ChemWiki - User contributions [en]

MRD:ql2018

2020-05-22T15:49:48Z

Ql2018:

== Molecular Reaction Dynamics Lab ==

=== Exercise 1- (H+H2 System). ===
{{fontcolor|blue|Q1ː 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 transition state can be found as a saddle point on the potential energy surface diagram. Mathematically, the transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish the transition state from local minima,this can be done by viewing the potential energy surface from different angles. The transition state is the only point that is a minimum point from one angle(Figure 1)but a maximum from second angle(Figure 2).
{{multiple image
| align = center
| direction = vertical
| width = 400
| header = Transition State at maximum and minimum
| image1 = Surface_Plot1_qw.png
| caption1 = Transition state is a maximum from one angle.
| image2 = Surface_Plot2_qw.png
| caption2 = Transition state is a minimum from another angle.
}}

{{fontcolor|blue|Q1ː 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.}}
My estimation for the transition state position rts is 90.7pm.Because for the transition state, the potential energies of both p1 and p2 are zero.There is no change of the energy which means that the gradients of potential energy surface is zero and there is no force acting on atoms.So r1 and r2 will keep constant.The graph corresponds should be a straight line since there is no oscillation.

[[File:Surface_Plot3_qw.png|thumb|center|Internuclear distances against time graph at r1=r2=90.7pm with zero momenta.]]

{{fontcolor|blue|Q3ːComment on how the mep and the trajectory you just calculated differ.}}
As the two graphs shown below, the difference is obvious that the trajectory on the contour plot of mep is shorter than that of dynamics. And there is also no oscillation compared with the graph generated by dynamics. The reason for this is because that there is zero kinetic energy for mep due to zero velocity and momentum, there will be no gain in vibtational energy as a result. Therefore the trajectory shows no oscillation. Also the change in total energy is different. Since there is no gain in kinetic energy, the total energy will drop as potential energy losses.

For dynamics, the total energy is conserved as there is gain in kinetic energy when H2 formed.And due to this bond forming, the vibrational energy results in the oscillations on the contour plot.

{{multiple image
| align = left
| direction = vertical
| width = 300
| header = MEP and Dynamics
| image1 = Surface_Plot4_qw.png
| caption1 = MEP contour plot
| image2 = Surface_Plot5_qw.png
| caption2 = Dynamics contour plot
}}

{{fontcolor|blue|Q4ːComplete 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
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot/ kJ.mol-1!! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || Yes || This reaction started with small AB distance and large BC distance. It has enough momentum to pass the transition state region. After that region, the bond between BC formed and the bond between AB broken. The trajectry shows no fluctuation before BC bond formed, which is because the energy is mostly transitional energy. When BC bond formed, the energy is mostly vibrational energy which causes oscillation. ||[[File:Surface_Plot6_qw.png|thumb|upright=0.8]]
|-
| -3.1 || -4.1 || -420.077 || No || This reaction started with small AB distance and large BC distance. However, the momentum is not large enough to pass the transition state region. There is no break in bond between AB and no form in bond between BC. Molecule AB moves away forom C and the bond between AB keeps vibrating due to the kinetic energy. ||[[File:Surface_Plot7_qw.png|thumb|upright=0.8]]
|-
| -3.1 || -5.1 || -413.977 || Yes || This time the BC momentum is large enough for the system to pass transition state. AB bond vibrates before bond breaking due to kinetic energy. The vibration is even larger for BC due to larger momentum after the bond forming. ||[[File:Surface_Plot8_qw.png|thumb|upright=0.8]]
|-
| -5.1 || -10.1 || -357.277 || No || The energy is too large for this system. Even the AB bond breaks and the trajectory passes the transition state region, the bond formed between BC vibrates too strongly due to large energy that the bond fromed eventually breaks. The trajectory goes back and recrosses the transition state region. AB forms a bond again and as AB moves away from C, there is no vibration between AB bond. ||[[File:Surface_Plot9_qw.png|thumb|upright=0.8]]
|-
| -5.1 || -10.6 || -349.477 || Yes || The energy for this system is also very large that the trajectory passes through the transition state region for a couple of times. Although the bond formed between BC after the trajectory passes through the transition state region for the first time. The bond of BC breaks due to large energy and recrosses the transition state. However, because the system has more energy than the previous one.it had the energy to collide for a third time, the bond between BC forms again and became stable as BC vibrates and moves away from A. ||[[File:Surface_Plot10_qw.png|thumb|upright=0.8]]
|}

{{fontcolor|blue|Q5ːGiven the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?}}

The transition state theory assumes that once the reactants have enough kinetic energy to pass through the transition state. The product must formed and the reaction would not go to reverse. However, the given experimental results indicate that it was not true. The products can recross the transition state and reform reactants. As a result, the transition state theory overestimates the reaction rate compared to experimental results. Also, due to the quantum tunneling effects, atoms with energy lower than activation energy can still pass through the barrier, which leads to a underestimation of reaction rate.

== Exercise 2ː F - H - H System ==
{{fontcolor|blue|Q6ː 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?}}

According to the potential energy surface graph F, H2 to H and HFis an exothermic reaction since it has higher potential energy for F and H2. Therefore H + HF to F, H2 is an endothermic reaction. This shows that the H-F bond is stronger than H-H bond. Because the formation of H-F bond releases more energy than the breaking of H-H bond.

[[File:Surface_Plot11_qw.png|thumb|center|Potential energy surface of F-H-H system]]

{{fontcolor|blue|Q7ː Locate the approximate position of the transition state.}}
The approximate position of transition state for this reaction is when F-H isr1 = 181.300 pm and H-H isr2 = 74.483 pm. The momentum at this point is zero.
[[File:Surface_Plot12_qw.png|thumb|center|approximate position of the transition state of F-H-H system]]

{{fontcolor|blue|Q8ː Report the activation energy for both reactions.}}
The potential energy of the reactants F + H2 is -434.625 kJ.mol-1. The potential energy of the transition state is -433.981 kJ.mol-1. The activation energy is equal to the energy of transition state minus the energy of the reactants, which is 0.644 kJ.mol-1.

The potential energy of the products H + HF is -556.231 kJ.mol-1. The potential energy of the transition state is -433.981 kJ.mol-1. The activation energy of this reverse reaction is equal to the energy of transition state minus the energy of the products, which is 122.25 kJ.mol-1.

{{multiple image
| align = center
| direction = vertical
| width = 300
| header = Activation Energies calculation
| image1 = Surface_Plot13_qw.png
| caption1 = Energy against time r1 = 184 pm, r2 = 74.483 pm
| image2 = Surface_Plot14_qw.png
| caption2 = Energy against time r1 = 176.000 pm, r2 = 74.483 pm
}}

{{fontcolor|blue|Q9ːIn 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 conditions are set that the the bond distance is 184pm between F and H and the bond distance is 75 between H and H. p1=-1 and p2= -2. From the graph, it can be seen that the product has greater vibration. This is because the potential energy transfer to kinetic energy and transitional energy.

The energy transfer can be confirmed by using IR spectroscopy. Because the vibration of HF bond can be detected by IR. Calorimetry can also be used to detect the heat generated during the reaction. However, this heat includes both vibrational and transitional energy.

{| class="wikitable" border="1"
! Momentum vs Time
|- !! Contour Plot
|-
| [[File:Surface_Plot15_qw.png|400px|thumb|left]] || [[File:Surface_Plot16_qw.png|400px|thumb|right]]
|}
{{fontcolor|blue|Q10ːDiscuss 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.}}

From Polanyi's rule, It is known that the transitional energy can be more efficient for a exothermic reaction as it helps the reactants to pass through early transition state. In endothermic reaction, it has late transition state that the vibrational energy is more effective. It helps the reactants to pass the late transition state.1

==Reference==
1.J.C. Polanyi. Some Concepts in Reaction Dynamics. Science 1987, 236 (4802): 680-690. doi:10.1126/science.236.4802.680

MRD:ql2018

2020-05-22T15:47:56Z

Ql2018:

== Molecular Reaction Dynamics Lab ==

=== Exercise 1- (H+H2 System). ===
{{fontcolor|blue|Q1ː 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 transition state can be found as a saddle point on the potential energy surface diagram. Mathematically, the transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish the transition state from local minima,this can be done by viewing the potential energy surface from different angles. The transition state is the only point that is a minimum point from one angle(Figure 1)but a maximum from second angle(Figure 2).
{{multiple image
| align = center
| direction = vertical
| width = 400
| header = Transition State at maximum and minimum
| image1 = Surface_Plot1_qw.png
| caption1 = Transition state is a maximum from one angle.
| image2 = Surface_Plot2_qw.png
| caption2 = Transition state is a minimum from another angle.
}}

{{fontcolor|blue|Q1ː 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.}}
My estimation for the transition state position rts is 90.7pm.Because for the transition state, the potential energies of both p1 and p2 are zero.There is no change of the energy which means that the gradients of potential energy surface is zero and there is no force acting on atoms.So r1 and r2 will keep constant.The graph corresponds should be a straight line since there is no oscillation.

[[File:Surface_Plot3_qw.png|thumb|center|Internuclear distances against time graph at r1=r2=90.7pm with zero momenta.]]

{{fontcolor|blue|Q3ːComment on how the mep and the trajectory you just calculated differ.}}
As the two graphs shown below, the difference is obvious that the trajectory on the contour plot of mep is shorter than that of dynamics. And there is also no oscillation compared with the graph generated by dynamics. The reason for this is because that there is zero kinetic energy for mep due to zero velocity and momentum, there will be no gain in vibtational energy as a result. Therefore the trajectory shows no oscillation. Also the change in total energy is different. Since there is no gain in kinetic energy, the total energy will drop as potential energy losses.

For dynamics, the total energy is conserved as there is gain in kinetic energy when H2 formed.And due to this bond forming, the vibrational energy results in the oscillations on the contour plot.

{{multiple image
| align = left
| direction = vertical
| width = 300
| header = MEP and Dynamics
| image1 = Surface_Plot4_qw.png
| caption1 = MEP contour plot
| image2 = Surface_Plot5_qw.png
| caption2 = Dynamics contour plot
}}

{{fontcolor|blue|Q4ːComplete 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
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot/ kJ.mol-1!! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || Yes || This reaction started with small AB distance and large BC distance. It has enough momentum to pass the transition state region. After that region, the bond between BC formed and the bond between AB broken. The trajectry shows no fluctuation before BC bond formed, which is because the energy is mostly transitional energy. When BC bond formed, the energy is mostly vibrational energy which causes oscillation. ||[[File:Surface_Plot6_qw.png|thumb|upright=0.8]]
|-
| -3.1 || -4.1 || -420.077 || No || This reaction started with small AB distance and large BC distance. However, the momentum is not large enough to pass the transition state region. There is no break in bond between AB and no form in bond between BC. Molecule AB moves away forom C and the bond between AB keeps vibrating due to the kinetic energy. ||[[File:Surface_Plot7_qw.png|thumb|upright=0.8]]
|-
| -3.1 || -5.1 || -413.977 || Yes || This time the BC momentum is large enough for the system to pass transition state. AB bond vibrates before bond breaking due to kinetic energy. The vibration is even larger for BC due to larger momentum after the bond forming. ||[[File:Surface_Plot8_qw.png|thumb|upright=0.8]]
|-
| -5.1 || -10.1 || -357.277 || No || The energy is too large for this system. Even the AB bond breaks and the trajectory passes the transition state region, the bond formed between BC vibrates too strongly due to large energy that the bond fromed eventually breaks. The trajectory goes back and recrosses the transition state region. AB forms a bond again and as AB moves away from C, there is no vibration between AB bond. ||[[File:Surface_Plot9_qw.png|thumb|upright=0.8]]
|-
| -5.1 || -10.6 || -349.477 || Yes || The energy for this system is also very large that the trajectory passes through the transition state region for a couple of times. Although the bond formed between BC after the trajectory passes through the transition state region for the first time. The bond of BC breaks due to large energy and recrosses the transition state. However, because the system has more energy than the previous one.it had the energy to collide for a third time, the bond between BC forms again and became stable as BC vibrates and moves away from A. ||[[File:Surface_Plot10_qw.png|thumb|upright=0.8]]
|}

{{fontcolor|blue|Q5ːGiven the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?}}

The transition state theory assumes that once the reactants have enough kinetic energy to pass through the transition state. The product must formed and the reaction would not go to reverse. However, the given experimental results indicate that it was not true. The products can recross the transition state and reform reactants. As a result, the transition state theory overestimates the reaction rate compared to experimental results. Also, due to the quantum tunneling effects, atoms with energy lower than activation energy can still pass through the barrier, which leads to a underestimation of reaction rate.

== Exercise 2ː F - H - H System ==
{{fontcolor|blue|Q6ː 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?}}

According to the potential energy surface graph F, H2 to H and HFis an exothermic reaction since it has higher potential energy for F and H2. Therefore H + HF to F, H2 is an endothermic reaction. This shows that the H-F bond is stronger than H-H bond. Because the formation of H-F bond releases more energy than the breaking of H-H bond.

[[File:Surface_Plot11_qw.png|thumb|center|Potential energy surface of F-H-H system]]

{{fontcolor|blue|Q7ː Locate the approximate position of the transition state.}}
The approximate position of transition state for this reaction is when F-H isr1 = 181.300 pm and H-H isr2 = 74.483 pm. The momentum at this point is zero.
[[File:Surface_Plot12_qw.png|thumb|center|approximate position of the transition state of F-H-H system]]

{{fontcolor|blue|Q8ː Report the activation energy for both reactions.}}
The potential energy of the reactants F + H2 is -434.625 kJ.mol-1. The potential energy of the transition state is -433.981 kJ.mol-1. The activation energy is equal to the energy of transition state minus the energy of the reactants, which is 0.644 kJ.mol-1.

The potential energy of the products H + HF is -556.231 kJ.mol-1. The potential energy of the transition state is -433.981 kJ.mol-1. The activation energy of this reverse reaction is equal to the energy of transition state minus the energy of the products, which is 122.25 kJ.mol-1.

{{multiple image
| align = center
| direction = vertical
| width = 300
| header = Activation Energies calculation
| image1 = Surface_Plot13_qw.png
| caption1 = Energy against time r1 = 184 pm, r2 = 74.483 pm
| image2 = Surface_Plot14_qw.png
| caption2 = Energy against time r1 = 176.000 pm, r2 = 74.483 pm
}}

{{fontcolor|blue|Q9ːIn 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 conditions are set that the the bond distance is 184pm between F and H and the bond distance is 75 between H and H. p1=-1 and p2= -2. From the graph, it can be seen that the product has greater vibration. This is because the potential energy transfer to kinetic energy and transitional energy.

The energy transfer can be confirmed by using IR spectroscopy. Because the vibration of HF bond can be detected by IR. Calorimetry can also be used to detect the heat generated during the reaction. However, this heat includes both vibrational and transitional energy.

{| class="wikitable" border="1"
! Momentum vs Time
|- !! Contour Plot
|-
| [[File:Surface_Plot15_qw.png|400px|thumb|left]] || [[File:Surface_Plot16_qw.png|400px|thumb|right]]
|}
{{fontcolor|blue|Q10ːDiscuss 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.}}

From Polanyi's rule, It is known that the transitional energy can be more efficient for a exothermic reaction as it helps the reactants to pass through early transition state. In endothermic reaction, it has late transition state that the vibrational energy is more effective. It helps the reactants to pass the late transition state.1

1.J.C. Polanyi. Some Concepts in Reaction Dynamics. Science 1987, 236 (4802): 680-690. doi:10.1126/science.236.4802.680

File:Surface Plot16 qw.png

2020-05-22T15:44:09Z

Ql2018:

File:Surface Plot15 qw.png

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Ql2018:

File:Surface Plot14 qw.png

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Ql2018:

File:Surface Plot13 qw.png

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File:Surface Plot12 qw.png

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File:Surface Plot11 qw.png

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MRD:ql2018

2020-05-22T14:24:35Z

Ql2018:

== Molecular Reaction Dynamics Lab ==

=== Exercise 1- (H+H2 System). ===
{{fontcolor|blue|Q1ː 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 transition state can be found as a saddle point on the potential energy surface diagram. Mathematically, the transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish the transition state from local minima,this can be done by viewing the potential energy surface from different angles. The transition state is the only point that is a minimum point from one angle(Figure 1)but a maximum from second angle(Figure 2).

{{fontcolor|blue|Q1ː 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.}}
My estimation for the transition state position rts is 90.7pm.Because for the transition state, the potential energies of both p1 and p2 are zero.There is no change of the energy which means that the gradients of potential energy surface is zero and there is no force acting on atoms.So r1 and r2 will keep constant.The graph corresponds should be a straight line since there is no oscillation.

{{fontcolor|blue|Q3ːComment on how the mep and the trajectory you just calculated differ.}}
As the two graphs shown below, the difference is obvious that the trajectory on the contour plot of mep is shorter than that of dynamics. And there is also no oscillation compared with the graph generated by dynamics. The reason for this is because that there is zero kinetic energy for mep due to zero velocity and momentum, there will be no gain in vibtational energy as a result. Therefore the trajectory shows no oscillation. Also the change in total energy is different. Since there is no gain in kinetic energy, the total energy will drop as potential energy losses.

For dynamics, the total energy is conserved as there is gain in kinetic energy when H2 formed.And due to this bond forming, the vibrational energy results in the oscillations on the contour plot.

{{fontcolor|green|Q4ːComplete 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
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot/ kJ.mol-1!! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || Yes || This reaction started with small AB distance and large BC distance. It has enough momentum to pass the transition state region. After that region, the bond between BC formed and the bond between AB broken. The trajectry shows no fluctuation before BC bond formed, which is because the energy is mostly transitional energy. When BC bond formed, the energy is mostly vibrational energy which causes oscillation. ||[[|thumb|upright=0.8]]
|-
| -3.1 || -4.1 || -420.077 || No || This reaction started with small AB distance and large BC distance. However, the momentum is not large enough to pass the transition state region. There is no break in bond between AB and no form in bond between BC. Molecule AB moves away forom C and the bond between AB keeps vibrating due to the kinetic energy. ||[[|thumb|upright=0.8]]
|-
| -3.1 || -5.1 || -413.977 || Yes || This time the BC momentum is large enough for the system to pass transition state. AB bond vibrates before bond breaking due to kinetic energy. The vibration is even larger for BC due to larger momentum after the bond forming. ||[[|thumb|upright=0.8]]
|-
| -5.1 || -10.1 || -357.277 || No || The energy is too large for this system. Even the AB bond breaks and the trajectory passes the transition state region, the bond formed between BC vibrates too strongly due to large energy that the bond fromed eventually breaks. The trajectory goes back and recrosses the transition state region. AB forms a bond again and as AB moves away from C, there is no vibration between AB bond. ||[[File:|thumb|upright=0.8]]
|-
| -5.1 || -10.6 || -349.477 || Yes || The energy for this system is also very large that the trajectory passes through the transition state region for a couple of times. Although the bond formed between BC after the trajectory passes through the transition state region for the first time. The bond of BC breaks due to large energy and recrosses the transition state. However, because the system has more energy than the previous one.it had the energy to collide for a third time, the bond between BC forms again and became stable as BC vibrates and moves away from A. ||[[|thumb|upright=0.8]]
|}

{{fontcolor|blue|Q5ːGiven the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?}}

The transition state theory assumes that once the reactants have enough kinetic energy to pass through the transition state. The product must formed and the reaction would not go to reverse. However, the given experimental results indicate that it was not true. The products can recross the transition state and reform reactants. As a result, the transition state theory overestimates the reaction rate compared to experimental results. Also, due to the quantum tunneling effects, atoms with energy lower than activation energy can still pass through the barrier, which leads to a underestimation of reaction rate.

== Exercise 2ː F - H - H System ==
{{fontcolor|green|Q6ː 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?}}

According to the potential energy surface graph F, H2 to H and HFis an exothermic reaction since it has higher potential energy for F and H2. Therefore H + HF to F, H2 is an endothermic reaction. This shows that the H-F bond is stronger than H-H bond. Because the formation of H-F bond releases more energy than the breaking of H-H bond.

{{fontcolor|blue|Q7ː Locate the approximate position of the transition state.}}
The approximate position of transition state for this reaction is when F-H isr1 = 181.300 pm and H-H isr2 = 74.483 pm. The momentum at this point is zero.

{{fontcolor|blue|Q8ː Report the activation energy for both reactions.}}
The potential energy of the reactants F + H2 is -434.215 kJ.mol-1. The potential energy of the transition state is -433.981 kJ.mol-1. The activation energy is equal to the energy of transition state minus the energy of the reactants, which is 0.233 kJ.mol-1.

The potential energy of the products H + HF is -556.079 kJ.mol-1. The potential energy of the transition state is -433.981 kJ.mol-1. The activation energy of this reverse reaction is equal to the energy of transition state minus the energy of the products, which is 122.098 kJ.mol-1.

{{fontcolor|green|Q9ːIn 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 conditions are set that the the bond distance is 185pm between F and H and the bond distance is 75 between H and H. p1=-1 and p2= -2. From the graph, it can be seen that the product has greater vibration. This is because the potential energy transfer to kinetic energy and transitional energy.

The energy transfer can be confirmed by using IR spectroscopy. Because the vibration of HF bond can be detected by IR. Calorimetry can also be used to detect the heat generated during the reaction. However, this heat includes both vibrational and transitional energy.

{{fontcolor|blue|Q10ːDiscuss 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.}}

From Polanyi's rule, It is known that the transitional energy can be more efficient for a exothermic reaction as it helps the reactants to pass through early transition state. In endothermic reaction, it has late transition state that the vibrational energy is more effective. It helps the reactants to pass the late transition state.

MRD:ql2018

2020-05-22T07:50:16Z

Ql2018:

MRD:ql2018

2020-05-22T03:51:23Z

Ql2018:

MRD:ql2018

2020-05-20T08:49:44Z

Ql2018: /* Molecular Reaction Dynamics Lab */

MRD:ql2018

2020-05-20T08:37:25Z

Ql2018: Created page with "== Molecular Reaction Dynamics Lab == === Exercise 1- (H+H2 System). === {{fontcolor|blue|Q1ː On a potential energy surface diagram, how is the transition..."

Rep:Mod:01500798

2019-03-07T20:20:25Z

Ql2018: /* Jmol of N2 */

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of H2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex DEKFUX'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022

Charge on O: -0.511

In expectation, the charge on O should be negative since O is more electronegative than C.

===Molecular Orbitals===

[[File:Ql mo12.png|200px]]

'''Molecular orbital 12'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Anitibonding

-Energy: 0.02992 au (LUMO)

-Occupied or unoccupied: Unoccupied

[[File:Ql mo11.png|200px]]

'''Molecular orbital 11'''

-AOs contribute to the MO: 2p(O) 2p(O)

-Antibonding or bonding: Antibonding

-Energy: -0.36997 au (HOMO)

-Occupied or unoccupied: Occupied

[[File:Ql mo8.png|200px]]

'''Molecular orbital 8'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.51277 au

-Occupied or unoccupied: Occupied

[[File:Ql mo4.png|200px]]

'''Molecular orbital 4'''

-AOs contribute to the MO: 2s(O) 2s(O)

-Antibonding or bonding: Bonding

-Energy: -1.16099 au (deep in energy)

-Occupied or unoccupied: Occupied

[[File:Ql mo7.png|200px]]

'''Molecular orbital 7'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Antibonding

-Energy: -0.51655 au

-Occupied or unoccupied: Occupied

==Extra: CO ==
===Molecule Information===
Molecular name: Carbon monoxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -113.30945314 au

Point Group: C*V

C-O bond distance:1.14Å

C-O bond angle:180°

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

===Jmol of CO===
<jmol><jmolApplet>
<title> CO </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO OPT.LOG]]

===CO Vibrations===
[[File:Ql2018 virat co.png|300px]]

=== Vibration mode of CO ===

{| class="wikitable" border="1"
|+ Vibrations mode of Carbon monoxide
|-
|'''Wavenumber''' cm-1 || 2209
|-
| '''Symmetry''' || SG
|-
| '''Intensity''' arbitrary units|| 68
|-
| Image || [[File:QL new2209.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge co.png|200px]]

Charge on C: 0.506

Charge on O: -0.506

In expectation, the charge on O should be negative since O is more electronegative than C.

===Molecular Orbitals===

[[File:Ql ex mo8.png|200px]]

'''Molecular orbital 8'''

-AOs contribute to the MO: 2p(C) 2p(O)

-Antibonding or bonding: Anitibonding

-Energy: -0.02177 au (LUMO)

-Occupied or unoccupied: Unoccupied

[[File:Ql ex mo7.png|200px]]

'''Molecular orbital 7'''

-AOs contribute to the MO: 2s(C) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.37145 au (HOMO)

-Occupied or unoccupied: Occupied

[[File:Ql ex mo6.png|200px]]

'''Molecular orbital 6'''

-AOs contribute to the MO: 2p(C) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.46743 au

-Occupied or unoccupied: Occupied

[[File:Ql ex mo4.png|200px]]

'''Molecular orbital 4'''

-AOs contribute to the MO: 2s(C) 2s(O)

-Antibonding or bonding: Antibonding

-Energy: -0.57004 au

-Occupied or unoccupied: Occupied

[[File:Ql ex mo3.png|200px]]

'''Molecular orbital 3'''

-AOs contribute to the MO: 2s(C) 2s(O)

-Antibonding or bonding: Bonding

-Energy: -1.15791 au

-Occupied or unoccupied: Occupied

Rep:Mod:01500798

2019-03-07T20:18:14Z

Ql2018: /* Extra for CO */

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex DEKFUX'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022

Charge on O: -0.511

In expectation, the charge on O should be negative since O is more electronegative than C.

===Molecular Orbitals===

[[File:Ql mo12.png|200px]]

'''Molecular orbital 12'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Anitibonding

-Energy: 0.02992 au (LUMO)

-Occupied or unoccupied: Unoccupied

[[File:Ql mo11.png|200px]]

'''Molecular orbital 11'''

-AOs contribute to the MO: 2p(O) 2p(O)

-Antibonding or bonding: Antibonding

-Energy: -0.36997 au (HOMO)

-Occupied or unoccupied: Occupied

[[File:Ql mo8.png|200px]]

'''Molecular orbital 8'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.51277 au

-Occupied or unoccupied: Occupied

[[File:Ql mo4.png|200px]]

'''Molecular orbital 4'''

-AOs contribute to the MO: 2s(O) 2s(O)

-Antibonding or bonding: Bonding

-Energy: -1.16099 au (deep in energy)

-Occupied or unoccupied: Occupied

[[File:Ql mo7.png|200px]]

'''Molecular orbital 7'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Antibonding

-Energy: -0.51655 au

-Occupied or unoccupied: Occupied

==Extra: CO ==
===Molecule Information===
Molecular name: Carbon monoxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -113.30945314 au

Point Group: C*V

C-O bond distance:1.14Å

C-O bond angle:180°

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

===Jmol of CO===
<jmol><jmolApplet>
<title> CO </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO OPT.LOG]]

===CO Vibrations===
[[File:Ql2018 virat co.png|300px]]

=== Vibration mode of CO ===

{| class="wikitable" border="1"
|+ Vibrations mode of Carbon monoxide
|-
|'''Wavenumber''' cm-1 || 2209
|-
| '''Symmetry''' || SG
|-
| '''Intensity''' arbitrary units|| 68
|-
| Image || [[File:QL new2209.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge co.png|200px]]

Charge on C: 0.506

Charge on O: -0.506

In expectation, the charge on O should be negative since O is more electronegative than C.

===Molecular Orbitals===

[[File:Ql ex mo8.png|200px]]

'''Molecular orbital 8'''

-AOs contribute to the MO: 2p(C) 2p(O)

-Antibonding or bonding: Anitibonding

-Energy: -0.02177 au (LUMO)

-Occupied or unoccupied: Unoccupied

[[File:Ql ex mo7.png|200px]]

'''Molecular orbital 7'''

-AOs contribute to the MO: 2s(C) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.37145 au (HOMO)

-Occupied or unoccupied: Occupied

[[File:Ql ex mo6.png|200px]]

'''Molecular orbital 6'''

-AOs contribute to the MO: 2p(C) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.46743 au

-Occupied or unoccupied: Occupied

[[File:Ql ex mo4.png|200px]]

'''Molecular orbital 4'''

-AOs contribute to the MO: 2s(C) 2s(O)

-Antibonding or bonding: Antibonding

-Energy: -0.57004 au

-Occupied or unoccupied: Occupied

[[File:Ql ex mo3.png|200px]]

'''Molecular orbital 3'''

-AOs contribute to the MO: 2s(C) 2s(O)

-Antibonding or bonding: Bonding

-Energy: -1.15791 au

-Occupied or unoccupied: Occupied

Rep:Mod:01500798

2019-03-07T20:15:30Z

Ql2018:

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex DEKFUX'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022

Charge on O: -0.511

In expectation, the charge on O should be negative since O is more electronegative than C.

===Molecular Orbitals===

[[File:Ql mo12.png|200px]]

'''Molecular orbital 12'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Anitibonding

-Energy: 0.02992 au (LUMO)

-Occupied or unoccupied: Unoccupied

[[File:Ql mo11.png|200px]]

'''Molecular orbital 11'''

-AOs contribute to the MO: 2p(O) 2p(O)

-Antibonding or bonding: Antibonding

-Energy: -0.36997 au (HOMO)

-Occupied or unoccupied: Occupied

[[File:Ql mo8.png|200px]]

'''Molecular orbital 8'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.51277 au

-Occupied or unoccupied: Occupied

[[File:Ql mo4.png|200px]]

'''Molecular orbital 4'''

-AOs contribute to the MO: 2s(O) 2s(O)

-Antibonding or bonding: Bonding

-Energy: -1.16099 au (deep in energy)

-Occupied or unoccupied: Occupied

[[File:Ql mo7.png|200px]]

'''Molecular orbital 7'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Antibonding

-Energy: -0.51655 au

-Occupied or unoccupied: Occupied

==Extra for CO ==
===Molecule Information===
Molecular name: Carbon monoxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -113.30945314 au

Point Group: C*V

C-O bond distance:1.14Å

C-O bond angle:180°

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

===Jmol of CO===
<jmol><jmolApplet>
<title> CO </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO OPT.LOG]]

===CO Vibrations===
[[File:Ql2018 virat co.png|300px]]

=== Vibration mode of CO ===

{| class="wikitable" border="1"
|+ Vibrations mode of Carbon monoxide
|-
|'''Wavenumber''' cm-1 || 2209
|-
| '''Symmetry''' || SG
|-
| '''Intensity''' arbitrary units|| 68
|-
| Image || [[File:QL new2209.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge co.png|200px]]

Charge on C: 0.506

Charge on O: -0.506

In expectation, the charge on O should be negative since O is more electronegative than C.

===Molecular Orbitals===

[[File:Ql ex mo8.png|200px]]

'''Molecular orbital 8'''

-AOs contribute to the MO: 2p(C) 2p(O)

-Antibonding or bonding: Anitibonding

-Energy: -0.02177 au (LUMO)

-Occupied or unoccupied: Unoccupied

[[File:Ql ex mo7.png|200px]]

'''Molecular orbital 7'''

-AOs contribute to the MO: 2s(C) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.37145 au (HOMO)

-Occupied or unoccupied: Occupied

[[File:Ql ex mo6.png|200px]]

'''Molecular orbital 6'''

-AOs contribute to the MO: 2p(C) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.46743 au

-Occupied or unoccupied: Occupied

[[File:Ql ex mo4.png|200px]]

'''Molecular orbital 4'''

-AOs contribute to the MO: 2s(C) 2s(O)

-Antibonding or bonding: Antibonding

-Energy: -0.57004 au

-Occupied or unoccupied: Occupied

[[File:Ql ex mo3.png|200px]]

'''Molecular orbital 3'''

-AOs contribute to the MO: 2s(C) 2s(O)

-Antibonding or bonding: Bonding

-Energy: -1.15791 au

-Occupied or unoccupied: Occupied

File:Ql ex mo7.png

2019-03-07T20:02:03Z

Ql2018:

File:Ql ex mo8.png

2019-03-07T20:01:34Z

Ql2018:

File:Ql ex mo6.png

2019-03-07T20:01:08Z

Ql2018:

File:Ql ex mo4.png

2019-03-07T20:00:51Z

Ql2018:

File:Ql ex mo3.png

2019-03-07T20:00:30Z

Ql2018:

File:Ql charge co.png

2019-03-07T19:51:01Z

Ql2018:

File:QL new2209.png

2019-03-07T19:48:29Z

Ql2018:

Rep:Mod:01500798

2019-03-07T19:42:41Z

Ql2018:

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex DEKFUX'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022

Charge on O: -0.511

In expectation, the charge on O should be negative since O is more electronegative than C.

===Molecular Orbitals===

[[File:Ql mo12.png|200px]]

'''Molecular orbital 12'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Anitibonding

-Energy: 0.02992 au (LUMO)

-Occupied or unoccupied: Unoccupied

[[File:Ql mo11.png|200px]]

'''Molecular orbital 11'''

-AOs contribute to the MO: 2p(O) 2p(O)

-Antibonding or bonding: Antionding

-Energy: -0.36997 au (HOMO)

-Occupied or unoccupied: Occupied

[[File:Ql mo8.png|200px]]

'''Molecular orbital 8'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.51277 au

-Occupied or unoccupied: Occupied

[[File:Ql mo4.png|200px]]

'''Molecular orbital 4'''

-AOs contribute to the MO: 2s(O) 2s(O)

-Antibonding or bonding: Bonding

-Energy: -1.16099 au (deep in energy)

-Occupied or unoccupied: Occupied

[[File:Ql mo7.png|200px]]

'''Molecular orbital 7'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Antibonding

-Energy: -0.51655 au

-Occupied or unoccupied: Occupied

==Extra for CO ==
===Molecule Information===
Molecular name: Carbon monoxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -113.30945314 au

Point Group: C*V

C-O bond distance:1.14Å

C-O bond angle:180°

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

===Jmol of CO===
<jmol><jmolApplet>
<title> CO </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO OPT.LOG]]

===CO Vibrations===
[[File:Ql2018 vibrat co.png|300px]]

=== Vibration mode of CO ===

{| class="wikitable" border="1"
|+ Vibrations mode of Carbon monoxide
|-
|'''Wavenumber''' cm-1 || 2209
|-
| '''Symmetry''' || SG
|-
| '''Intensity''' arbitrary units|| 68
|-
| Image || [[File:QL 2209.png|150px]]
|}

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022

Charge on O: -0.511

In expectation, the charge on O should be negative since O is more electronegative than C.

===Molecular Orbitals===

[[File:Ql mo12.png|200px]]

'''Molecular orbital 12'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Anitibonding

-Energy: 0.02992 au (LUMO)

-Occupied or unoccupied: Unoccupied

[[File:Ql mo11.png|200px]]

'''Molecular orbital 11'''

-AOs contribute to the MO: 2p(O) 2p(O)

-Antibonding or bonding: Antionding

-Energy: -0.36997 au (HOMO)

-Occupied or unoccupied: Occupied

[[File:Ql mo8.png|200px]]

'''Molecular orbital 8'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.51277 au

-Occupied or unoccupied: Occupied

[[File:Ql mo4.png|200px]]

'''Molecular orbital 4'''

-AOs contribute to the MO: 2s(O) 2s(O)

-Antibonding or bonding: Bonding

-Energy: -1.16099 au (deep in energy)

-Occupied or unoccupied: Occupied

[[File:Ql mo7.png|200px]]

'''Molecular orbital 7'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Antibonding

-Energy: -0.51655 au

-Occupied or unoccupied: Occupied

File:QL 2209.png

2019-03-07T19:41:22Z

Ql2018:

Rep:Mod:01500798

2019-03-07T19:12:56Z

Ql2018:

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex DEKFUX'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022

Charge on O: -0.511

In expectation, the charge on O should be negative since O is more electronegative than C.

===Molecular Orbitals===

[[File:Ql mo12.png|200px]]
'''Molecular orbital 12'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Anitibonding

-Energy: 0.02992 au (LUMO)

-Occupied or unoccupied: Unoccupied

[[File:Ql mo11.png|200px]]
'''Molecular orbital 11'''

-AOs contribute to the MO: 2p(O) 2p(O)

-Antibonding or bonding: Antionding

-Energy: -0.36997 au (HOMO)

-Occupied or unoccupied: Occupied

[[File:Ql mo8.png|200px]]
'''Molecular orbital 8'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Bonding

-Energy: -0.51277 au

-Occupied or unoccupied: Occupied

[[File:Ql mo4.png|200px]]
'''Molecular orbital 4'''

-AOs contribute to the MO: 2s(O) 2s(O)

-Antibonding or bonding: Bonding

-Energy: -1.16099 au (deep in energy)

-Occupied or unoccupied: Occupied

[[File:Ql mo7.png|200px]]
'''Molecular orbital 7'''

-AOs contribute to the MO: 2p(C) 2p(O) 2p(O)

-Antibonding or bonding: Antibonding

-Energy: -0.51655 au

-Occupied or unoccupied: Occupied

File:Ql mo7.png

2019-03-07T19:10:20Z

Ql2018:

File:Ql mo12.png

2019-03-07T18:30:51Z

Ql2018:

File:Ql mo11.png

2019-03-07T18:30:39Z

Ql2018:

File:Ql mo8.png

2019-03-07T18:30:27Z

Ql2018:

File:Ql mo4.png

2019-03-07T18:30:12Z

Ql2018:

Rep:Mod:01500798

2019-03-07T13:23:17Z

Ql2018: /* Charge Analysis */

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex DEKFUX'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022

Charge on O: -0.511

In expectation, the charge on O should be negative since O is more electronegative than C.

Rep:Mod:01500798

2019-03-07T13:22:47Z

Ql2018: /* Vibration mode of H2 */

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex DEKFUX'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022
Charge on O: -0.511
In expectation, the charge on O should be negative since O is more electronegative than C.

Rep:Mod:01500798

2019-03-07T13:22:22Z

Ql2018: /* Vibration mode of H2 */

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration modes
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration mode
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex DEKFUX'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022
Charge on O: -0.511
In expectation, the charge on O should be negative since O is more electronegative than C.

Rep:Mod:01500798

2019-03-07T13:21:31Z

Ql2018: /* Structure and Reactivity */

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration modes
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration modes
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex DEKFUX'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022
Charge on O: -0.511
In expectation, the charge on O should be negative since O is more electronegative than C.

Rep:Mod:01500798

2019-03-07T13:20:35Z

Ql2018:

== NH3 ==
===Molecule Information===
Molecular name: Ammonia

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy:-56.55776873 au

Point Group: C3V

N-H bond distance:1.02Å

H-N-H bond angle:37°

===Item Table===

<pre> Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

===Jmol of NH3===
<jmol><jmolApplet>
<title> Ammonia </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===link===
[[File:QUANWENT NH3 OPTF POP.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT_NH3_OPTF_POP.LOG]]

===NH3 Vibrations===
[[File:Ql2018_vibrat.png|300px]]

{| class="wikitable" border="1"
|+ Vibrations modes of Ammonia
|-
|'''Wavenumber''' cm-1 || 1090||1694||1694||3461||3590||3590
|-
| '''Symmetry''' || A1||E||E||A1||E||E
|-
| '''Intensity''' arbitrary units|| 145||14||14||1||0||0
|-
| Image || [[File:1090mode.png|150px]]|| [[File:1694mode.png|150px]]|| [[File:1694mode2.png|150px]]|| [[File:3461mode.png|150px]]|| [[File:3590mode.png|150px]]|| [[File:3590mode2.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-6 rule?

- 3 x 4 - 6 = 6 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 1694 cm^-1 and 3590 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 1090 cm^-1 and 1694 cm^-1 are "bending" vibrations,modes with the wavenumber of 3461 cm^-1 and 3590 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 3461 cm^-1.

one mode is known as the "umbrella" mode, which one is this?

- Mode with the wavenumber of 1090 cm^-1.

how many bands would you expect to see in an experimental spectrum of gaseous ammonia?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 3461 cm^-1 has intensity 1.

===Charge Analysis===

[[File:NBO charge lqw.png|200px]]

In expectation, N is more electronegative than H and should have negative charge,H should have positive charge. The results show that the charge is -1.125 on N and 0.375 on H.

== N2 ==
===Molecule Information===
Molecular name: Nitrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -109.52412868 au

Point Group: D*H

N-N bond distance:1.11Å

N-N bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000001 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> N2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWENT N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWENT N2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWENT N2 OPT.LOG]]

===N2 Vibrations===
[[File:Ql2018 vibrat n2.png|300px]]

=== Vibration mode of N2 ===
{| class="wikitable" border="1"
|+ Vibration modes
|-
| Wavenumber cm^-1 || 2457
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode n2.png|150px]]
|}

===Charge Analysis===

[[File:Charge n2.png|200px]]

In expectation, the charge on both N should be zero since there is no resultant dipole moment. The results show that the charge is on both N is 0.

== H2 ==
===Molecule Information===
Molecular name: Hydrogen

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -1.17853936 au

Point Group: D*H

H-H bond distance:0.74Å

H-H bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
</pre>

===Jmol of N2===
<jmol><jmolApplet>
<title> H2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN H2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN H2 OPT.LOG]]

===H2 Vibrations===
[[File:Ql2018 vibrat h2.png|300px]]

=== Vibration mode of H2 ===
{| class="wikitable" border="1"
|+ Vibration modes
|-
| Wavenumber cm^-1 || 4466
|-
| Symmetry || SGG
|-
| Intensity Arbitrary Units || 0
|-
| Image || [[File:Mode h2.png|150px]]
|}

===Charge Analysis===

[[File:Ql charge h2.png|200px]]

In expectation, the charge on both H should be zero since there is no resultant dipole moment. The results show that the charge is on both H is 0.

==Structure and Reactivity==
'''mono-metallic TM complex'''

[[File:QUANWEN DEKFUX.png|250px]]

Link to the complex:[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=DEKFUX&DatabaseToSearch=Published]

There is one N-N triple bond in the complex. The bong length of this triple bod is 1.086. The N-N triple bond length in Nitrogen gas is 1.10550 which is slightly longer. I think the reason that causes the difference in bond length is that the bond length calculated for Nitrogen gas is under perfect condition whereas there are other factors influencing the value in reality. The transition metal attached in crystal structure help to stabilize the N-N triple bond. So the bong length in crystal structure is shorter.

==Energy for Reaction==

E(NH3)= -56.557769 au

2*E(NH3)= -113.115538 au

E(N2)= -109.5241287 au

E(H2)= -1.1785394 au

3*E(H2)= -3.5356180 au

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907 au = -146.8 kJ/mol

The ammonia product is more stable since the change in energy is negative.

== CO2 ==
===Molecule Information===
Molecular name: Carbon dioxide

Calculation Type: FREQ

Calculation Method: RB3LYP

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

Final Energy: -188.58093945 au

Point Group: D*H

C-O bond distance:1.17Å

C-O bond angle:180°

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000021 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
</pre>

===Jmol of CO2===
<jmol><jmolApplet>
<title> CO2 </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>QUANWEN CO2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Link===
[[File:QUANWEN CO2 OPT.LOG| https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:QUANWEN CO2 OPT.LOG]]

===CO2 Vibrations===
[[File:Ql2018 co2 vibrat.png|300px]]

=== Vibration mode of CO2 ===

{| class="wikitable" border="1"
|+ Vibrations modes of Carbon dioxide
|-
|'''Wavenumber''' cm-1 || 640||640||1372||2436
|-
| '''Symmetry''' || PIU||PIU||SGG||SGU
|-
| '''Intensity''' arbitrary units|| 31||31||0||546
|-
| Image || [[File:QL 640.png|150px]]|| [[File:QL 640 2.png|150px]]|| [[File:QL 13XX.png|150px]]|| [[File:QL 24XX.png|150px]]
|}

=== Answer of Questions ===
how many modes do you expect from the 3N-5 rule?

- 3 x 4 - 6 = 4 modes

which modes are degenerate (ie have the same energy)?

- Modes with wavenumbers of 640 cm^-1.

which modes are "bending" vibrations and which are "bond stretch" vibrations?

- Modes with the wavenumber of 640 cm^-1 are "bending" vibrations,modes with the wavenumber of 1372 cm^-1 and 2436 cm^-1 are "bond stretch" vibrations.

which mode is highly symmetric?

- Mode with the wavenumber of 1372 cm^-1.

how many bands would you expect to see?

- Two bands. Because degenerate modes show one band.And the mode with the wavenumber of 1372 cm^-1 has intensity 0.

===Charge Analysis===

[[File:Ql Charge co2.png|200px]]

Charge on C: 1.022
Charge on O: -0.511
In expectation, the charge on O should be negative since O is more electronegative than C.

File:Ql Charge co2.png

2019-03-07T13:17:15Z

Ql2018:

Rep:Mod:01500798

2019-03-07T13:10:02Z

Ql2018:

File:QL 640 2.png

2019-03-07T13:09:33Z

Ql2018:

File:QL 640.png

2019-03-07T13:08:55Z

Ql2018: