File:Bl1718 14.png

2020-05-22T09:59:13Z

Bl1718:

MRD:Bl1718

2020-05-22T09:32:31Z

2020-05-22T09:04:44Z

Bl1718: /* Reaction dynamics */

== Exercise 1: H-H-H system ==
=== Dynamics from the transition state region ===
==== 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? ====
δV(ri)/δri=0

Transition state is defined as the derivative of potential energy at a local maximum. To distinguish from a local minimum, you can look at the second derivative of the point, if it is smaller than zero it is a maximum.

=== Trajectories from r1 = r2: locating the transition state ===
==== 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 ====

The best estimate of the transition state position is 90.82 pm.

As H + H2 surface is symmetric, the transition state must have r1 = r2 which means rAB = rBC. At transition state, the potential energy reaches its maximum while kinetic energy equals to zero. The transition state distance is found by minimizing the force between atoms,as shown in Figure 1.

The ' Internuclear Distance vs Time' plot (Figure 2) at 90.82 pm shows a straight line suggesting there is no vibration between atoms.The internuclear distance is constant in time because there is no force at transition state.The kinetic energy is close to zero at this point.

[[File:Setting1bl1718.png |500 px|thumb|center|Figure 1: Setting for H + H2 reaction at transition state]]
[[File:Animation1.png |500 px|thumb|center|Figure 2: Internuclear Distance vs Time plot for H + H2 reaction at transition state]]

=== Trajectories from r1 = rts+δ, r2 = rts ===
==== Comment on how the mep and the trajectory you just calculated differ ====

The graphs of mep are smooth line while all graph of trajectory occur as oscillation.
This is because dynamic calculation taken atomic mass and phase conditions into account, the energy is converting between kinetic energy and potential energy. Therefore, the inertial motion causes in oscillation on the graph. As for mep, no potential energy is encountered so it shows a smooth trajectory.It is also aware that the r1 of mep stops at 194 and r1 of dynamic goes to infinity.

[[File:bl1718_1.png |600 px|thumb|center|Figure 3: Contour plot for H + H2 reaction]]
[[File:bl1718_2.png |600 px|thumb|center|Figure 4: Skew plot for H + H2 reaction]]
[[File:bl1718_3.png |600 px|thumb|center|Figure 5: Surface plot for H + H2 reaction]]
[[File:bl1718_4.png |600 px|thumb|center|Figure 6: Internuclear Distance vs Time plot for H + H2 reaction]]
[[File:bl1718_5.png |600 px|thumb|center|Figure 7: Internuclear Velocities vs Time for H + H2 reaction]]
[[File:bl1718_6.png |600 px|thumb|center|Figure 8: Momenta vs Time for H + H2 reaction]]
[[File:bl1718_7.png |600 px|thumb|center|Figure 9: Energy vs Time for H + H2 reaction]]

By switching the values of r1 and r2, the shape of the trajectory does not change. This shows that the trajectory is the same for both side of transition state.(Figure 10)

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

{| class="wikitable"
!p1/g.mol-1.pm.fs-1
!p2/g.mol-1.pm.fs-1
!Etot
!Reactive?
!Description of the dynamics
!Illustration of the trajectory
|-
|<nowiki>-2.56</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-414.280</nowiki>
|Yes
|The reaction curve smoothly passes through transition state region then go to the product side showing reaction products are formed and the reaction is occurring.
|[[File:Animation7.png |300px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-4.1</nowiki>
|<nowiki>-420.077</nowiki>
|No
|The graph shows that the AB distance decreases then bounces back without reaching transition state region. This suggests that there is no product formed.
|[[File:Animation8.png |300px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-413.977</nowiki>
|Yes
|The reaction curve smoothly passes through transition state region then go to the product side showing reaction products are formed and the reaction is occurring.
|[[File:Animation9.png |300px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.1</nowiki>
|<nowiki>-357.277</nowiki>
|No
|The curve line in the plot shows that some products has been formed as it passes through the transition state region, but immediately react backwards to reform reactants.
|[[File:Animation10.png |300px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.6</nowiki>
|<nowiki>-349.477</nowiki>
|Yes
|The curve bounces forwards and backwards in transition state region then go to product region representing the presence of reaction products.
|[[File:Animation11.png |300px]]
|}
In conclusion, the reactivity of a reaction is not related to its kinetic energy. Although some systems have enough energy to cross the activation barrier. The reactants can be reformed by recrossing the barrier.

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

First, the idea of barrier recrossing breaks the assumption of Transition State Theory (TST). TST predictions calculate the rate without counting the recrossing product ,which will overestimate the reaction rate.

Second, energy is considered classic in TST while are quantized in molecular level. This will lead to the overestimate calculation in partition functions and activation energy of the system, which will affect the value of reaction rates.

== Exercise 2: F-H-H system ==
=== PES inspection ===
==== By inspecting the potential energy surfaces, classify the F + H2 and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved? ====
F + H2 reaction is exothermic and H + HF reaction is endothermic. By look at the surface plot of two reactions, the reaction occur with an increase in BC distance and a decrease in AB distance. For F + H2 reaction, the energy curve starts at a higher value and ends in a lower value, suggesting the reaction is exothermic. For H + HF reaction, the curve starts at a lower value and ends in a high value, suggesting it is endothermic.

In the reaction, if the total energy of bond breaking is higher than the total energy of bond forming, the reaction is exothermic. This suggests that the bond strength of H-H bond in H2 is higher than the H-F bond.
[[File:Surface_Plot1_2.png |500px |thumb|center|Figure 11: A graph of F + H2 reaction]]
[[File:Surface_Plot2_2.png |500px |thumb|center|Figure 12: A graph of H + HF reaction]]

==== Locate the approximate position of the transition state ====
For F + H2 reaction, the approximate position of the transition state is where rAB = 181.10 pm and rBC = 74.49 pm. For H + HF reaction, the approximate position of the transition state is where rAB = 74.49 pm and rBC = 181.10 pm. In both situations, rAB = r2 and rBC = r1.
This is determined by finding the distance when force equals or closes to zero. As F is a bigger atom, the distance between F and H are expected to be bigger.

[[File:Surface_Plot3bl1718.png |500 px|thumb|center|Figure 13: Trajectory for F + H2 reaction at transition state]]
[[File:Surface_Plot4bl1718.png |500 px|thumb|center|Figure 14: Trajectory for H + HF reaction at transition state]]

==== Report the activation energy for both reactions ====

The activation energy is the energy at saddle point - energy of reactants.The energy of reactants is determined as the minimum energy by changing r1 while keeping r2 large. For F + H2 reaction, the energy at transition state is -433.981 kJmol-1, the energy of reactants is -435.100 kJmol-1.Thus, the activation energy is 1.12 kJmol-1 for F + H2 reaction. For H + HF reaction, the energy at transition state is -433.981 kJmol-1 and the energy of reactants is -560.600 kJmol-1.Thus, the activation energy for H + HF reaction is 126.6 kJmol-1.

[[File:bl1718_8.png |500 px|thumb|center|Figure 15: Reactant energy in F + H2 reaction]]
[[File:bl1718_9.png |500 px|thumb|center|Figure 16: reactant energy in H + HF reaction]]

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

The condition of reaction trajectory is set as the same rHH as its saddle point but a smaller rFH, both momenta are set at zero (i.e. zero initial kinetic energy). From the Animation, the H2 molecule approaches F atom as it vibrates. At a point, the closer H atom is attracted by F and the formed HF molecule starts to vibrate. The rest H atom gains kinetic energy and repulse from the HF molecule. Since the initial kinetic energy in the system is zero, the Animation shows that some vibrational energy is transferred into kinetic energy. This is also shown in Momenta vs Time plot (Figure 17). The increase in amplitude suggests that a gain in kinetic energy. According to the reference, the reaction is occurred on a highly repulsive surface. When the bimolecule approaches F, the repulsion between Hs causes the closer H atom to recoil, pushing the H atom to F and AB vibration is produced.A schematic representation is also shown in the reference. (Figure 17) (reference)

As the reaction is exothermic, the release of energy can be measured by a thermometer. However, it may be hard to measure as the reaction is carried out in gas phase. A more accurate way is to use a bomb calorimetry. The reaction takes place in a sealed container in water. Heat from reaction in the sealed metal container flow to the water. The temperature difference of water can be measured and the heat flow can be determined.

[[File:Animation14bl1718.png |500 px|thumb|center|Figure 18: Momenta vs Time plot of F + H2 reaction]]

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

'''Observation of changing initial conditions in F + H2 reaction'''
rFH is set at 181.10 pm and rHH is set at 74.49 pm, so the initial potential energy is the same as its transition state.By increasing the momenta, the kinetic energy of biomolecule increases.From the Contour plots, some curves show the presence of barrier recrossing. This suggests that in translation mode, most released energy is gone to vibration energy causing the increase possibility of barrier recrossing. Whereas in vibration mode, most released energy is gone to translation energy, so the repulsed H atom has more kinetic energy. The distribution of energy in two difference modes affect the efficiency of reaction. Vibration mode is more efficient than translation mode.

The position of transition state in F + H2 reaction suggests its surface being a Type-II barrier.

'''Observation of changing initial conditions in H + HF reaction'''

MRD:Bl1718

2020-05-22T06:24:21Z

Bl1718: /* Reaction dynamics */

== Exercise 1: H-H-H system ==
=== Dynamics from the transition state region ===
==== 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? ====
δV(ri)/δri=0

Transition state is defined as the derivative of potential energy at a local maximum. To distinguish from a local minimum, you can look at the second derivative of the point, if it is smaller than zero it is a maximum.

=== Trajectories from r1 = r2: locating the transition state ===
==== 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 ====

The best estimate of the transition state position is 90.82 pm.

As H + H2 surface is symmetric, the transition state must have r1 = r2 which means rAB = rBC. At transition state, the potential energy reaches its maximum while kinetic energy equals to zero. The transition state distance is found by minimizing the force between atoms,as shown in Figure 1.

The ' Internuclear Distance vs Time' plot (Figure 2) at 90.82 pm shows a straight line suggesting there is no vibration between atoms.The internuclear distance is constant in time because there is no force at transition state.The kinetic energy is close to zero at this point.

[[File:Setting1bl1718.png |500 px|thumb|center|Figure 1: Setting for H + H2 reaction at transition state]]
[[File:Animation1.png |500 px|thumb|center|Figure 2: Internuclear Distance vs Time plot for H + H2 reaction at transition state]]

=== Trajectories from r1 = rts+δ, r2 = rts ===
==== Comment on how the mep and the trajectory you just calculated differ ====

The graphs of mep are smooth line while all graph of trajectory occur as oscillation.
This is because dynamic calculation taken atomic mass and phase conditions into account, the energy is converting between kinetic energy and potential energy. Therefore, the inertial motion causes in oscillation on the graph. As for mep, no potential energy is encountered so it shows a smooth trajectory.It is also aware that the r1 of mep stops at 194 and r1 of dynamic goes to infinity.

[[File:bl1718_1.png |600 px|thumb|center|Figure 3: Contour plot for H + H2 reaction]]
[[File:bl1718_2.png |600 px|thumb|center|Figure 4: Skew plot for H + H2 reaction]]
[[File:bl1718_3.png |600 px|thumb|center|Figure 5: Surface plot for H + H2 reaction]]
[[File:bl1718_4.png |600 px|thumb|center|Figure 6: Internuclear Distance vs Time plot for H + H2 reaction]]
[[File:bl1718_5.png |600 px|thumb|center|Figure 7: Internuclear Velocities vs Time for H + H2 reaction]]
[[File:bl1718_6.png |600 px|thumb|center|Figure 8: Momenta vs Time for H + H2 reaction]]
[[File:bl1718_7.png |600 px|thumb|center|Figure 9: Energy vs Time for H + H2 reaction]]

By switching the values of r1 and r2, the shape of the trajectory does not change. This shows that the trajectory is the same for both side of transition state.(Figure 10)

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

{| class="wikitable"
!p1/g.mol-1.pm.fs-1
!p2/g.mol-1.pm.fs-1
!Etot
!Reactive?
!Description of the dynamics
!Illustration of the trajectory
|-
|<nowiki>-2.56</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-414.280</nowiki>
|Yes
|The reaction curve smoothly passes through transition state region then go to the product side showing reaction products are formed and the reaction is occurring.
|[[File:Animation7.png |300px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-4.1</nowiki>
|<nowiki>-420.077</nowiki>
|No
|The graph shows that the AB distance decreases then bounces back without reaching transition state region. This suggests that there is no product formed.
|[[File:Animation8.png |300px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-413.977</nowiki>
|Yes
|The reaction curve smoothly passes through transition state region then go to the product side showing reaction products are formed and the reaction is occurring.
|[[File:Animation9.png |300px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.1</nowiki>
|<nowiki>-357.277</nowiki>
|No
|The curve line in the plot shows that some products has been formed as it passes through the transition state region, but immediately react backwards to reform reactants.
|[[File:Animation10.png |300px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.6</nowiki>
|<nowiki>-349.477</nowiki>
|Yes
|The curve bounces forwards and backwards in transition state region then go to product region representing the presence of reaction products.
|[[File:Animation11.png |300px]]
|}
In conclusion, the reactivity of a reaction is not related to its kinetic energy. Although some systems have enough energy to cross the activation barrier. The reactants can be reformed by recrossing the barrier.

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

First, the idea of barrier recrossing breaks the assumption of Transition State Theory (TST). TST predictions calculate the rate without counting the recrossing product ,which will overestimate the reaction rate.

Second, energy is considered classic in TST while are quantized in molecular level. This will lead to the overestimate calculation in partition functions and activation energy of the system, which will affect the value of reaction rates.

== Exercise 2: F-H-H system ==
=== PES inspection ===
==== By inspecting the potential energy surfaces, classify the F + H2 and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved? ====
F + H2 reaction is exothermic and H + HF reaction is endothermic. By look at the surface plot of two reactions, the reaction occur with an increase in BC distance and a decrease in AB distance. For F + H2 reaction, the energy curve starts at a higher value and ends in a lower value, suggesting the reaction is exothermic. For H + HF reaction, the curve starts at a lower value and ends in a high value, suggesting it is endothermic.

In the reaction, if the total energy of bond breaking is higher than the total energy of bond forming, the reaction is exothermic. This suggests that the bond strength of H-H bond in H2 is higher than the H-F bond.
[[File:Surface_Plot1_2.png |500px |thumb|center|Figure 11: A graph of F + H2 reaction]]
[[File:Surface_Plot2_2.png |500px |thumb|center|Figure 12: A graph of H + HF reaction]]

==== Locate the approximate position of the transition state ====
For F + H2 reaction, the approximate position of the transition state is where rAB = 181.10 pm and rBC = 74.49 pm. For H + HF reaction, the approximate position of the transition state is where rAB = 74.49 pm and rBC = 181.10 pm. In both situations, rAB = r2 and rBC = r1.
This is determined by finding the distance when force equals or closes to zero. As F is a bigger atom, the distance between F and H are expected to be bigger.

[[File:Surface_Plot3bl1718.png |500 px|thumb|center|Figure 13: Trajectory for F + H2 reaction at transition state]]
[[File:Surface_Plot4bl1718.png |500 px|thumb|center|Figure 14: Trajectory for H + HF reaction at transition state]]

==== Report the activation energy for both reactions ====

The activation energy is the energy at saddle point - energy of reactants.The energy of reactants is determined as the minimum energy by changing r1 while keeping r2 large. For F + H2 reaction, the energy at transition state is -433.981 kJmol-1, the energy of reactants is -435.100 kJmol-1.Thus, the activation energy is 1.12 kJmol-1 for F + H2 reaction. For H + HF reaction, the energy at transition state is -433.981 kJmol-1 and the energy of reactants is -560.600 kJmol-1.Thus, the activation energy for H + HF reaction is 126.6 kJmol-1.

[[File:bl1718_8.png |500 px|thumb|center|Figure 15: Reactant energy in F + H2 reaction]]
[[File:bl1718_9.png |500 px|thumb|center|Figure 16: reactant energy in H + HF reaction]]

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

The condition of reaction trajectory is set as the same rHH as its saddle point but a smaller rFH, both momenta are set at zero (i.e. zero initial kinetic energy). From the Animation, the H2 molecule approaches F atom as it vibrates. At a point, the closer H atom is attracted by F and the formed HF molecule starts to vibrate. The rest H atom gains kinetic energy and moves away from the HF molecule. Since the initial kinetic energy in the system is zero, the Animation shows that some vibrational energy is transferred into kinetic energy. This is also shown in Momenta vs Time plot (Figure 17). The increase in amplitude suggests that a gain in kinetic energy.
As the reaction is exothermic, the release of energy can be measured by a thermometer. However, it may be hard to measure as the reaction is carried out in gas phase. A more accurate way is to use a bomb calorimetry. The reaction takes place in a sealed container in water. Heat from reaction in the sealed metal container flow to the water. The temperature difference of water can be measured and the heat flow can be determined.

[[File:Animation14bl1718.png |500 px|thumb|center|Figure 17: Momenta vs Time plot of F + H2 reaction]]

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

MRD:Bl1718

2020-05-22T06:07:22Z

Bl1718: /* Reaction dynamics */

== Exercise 1: H-H-H system ==
=== Dynamics from the transition state region ===
==== 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? ====
δV(ri)/δri=0

Transition state is defined as the derivative of potential energy at a local maximum. To distinguish from a local minimum, you can look at the second derivative of the point, if it is smaller than zero it is a maximum.

=== Trajectories from r1 = r2: locating the transition state ===
==== 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 ====

The best estimate of the transition state position is 90.82 pm.

As H + H2 surface is symmetric, the transition state must have r1 = r2 which means rAB = rBC. At transition state, the potential energy reaches its maximum while kinetic energy equals to zero. The transition state distance is found by minimizing the force between atoms,as shown in Figure 1.

The ' Internuclear Distance vs Time' plot (Figure 2) at 90.82 pm shows a straight line suggesting there is no vibration between atoms.The internuclear distance is constant in time because there is no force at transition state.The kinetic energy is close to zero at this point.

[[File:Setting1bl1718.png |500 px|thumb|center|Figure 1: Setting for H + H2 reaction at transition state]]
[[File:Animation1.png |500 px|thumb|center|Figure 2: Internuclear Distance vs Time plot for H + H2 reaction at transition state]]

=== Trajectories from r1 = rts+δ, r2 = rts ===
==== Comment on how the mep and the trajectory you just calculated differ ====

The graphs of mep are smooth line while all graph of trajectory occur as oscillation.
This is because dynamic calculation taken atomic mass and phase conditions into account, the energy is converting between kinetic energy and potential energy. Therefore, the inertial motion causes in oscillation on the graph. As for mep, no potential energy is encountered so it shows a smooth trajectory.It is also aware that the r1 of mep stops at 194 and r1 of dynamic goes to infinity.

[[File:bl1718_1.png |600 px|thumb|center|Figure 3: Contour plot for H + H2 reaction]]
[[File:bl1718_2.png |600 px|thumb|center|Figure 4: Skew plot for H + H2 reaction]]
[[File:bl1718_3.png |600 px|thumb|center|Figure 5: Surface plot for H + H2 reaction]]
[[File:bl1718_4.png |600 px|thumb|center|Figure 6: Internuclear Distance vs Time plot for H + H2 reaction]]
[[File:bl1718_5.png |600 px|thumb|center|Figure 7: Internuclear Velocities vs Time for H + H2 reaction]]
[[File:bl1718_6.png |600 px|thumb|center|Figure 8: Momenta vs Time for H + H2 reaction]]
[[File:bl1718_7.png |600 px|thumb|center|Figure 9: Energy vs Time for H + H2 reaction]]

By switching the values of r1 and r2, the shape of the trajectory does not change. This shows that the trajectory is the same for both side of transition state.(Figure 10)

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

{| class="wikitable"
!p1/g.mol-1.pm.fs-1
!p2/g.mol-1.pm.fs-1
!Etot
!Reactive?
!Description of the dynamics
!Illustration of the trajectory
|-
|<nowiki>-2.56</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-414.280</nowiki>
|Yes
|The reaction curve smoothly passes through transition state region then go to the product side showing reaction products are formed and the reaction is occurring.
|[[File:Animation7.png |300px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-4.1</nowiki>
|<nowiki>-420.077</nowiki>
|No
|The graph shows that the AB distance decreases then bounces back without reaching transition state region. This suggests that there is no product formed.
|[[File:Animation8.png |300px]]
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-413.977</nowiki>
|Yes
|The reaction curve smoothly passes through transition state region then go to the product side showing reaction products are formed and the reaction is occurring.
|[[File:Animation9.png |300px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.1</nowiki>
|<nowiki>-357.277</nowiki>
|No
|The curve line in the plot shows that some products has been formed as it passes through the transition state region, but immediately react backwards to reform reactants.
|[[File:Animation10.png |300px]]
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.6</nowiki>
|<nowiki>-349.477</nowiki>
|Yes
|The curve bounces forwards and backwards in transition state region then go to product region representing the presence of reaction products.
|[[File:Animation11.png |300px]]
|}
In conclusion, the reactivity of a reaction is not related to its kinetic energy. Although some systems have enough energy to cross the activation barrier. The reactants can be reformed by recrossing the barrier.

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

First, the idea of barrier recrossing breaks the assumption of Transition State Theory (TST). TST predictions calculate the rate without counting the recrossing product ,which will overestimate the reaction rate.

Second, energy is considered classic in TST while are quantized in molecular level. This will lead to the overestimate calculation in partition functions and activation energy of the system, which will affect the value of reaction rates.

== Exercise 2: F-H-H system ==
=== PES inspection ===
==== By inspecting the potential energy surfaces, classify the F + H2 and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved? ====
F + H2 reaction is exothermic and H + HF reaction is endothermic. By look at the surface plot of two reactions, the reaction occur with an increase in BC distance and a decrease in AB distance. For F + H2 reaction, the energy curve starts at a higher value and ends in a lower value, suggesting the reaction is exothermic. For H + HF reaction, the curve starts at a lower value and ends in a high value, suggesting it is endothermic.

In the reaction, if the total energy of bond breaking is higher than the total energy of bond forming, the reaction is exothermic. This suggests that the bond strength of H-H bond in H2 is higher than the H-F bond.
[[File:Surface_Plot1_2.png |500px |thumb|center|Figure 11: A graph of F + H2 reaction]]
[[File:Surface_Plot2_2.png |500px |thumb|center|Figure 12: A graph of H + HF reaction]]

==== Locate the approximate position of the transition state ====
For F + H2 reaction, the approximate position of the transition state is where rAB = 181.10 pm and rBC = 74.49 pm. For H + HF reaction, the approximate position of the transition state is where rAB = 74.49 pm and rBC = 181.10 pm. In both situations, rAB = r2 and rBC = r1.
This is determined by finding the distance when force equals or closes to zero. As F is a bigger atom, the distance between F and H are expected to be bigger.

[[File:Surface_Plot3bl1718.png |500 px|thumb|center|Figure 13: Trajectory for F + H2 reaction at transition state]]
[[File:Surface_Plot4bl1718.png |500 px|thumb|center|Figure 14: Trajectory for H + HF reaction at transition state]]

==== Report the activation energy for both reactions ====

The activation energy is the energy at saddle point - energy of reactants.The energy of reactants is determined as the minimum energy by changing r1 while keeping r2 large. For F + H2 reaction, the energy at transition state is -433.981 kJmol-1, the energy of reactants is -435.100 kJmol-1.Thus, the activation energy is 1.12 kJmol-1 for F + H2 reaction. For H + HF reaction, the energy at transition state is -433.981 kJmol-1 and the energy of reactants is -560.600 kJmol-1.Thus, the activation energy for H + HF reaction is 126.6 kJmol-1.

[[File:bl1718_8.png |500 px|thumb|center|Figure 15: Reactant energy in F + H2 reaction]]
[[File:bl1718_9.png |500 px|thumb|center|Figure 16: reactant energy in H + HF reaction]]

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

[[File:Animation14bl1718.png |500 px|thumb|center|Figure 17: Momenta vs Time plot of F + H2 reaction]]

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

File:Animation14bl1718.png

2020-05-22T06:04:42Z

Bl1718:

MRD:Bl1718

2020-05-22T05:46:47Z

2020-05-21T13:42:35Z

Bl1718: /* 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? */