic energy is much lower when more energy in the system is the translational mode. Because the early transition state can be more easily overcomed by translational energy.<ref name="RefTS1" /> This is realated to the position of transition state.

[[File:-10.6cd1618.png|250px]]
p1= -1 g.mol-1.pm.fs-1 p2= 0.6 g.mol-1.pm.fs-1 Ek= +1.486 kJmol-1

[[File:-1.050cd1618.png|250px]]
p1= -1.05 g.mol-1.pm.fs-1 p2= 0 g.mol-1.pm.fs-1 Ek= +0.580 kJmol-1

In the endothermic process, FH + H, vibrational energy is more effective to promote reaction. The initial condition with higher vibrational energy requies less total kinetic energy to reach TS.

[[File:-0.2-19gcd1618.png|250px]]
p1= -0.2 g.mol-1.pm.fs-1 p2= -19 g.mol-1.pm.fs-1 Ek= +357.221 kJmol-1

[[File:13.2-2.4gcd1618.png|250px]]
p1= 13.2 g.mol-1.pm.fs-1 p2= -2.4 g.mol-1.pm.fs-1 Ek= +129.145 kJmol-1

== References ==
<references>
<ref name="RefTS1">Polanyi, J. C. "Some Concepts in Reaction Dynamics." Science 236.4802 (1987): 680-90.</ref>
</references>

MRD:cd1618

2020-05-08T13:59:57Z

Cd1618:

== Questions and Answers ==

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?

A saddle point is a point on the potential surface that the slope in orthogonal directions are zero and is not a local minimum or maximum.
It can be identified by finding the first-order saddle point on potential energy surface.
To differentiate saddle point from a local minimum, second partial derivative test can be done. Taking two orthogonal curves on potential surface both orthogonal to z axis, if the product of the second derivatives of the is negative, then it is a saddle point. However for a local minimum, the product of second derivatives and the curvature are positive, which indicates the energy goes up in all directions.

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.

rts= 91 pm All atoms in this system are hydrogen atoms. In this case, a symmetric transition state is expected, the Internuclear Distances vs Time graph confirmed that the distances between AB and BC are the same.

[[File:TScd1618.png|250px]]

3.Comment on how the mep and the trajectory you just calculated differ.

Dynamic calculation makes trajectory vibrate more at the valley, because it considers the vibration of the bond.
Minimum energy path calculation resets momenta to zero in each step, so there is no bond vibration, the trajectory is more like a smooth curve.

4.Complete the table above by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?

{| class="wikitable" border="1"
|+ Reactive and unreactive trajectories
! 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 || Reactive || after TS, more bond vibration is observed || [[File:-2.56-5.1cd1618.png|150px]]
|-
| -3.1 || -4.1 || -420.077 || Unreactive || fail to reach TS || [[File:-3.1-4.1cd1618.png|150px]]
|-
| -3.1 || -5.1 || -413.977 || Reactive || a reactive trajectory with more vibrational energy || [[File:-3.1-5.1cd1618.png|150px]]
|-
| -5.1 || -10.1 || -357.277 || Unreactive || energy is too high, barrier recrossed || [[File:-5.1-10.1cd1618.png|150px]]
|-
| -5.1 || -10.6 || -349.477 || Reavtive || energy high enough to pass TS after recrossing || [[File:-5.1-10.6cd1618.png|150px]]
|}

Even with high enough energy, a trajectory is not always reactive. Right amount of energy is required for the reaction to happen. The system can go beyond the transition state and recross the energy barrier back to reactant.

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

TST will overestimate reaction rate, because it assumes any trajectory with kinetic energy higher than activation energy will be reactive, but from the simulation, it can be found that even with higher energy can recross the transition state and goes back to reactant. So experimentally, the rate will be lower than the estimated value.

6.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?

Exothermic for F + H2 and endo thermic for H + HF, this indicates that the bond strength for H-F is higher than H-H. So breaking a weak H-H bond to form a strong H-F bond will be exothermic and vice versa

[[File:PEScd1618.png|250px]]

7.Locate the approximate position of the transition state.

F-H distance 181 pm H-H distance 75 pm

8.Report the activation energy for both reactions.

-433.940 kJmol-1 for transition state
0.066 kJmol-1 for F + H2 It is very close to 0 and hard to determine.
125.367 kJmol-1 for H + HF

9.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.

The energy of bond forming is transferred to the vibration of F-H bond, shown in the Momenta vs Time diagram. The Momentum of F-H experienced a huge increase when the system goes over the transition state. In the experiment, this can be confirmed by infrared chemiluminiscence.
Also, the internal vibration will be converted to translational energy and transferred to the surrendering molecules.

10.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.

In the exothermic process examined here, F + H2, translational energy is more effective in overcoming the activation energy barrier. This can be confirmed by calculation, the total kinetic energy is much lower when more energy in the system is the translational mode. Because the early transition state can be more easily overcomed by translational energy.<ref name="RefTS1" />

[[File:-10.6cd1618.png|250px]]
p1= -1 g.mol-1.pm.fs-1 p2= 0.6 g.mol-1.pm.fs-1 Ek= +1.486 kJmol-1

[[File:-1.050cd1618.png|250px]]
p1= -1.05 g.mol-1.pm.fs-1 p2= 0 g.mol-1.pm.fs-1 Ek= +0.580 kJmol-1

In the endothermic process, FH + H, vibrational energy is more effective to promote reaction. The initial condition with higher vibrational energy requies less total kinetic energy to reach TS.

[[File:-0.2-19gcd1618.png|250px]]
p1= -0.2 g.mol-1.pm.fs-1 p2= -19 g.mol-1.pm.fs-1 Ek= +357.221 kJmol-1

[[File:13.2-2.4gcd1618.png|250px]]
p1= 13.2 g.mol-1.pm.fs-1 p2= -2.4 g.mol-1.pm.fs-1 Ek= +129.145 kJmol-1

== References ==
<references>
<ref name="RefTS1">Polanyi, J. C. "Some Concepts in Reaction Dynamics." Science 236.4802 (1987): 680-90.</ref>
</references>

MRD:cd1618

2020-05-08T13:51:15Z

Cd1618:

== Questions and Answers ==

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?

A saddle point is a point on the potential surface that the slope in orthogonal directions are zero and is not a local minimum or maximum.
It can be identified by finding the first-order saddle point on potential energy surface.
To differentiate saddle point from a local minimum, second partial derivative test can be done. Taking two orthogonal curves on potential surface both orthogonal to z axis, if the product of the second derivatives of the is negative, then it is a saddle point. However for a local minimum, the product of second derivatives and the curvature are positive, which indicates the energy goes up in all directions.

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.

rts= 91 pm All atoms in this system are hydrogen atoms. In this case, a symmetric transition state is expected, the Internuclear Distances vs Time graph confirmed that the distances between AB and BC are the same.

[[File:TScd1618.png|250px]]

3.Comment on how the mep and the trajectory you just calculated differ.

Dynamic calculation makes trajectory vibrate more at the valley, because it considers the vibration of the bond.
Minimum energy path calculation resets momenta to zero in each step, so there is no bond vibration, the trajectory is more like a smooth curve.

4.Complete the table above by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?

{| class="wikitable" border="1"
|+ Reactive and unreactive trajectories
! 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 || Reactive || after TS, more bond vibration is observed || [[File:-2.56-5.1cd1618.png|150px]]
|-
| -3.1 || -4.1 || -420.077 || Unreactive || fail to reach TS || [[File:-3.1-4.1cd1618.png|150px]]
|-
| -3.1 || -5.1 || -413.977 || Reactive || a reactive trajectory with more vibrational energy || [[File:-3.1-5.1cd1618.png|150px]]
|-
| -5.1 || -10.1 || -357.277 || Unreactive || energy is too high, barrier recrossed || [[File:-5.1-10.1cd1618.png|150px]]
|-
| -5.1 || -10.6 || -349.477 || Reavtive || energy high enough to pass TS after recrossing || [[File:-5.1-10.6cd1618.png|150px]]
|}

Even with high enough energy, a trajectory is not always reactive. Right amount of energy is required for the reaction to happen. The system can go beyond the transition state and recross the energy barrier back to reactant.

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

TST will overestimate reaction rate, because it assumes any trajectory with kinetic energy higher than activation energy will be reactive, but from the simulation, it can be found that even with higher energy can recross the transition state and goes back to reactant. So experimentally, the rate will be lower than the estimated value.

6.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?

Exothermic for F + H2 and endo thermic for H + HF, this indicates that the bond strength for H-F is higher than H-H. So breaking a weak H-H bond to form a strong H-F bond will be exothermic and vice versa

[[File:PEScd1618.png|250px]]

7.Locate the approximate position of the transition state.

F-H distance 181 pm H-H distance 75 pm

8.Report the activation energy for both reactions.

-433.940 kJmol-1 for transition state
0.066 kJmol-1 for F + H2 It is very close to 0 and hard to determine.
125.367 kJmol-1 for H + HF

9.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.

The energy of bond forming is transferred to the vibration of F-H bond, shown in the Momenta vs Time diagram. The Momentum of F-H experienced a huge increase when the system goes over the transition state. In the experiment, this can be confirmed by infrared chemiluminiscence.
Also, the internal vibration will be converted to translational energy and transferred to the surrendering molecules.

10.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.

In the exothermic process examined here, F + H2, translational energy is more effective in overcoming the activation energy barrier. This can be confirmed by calculation, the total kinetic energy is much lower when more energy in the system is the translational mode. Because the early transition state can be more easily overcomed by translational energy.<ref name="RefTS1" /><ref name="RefTS2" />

[[File:-10.6cd1618.png|250px]]
p1= -1 g.mol-1.pm.fs-1 p2= 0.6 g.mol-1.pm.fs-1 Ek= +1.486 kJmol-1

[[File:-1.050cd1618.png|250px]]
p1= -1.05 g.mol-1.pm.fs-1 p2= 0 g.mol-1.pm.fs-1 Ek= +0.580 kJmol-1

In the endothermic process, FH + H, vibrational energy is more effective to promote reaction. The initial condition with higher vibrational energy requies less total kinetic energy to reach TS.

[[File:-0.2-19gcd1618.png|250px]]
p1= -0.2 g.mol-1.pm.fs-1 p2= -19 g.mol-1.pm.fs-1 Ek= +357.221 kJmol-1

[[File:13.2-2.4gcd1618.png|250px]]
p1= 13.2 g.mol-1.pm.fs-1 p2= -2.4 g.mol-1.pm.fs-1 Ek= +129.145 kJmol-1

== References ==
<references>
<ref name="RefTS1">Polanyi, J. C. "Some Concepts in Reaction Dynamics." Science 236.4802 (1987): 680-90.</ref>
</references>
<references>
<ref name="RefTS2">Polanyi, J. C. "Energy Distribution Among Reagents and Products of Atomic Reactions." The Journal of Chemical Physics 31.5 (1959): 1338-351.</ref>
</references>

File:13.2-2.4gcd1618.png

2020-05-08T13:45:29Z

Cd1618:

File:-0.2-19gcd1618.png

2020-05-08T13:44:17Z

Cd1618:

File:-1.050cd1618.png

2020-05-08T13:42:51Z

Cd1618:

File:-10.6cd1618.png

2020-05-08T13:41:34Z

Cd1618:

File:PEScd1618.png

2020-05-08T13:21:56Z

Cd1618:

MRD:cd1618

2020-05-08T13:13:02Z

Cd1618:

== Questions and Answers ==

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?

A saddle point is a point on the potential surface that the slope in orthogonal directions are zero and is not a local minimum or maximum.
It can be identified by finding the first-order saddle point on potential energy surface.
To differentiate saddle point from a local minimum, second partial derivative test can be done. Taking two orthogonal curves on potential surface both orthogonal to z axis, if the product of the second derivatives of the is negative, then it is a saddle point. However for a local minimum, the product of second derivatives and the curvature are positive, which indicates the energy goes up in all directions.

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.

rts= 91 pm All atoms in this system are hydrogen atoms. In this case, a symmetric transition state is expected, the Internuclear Distances vs Time graph confirmed that the distances between AB and BC are the same.

[[File:TScd1618.png|250px]]

3.Comment on how the mep and the trajectory you just calculated differ.

Dynamic calculation makes trajectory vibrate more at the valley, because it considers the vibration of the bond.
Minimum energy path calculation resets momenta to zero in each step, so there is no bond vibration, the trajectory is more like a smooth curve.

4.Complete the table above by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?

{| class="wikitable" border="1"
|+ Reactive and unreactive trajectories
! 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 || Reactive || after TS, more bond vibration is observed || [[File:-2.56-5.1cd1618.png|150px]]
|-
| -3.1 || -4.1 || -420.077 || Unreactive || fail to reach TS || [[File:-3.1-4.1cd1618.png|150px]]
|-
| -3.1 || -5.1 || -413.977 || Reactive || a reactive trajectory with more vibrational energy || [[File:-3.1-5.1cd1618.png|150px]]
|-
| -5.1 || -10.1 || -357.277 || Unreactive || energy is too high, barrier recrossed || [[File:-5.1-10.1cd1618.png|150px]]
|-
| -5.1 || -10.6 || -349.477 || Reavtive || energy high enough to pass TS after recrossing || [[File:-5.1-10.6cd1618.png|150px]]
|}

Even with high enough energy, a trajectory is not always reactive. Right amount of energy is required for the reaction to happen. The system can go beyond the transition state and recross the energy barrier back to reactant.

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

TST will overestimate reaction rate, because it assumes any trajectory with kinetic energy higher than activation energy will be reactive, but from the simulation, it can be found that even with higher energy can recross the transition state and goes back to reactant. So experimentally, the rate will be lower than the estimated value.

6.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?

Exothermic for F + H2 and endo thermic for H + HF, this indicates that the bond strength for H-F is higher than H-H. So breaking a weak H-H bond to form a strong H-F bond will be exothermic and vice versa

7.Locate the approximate position of the transition state.

F-H distance 181 pm H-H distance 75 pm

8.Report the activation energy for both reactions.

-433.940 kJmol-1 for transition state
0.066 kJmol-1 for F + H2 It is very close to 0 and hard to determine.
125.367 kJmol-1 for H + HF

9.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.
AB distance 230 pm Momentum -1.6
BC 75 -0.2
The energy of bond forming is transferred to the vibration of F-H bond, shown in the Momenta vs Time diagram. The Momentum of F-H experienced a huge increase when the system goes over the transition state. In the experiment, this can be confirmed by infrared chemiluminiscence.
Also, the internal vibration will be converted to translational energy and transferred to the surrendering molecules.

10.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.

In the exothermic process examined here, F + H2, translational energy is more effective in overcoming the activation energy barrier. This can be confirmed by calculation, the total kinetic energy is much lower when more energy in the system is the translational mode
210 -1 0.6 +1.486
210 -1.05 0 +0.580

In the endothermic process, FH + H, vibrational energy is more effective to promote reaction.
-0.2 -19 +357.221
13.2 -2.4 +129.145

== References ==

File:-5.1-10.1cd1618.png

2020-05-08T13:10:47Z

Cd1618:

File:-5.1-10.6cd1618.png

2020-05-08T13:08:34Z

Cd1618:

File:-3.1-5.1cd1618.png

2020-05-08T13:08:05Z

Cd1618:

File:-3.1-4.1cd1618.png

2020-05-08T13:04:01Z

Cd1618:

File:-2.56-5.1cd1618.png

2020-05-08T13:03:18Z

Cd1618:

File:TScd1618.png

2020-05-08T13:01:41Z

Cd1618:

MRD:cd1618

2020-05-08T12:22:09Z

Cd1618: Created page with "== Questions and Answers == On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can..."

== Questions and Answers ==

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?

A saddle point is a point on the potential surface that the slope in orthogonal directions are zero and is not a local minimum or maximum.
It can be identified by finding the first-order saddle point on potential energy surface.
To differentiate saddle point from a local minimum, second partial derivative test can be done. Taking two orthogonal curves on potential surface both orthogonal to z axis, if the product of the second derivatives of the is negative, then it is a saddle point. However for a local minimum, the product of second derivatives and the curvature are positive, which indicates the energy goes up in all directions.

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.

rts= 91 pm All atoms in this system are hydrogen atoms. In this case, a symmetric transition state is expected, the Internuclear Distances vs Time graph confirmed that the distances between AB and BC are the same.

Comment on how the mep and the trajectory you just calculated differ.

Dynamic calculation makes trajectory vibrate more at the valley, because it considers the vibration of the bond.
Minimum energy path calculation resets momenta to zero in each step, so there is no bond vibration, the trajectory is more like a smooth curve.

90 90.5 0 0
75 247 -5.1 -2.6

Does not go back to transition state
No reaction occurs

Complete the table above by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?

-2.56-5.1
-413 Reactive
-3.1-4.1
-420 Unreactive
-3.1-5.1
-413 Reactive
-5.1-10.1
-358 Unreactive
-5.1-10.6
-351 Reactive

{| class="wikitable" border="1"
|+ Reactive and unreactive trajectories
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| cell || cell || cell || cell || cell || cell
|-
| cell || cell || cell || cell || cell || cell
|-
| cell || cell || cell || cell || cell || cell
|-
| cell || cell || cell || cell || cell || cell
|-
| cell || cell || cell || cell || cell || cell
|}

Even with high enough energy, a trajectory is not always reactive. Right amount of energy is required for the reaction to happen. The system can go beyond the transition state and recross the energy barrier back to reactant.

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

TST will overestimate reaction rate, because it assumes any trajectory with kinetic energy higher than activation energy will be reactive, but from the simulation, it can be found that even with higher energy can recross the transition state and goes back to reactant. So experimentally, the rate will be lower than the estimated value.

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?

Exothermic for F + H2 and endo thermic for H + HF, this indicates that the bond strength for H-F is higher than H-H. So breaking a weak H-H bond to form a strong H-F bond will be exothermic and vice versa

Locate the approximate position of the transition state.
F-H distance 181 pm H-H distance 75 pm

Report the activation energy for both reactions.
-433.940

-434.006 0.066 kJmol-1 for F + H2 It is very close to 0 and hard to determine.
-559.307 125.367 kJmol-1 for H + HF

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.
AB distance 230 pm Momentum -1.6
BC 75 -0.2
The energy of bond forming is transferred to the vibration of F-H bond, shown in the Momenta vs Time diagram. The Momentum of F-H experienced a huge increase when the system goes over the transition state. In the experiment, this can be confirmed by infrared chemiluminiscence.
Also, the internal vibration will be converted to translational energy and transferred to the surrendering molecules.

92 -13.1
177 2.2

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.

In the exothermic process examined here, F + H2, translational energy is more effective in overcoming the activation energy barrier. This can be confirmed by calculation, the total kinetic energy is much lower when more energy in the system is the translational mode
210 -1 0.6 +1.486
210 -1.05 0 +0.580

In the endothermic process, FH + H, vibrational energy is more effective to promote reaction.
-0.2 -19 +357.221
13.2 -2.4 +129.145

Rep:Mod:lc2.25.19

2019-03-01T11:58:53Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

In the complex, the bond length of N2 and H2 is longer than the calculated value. Theoretically, when forming a dative bond, the electron from the metal is feed into the LUMO of the ligand molecule, so the bond order of ligand molecule decreases and the anti-bonding character increases. Thus a longer and weaker bond is observed.

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

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

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

-0.47310 a.u.

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

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

-0.45487 a.u.

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

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

-0.43685 a.u.

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

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

-0.41452 a.u.

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

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

-0.41452 a.u.

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

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

0.00039 a.u.

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

Rep:Mod:lc2.25.19

2019-03-01T11:57:56Z

Cd1618: /* N2 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

In the complex, the bond length of N2 and H2 is longer than the calculated value. Theoretically, when forming a dative bond, the electron from the metal is feed into the LUMO of the ligand molecule, so the bond order of ligand molecule decreases and the anti-bonding character increases. Thus a longer and weaker bond is observed.

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

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

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

-0.47310
Three 2p orbitals from equatorial F atoms, there is three nodal planes and each orbital is out of phase with the orbital next to it.

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

-0.45487
Three 2pz orbitals from equatorial F atoms art in phase and two axial 2pz orbitals are out of phase with each other and equatorial orbitals.

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

-0.43685
Three 2p orbitals from equatorial F atoms are interacting, but the electron density is mainly on the axial F atoms,and these 2p orbitals are in phase with each other.

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

-0.41452
This MO has a nodal plane going across the P-F bond and all the 2p orbitals from the other F atoms are out of phase.

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

-0.41452
A pair of 2pz orbitals from equatorial F atoms art in phase but out of phase with the last one and two axial 2pz orbitals are out of phase with each other and equatorial orbitals. This is the HOMO

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

0.00039
The 4s orbial of central P is out of phase with each of the 2p orbital from F atoms.
THis is the LUMO

Rep:Mod:lc2.25.19

2019-03-01T11:52:02Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

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

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

-0.47310
Three 2p orbitals from equatorial F atoms, there is three nodal planes and each orbital is out of phase with the orbital next to it.

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

-0.45487
Three 2pz orbitals from equatorial F atoms art in phase and two axial 2pz orbitals are out of phase with each other and equatorial orbitals.

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

-0.43685
Three 2p orbitals from equatorial F atoms are interacting, but the electron density is mainly on the axial F atoms,and these 2p orbitals are in phase with each other.

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

-0.41452
This MO has a nodal plane going across the P-F bond and all the 2p orbitals from the other F atoms are out of phase.

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

-0.41452
A pair of 2pz orbitals from equatorial F atoms art in phase but out of phase with the last one and two axial 2pz orbitals are out of phase with each other and equatorial orbitals. This is the HOMO

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

0.00039
The 4s orbial of central P is out of phase with each of the 2p orbital from F atoms.
THis is the LUMO

Rep:Mod:lc2.25.19

2019-03-01T11:44:35Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

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

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

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

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

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

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

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

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

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

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

Rep:Mod:lc2.25.19

2019-03-01T11:38:05Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

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

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

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

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

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

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

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

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

Rep:Mod:lc2.25.19

2019-03-01T11:25:49Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

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

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

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

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

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

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

File:Cd1618mo31.png

2019-03-01T11:25:26Z

Cd1618:

File:Cd1618mo30.png

2019-03-01T11:25:13Z

Cd1618:

File:Cd1618mo29.png

2019-03-01T11:24:50Z

Cd1618:

File:Cd1618mo28.png

2019-03-01T11:24:28Z

Cd1618:

File:CD1618MO25.png

2019-03-01T11:23:53Z

Cd1618:

Rep:Mod:lc2.25.19

2019-03-01T11:20:56Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

[[File:Cd1618MO25.tig|350px]]

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

[[File:Cd1618MO25.tif|350px]]

[[File:Cd1618MO25.tif|350px]]

[[File:Cd1618MO25.tif|350px]]

[[File:Cd1618MO25.tif|350px]]

Rep:Mod:lc2.25.19

2019-03-01T11:20:20Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

[[File:Cd1618MO25.tif|350px]]

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

[[File:Cd1618MO25.tif|350px]]

[[File:Cd1618MO25.tif|350px]]

[[File:Cd1618MO25.tif|350px]]

[[File:Cd1618MO25.tif|350px]]

File:Cd1618mo26.png

2019-03-01T11:19:46Z

Cd1618:

Rep:Mod:lc2.25.19

2019-03-01T11:16:42Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

[[File:Cd1618MO25.tif|350px]]

Rep:Mod:lc2.25.19

2019-03-01T11:16:27Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

[[File:Cd1618MO25.tif|250px]]

File:Cd1618MO25.tif

2019-03-01T11:15:27Z

Cd1618: Cd1618 uploaded a new version of File:Cd1618MO25.tif

Rep:Mod:lc2.25.19

2019-03-01T11:13:40Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

MO

[[File:Cd1618MO25.tif]]

File:Cd1618MO25.tif

2019-03-01T11:12:46Z

Cd1618:

Rep:Mod:lc2.25.19

2019-03-01T10:55:05Z

Cd1618: /* H2 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

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

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

Rep:Mod:lc2.25.19

2019-03-01T10:53:49Z

Cd1618: /* N2 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

Rep:Mod:lc2.25.19

2019-03-01T10:53:33Z

Cd1618: /* N2 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

Complex Structure

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

Rep:Mod:lc2.25.19

2019-03-01T10:53:04Z

Cd1618: /* N2 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

Complex Structure

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

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

Rep:Mod:lc2.25.19

2019-03-01T10:51:37Z

Cd1618: /* N2 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: VEJFOI

Bond length in the complex: 1.092Å

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

Rep:Mod:lc2.25.19

2019-03-01T10:34:27Z

Cd1618: /* Energy in Harbor Process */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

The ammonia product is more stable.

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

File:CD1618PF5INPUT.LOG

2019-03-01T10:29:07Z

Cd1618: Cd1618 uploaded a new version of File:CD1618PF5INPUT.LOG

Rep:Mod:lc2.25.19

2019-03-01T10:27:50Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Charge on F: -0.578

Charge on P: 2.748

Rep:Mod:lc2.25.19

2019-03-01T10:18:10Z

Cd1618: /* Energy in Harbor Process */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å

===Energy in Harbor Process===

E(NH3)= -56.55776873 a.u.

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

E(N2)= -109.52412868 a.u.

E(H2)= -1.17853935 a.u.

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

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

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Rep:Mod:lc2.25.19

2019-03-01T10:15:03Z

Cd1618: /* PF5 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å

===Energy in Harbor Process===

E(NH3)=

2*E(NH3)=

E(N2)=

E(H2)=

3*E(H2)=

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Rep:Mod:lc2.25.19

2019-03-01T10:14:42Z

Cd1618: /* N2 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

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

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å

===Energy in Harbor Process===

E(NH3)=

2*E(NH3)=

E(N2)=

E(H2)=

3*E(H2)=

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å

File:CD1618N2OUTPUT.LOG

2019-03-01T10:14:15Z

Cd1618:

File:CD16118N2input.LOG

2019-03-01T10:05:42Z

Cd1618:

Rep:Mod:lc2.25.19

2019-03-01T10:04:56Z

Cd1618: /* N2 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

Log File: [[File:File:CD16118N2input.LOG | Log File]]

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å

===Energy in Harbor Process===

E(NH3)=

2*E(NH3)=

E(N2)=

E(H2)=

3*E(H2)=

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å

Rep:Mod:lc2.25.19

2019-03-01T10:04:44Z

Cd1618: /* N2 */

== Molecular Modelling 2 ==
Molecules examined in this workshop: NO3, H2, N2, PF5,

=== NH3 ===
Calculation method: B3LYP

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

final energy: -56.55776873 a.u.

RMS gradient: 0.00000485 a.u.

point group: C3v

Bond length: 1.018Å

Bond angle: 105.7°

{| class="wikitable" border="1"
|+ Optimisation Table
! !! Item !! Value !! Threshold !! Converge?
|-
| Maximum || Force || 0.000004 || 0.000450 || YES
|-
| RMS || Force || 0.000004 || 0.000300 || YES
|-
| Maximum || Displacement || 0.000072 || 0.001800 || YES
|-
| RMS || Displacement || 0.000035 || 0.001200 || YES
|}

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

[[File:Cd1618 pic.PNG]]

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

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

Charge distribution: N: -1.125 H: 0.375

Questions

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

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

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

4. 1090cm-1 3461cm-1

5. 1090cm-1

6. 2 bands since there are six vibration modes

=== H2 ===

Calculation method: B3LYP

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

final energy: -1.17853935 a.u.

RMS gradient: 0.00003809 a.u.

point group: D∞h

Bond length: 0.743Å

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

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

[[File:Cd1618H2 pic.PNG]]

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

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

Identifier for the complex: CILXAX

Bond length in the complex: 0.8Å

===N2 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D∞h

Bond length: 1.106Å

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

Log File: [[File:File:CD16118Ninput.LOG | Log File]]

[[File:Cd1618N2pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å

===Energy in Harbor Process===

E(NH3)=

2*E(NH3)=

E(N2)=

E(H2)=

3*E(H2)=

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=

=== PF5 ===

Calculation method: B3LYP

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

final energy: -109.52412868 a.u.

RMS gradient: 0.00000365 a.u.

point group: D3h

axial P-F bond length: 1.597Å

planar P-F bond length: 1.569Å

F-P-F bond angle: 90°

F-P-F bond angle: 120°

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

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

[[File:Cd1618PF5pic.PNG]]

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

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

Identifier for the complex: AZOSUL01

Bond length in the complex: 1.091Å