ChemWiki - User contributions [en]

MRD:ti1918

2020-05-15T22:54:53Z

Ti1918: /* Question 5: */

[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.|323x323px]]

= Thomas Imperato MRD Report =

=== Exercise 1: ===

==== Question 1: ====
The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.

==== Question 2: ====
The best estimate for the transition state position was 90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.|centre]]

==== Question 3: ====
The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule. Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.
[[File:Screenshot 2020-05-12 at 14.16.26.png|thumb|Figure 3 - Reactive and Unreactive Trajectory Table.|centre]]

==== Question 4: ====
We can conclude from Figure 3 that even if the total energy is greater than the activation energy a reaction won't always occur as the translational and rotational also needs to be in the correct composition.

==== Question 5: ====
From the results in Figure 3 we can see that the total energy does not always predict the outcome of the interaction. So therefore experimental data will differ from the theoretical as the theoretical assumes that whenever the energy is greater than the activation energy a reaction will occur. But the experimental data won't always agree with this as in reality (experimental) the distribution of energy to vibrational etc components is more important.

=== Exercise 2: ===
[[File:SurfacePlotEndo.png|thumb|Figure 4 - Surface Plot for HF, H reaction.|centre]] [[File:SurfacePlotExo1.png|thumb|Figure 5 - Surface Plot for HH, F reaction.|right]]
==== Question 1: ====
From Figure 4 we can see that the reaction between HF and H is endothermic as the potential energy of the system becomes more positive due to the large energy input required to break the H-F bond overpowers the release of energy when the smaller H-H bond is formed. In Figure 5 we see that the HH and F reaction is exothermic as the potential energy of the system becomes more negative due to the release of energy when the strong H-F bond is formed. It all revolves around the fact that the H-F bond has greater bond energy than the H-H bond.

==== Question 2: ====
The approximate transition state for the reactions was 74 pm distance between the hydrogens and 182 pm between the hydrogen and fluorine. In Figure 6 we see that there is only a single dot on the plot using a MEP calculation, a classic property of a transition state.
[[File:TSDot1.png|thumb|Figure 6 - Contour Plot of Reaction, MEP.|centre]]

==== Question 3: ====
In order to find the activation energy you must find the difference between the potential energy of the transition state and the potential energy of the reactants. The potential energy of the transition state was found to be -433.945 Kj/mol by using a MEP calculation at the TS point. The potential energy of the reactants that form a hydrogen molecule is -558 Kj/mol so the activation energy is 124.055 Kj/mol. For the reverse reaction that forms a HF molecule has reactants with a potential energy of -434.245 Kj/mol so the activation energy is 0.300 Kj/mol.

==== Question 4: ====
The release of the reactant energy is carried out by the mechanism known as chemiluminescence, where light energy is emitted in response to the exothermic chemical reaction. After the reaction the product is in a quantum excited state and returns to the ground state by emitting a photon. This can be analysed by a technique called IRCL which provides data so that we can tell if the energy released is more vibrational or rotational depending on how intense the IRCL feedback is. To calculate the actual value of the energy released calorimetry should be carried out which is a straight forward experimental procedure.

==== Question 5: ====
The distribution of vibrational and rotational is very important in affecting the efficiency of the reaction as even with a large enough potential energy, if the vibrational and rotational aren't correct then a reaction can't occur. According to Polanyi's rules, if the reactant is similar to the transition state then the reaction is exothermic and vibrational energy is very important in allowing the reaction to occur. If the product is similar to the transition state then the reaction is endothermic and the vibrational energy is not that vital for the reaction to take place.

MRD:ti1918

2020-05-15T18:14:43Z

Ti1918: /* Question 4: */

MRD:ti1918

2020-05-15T11:05:38Z

Ti1918: /* Question 3: */

MRD:ti1918

2020-05-15T10:40:26Z

Ti1918:

File:TSDot1.png

2020-05-14T18:01:29Z

Ti1918:

MRD:ti1918

2020-05-14T18:01:17Z

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2020-05-14T18:00:32Z

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MRD:ti1918

2020-05-14T17:48:24Z

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MRD:ti1918

2020-05-14T17:48:13Z

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MRD:ti1918

2020-05-14T17:47:07Z

Ti1918:

File:TSDot.png

2020-05-14T17:46:26Z

Ti1918:

MRD:ti1918

2020-05-14T17:45:53Z

Ti1918:

MRD:ti1918

2020-05-14T14:49:17Z

Ti1918:

File:SurfacePlotEndo.png

2020-05-14T14:48:51Z

Ti1918:

MRD:ti1918

2020-05-14T14:47:07Z

Ti1918:

File:SurfacePlotExo1.png

2020-05-14T14:46:50Z

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MRD:ti1918

2020-05-14T14:45:35Z

Ti1918:

File:SurfacePlotExo.png

2020-05-14T14:45:03Z

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MRD:ti1918

2020-05-14T14:43:17Z

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MRD:ti1918

2020-05-14T14:42:57Z

Ti1918:

File:HFTransitionState.png

2020-05-14T14:42:34Z

Ti1918:

File:Animation.png

2020-05-14T14:31:17Z

Ti1918: Ti1918 uploaded a new version of File:Animation.png

MRD:ti1918

2020-05-14T14:27:35Z

Ti1918:

File:Animation.png

2020-05-14T14:26:24Z

Ti1918: Ti1918 uploaded a new version of File:Animation.png

MRD:ti1918

2020-05-14T14:25:19Z

Ti1918:

MRD:ti1918

2020-05-14T13:51:44Z

Ti1918:

MRD:ti1918

2020-05-14T13:50:34Z

Ti1918:

File:Surface Plot-1.png

2020-05-14T13:49:22Z

Ti1918: Ti1918 uploaded a new version of File:Surface Plot-1.png

MRD:ti1918

2020-05-14T13:48:57Z

Ti1918:

MRD:ti1918

2020-05-14T13:40:44Z

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MRD:ti1918

2020-05-14T13:39:29Z

Ti1918:

File:Surface Plot.png

2020-05-14T13:37:19Z

Ti1918: Ti1918 uploaded a new version of File:Surface Plot.png

MRD:ti1918

2020-05-14T13:37:03Z

Ti1918:

MRD:ti1918

2020-05-14T13:17:49Z

Ti1918:

MRD:ti1918

2020-05-14T13:17:13Z

Ti1918:

MRD:ti1918

2020-05-14T13:15:22Z

Ti1918:

[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.|323x323px]]

=== Question 1: ===
The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.

=== Question 2: ===
The best estimate for the transition state position was 0.90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.|centre]]

=== Question 3: ===
The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule. Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.
#[[File:Screenshot 2020-05-12 at 14.16.26.png|thumb|Figure 3 - Reactive and Unreactive Trajectory Table.|centre]]

=== Question 4: ===
We can conclude from Figure 3 that even if the total energy is greater than the activation energy a reaction won't always occur as the translational and rotational also needs to be taken in the correct composition.

=== Question 5: ===
From the results in Figure 3 we can see that the total energy does not always predict the outcome of the interaction. So therefore experimental data will differ from the theoretical as the theoretical assumes that whenever the energy is greater than the activation energy a reaction will occur. But the experimental data won't always agree with this as in reality (experimental) the distribution of energy to vibrational etc components is more important.

MRD:ti1918

2020-05-14T13:11:52Z

Ti1918:

[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.|323x323px]]
# The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.

# The best estimate for the transition state position was 0.90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.|centre]]

#The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule. Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.

#[[File:Screenshot 2020-05-12 at 14.16.26.png|thumb|Figure 3 - Reactive and Unreactive Trajectory Table.|centre]] We can conclude that even if the total energy is greater than the activation energy a reaction won't always occur as the translational and rotational also needs to be taken in the correct composition.

# From the results in Figure 3 we can see that the total energy does not always predict the outcome of the interaction. So therefore experimental data will differ from the theoretical as the theoretical assumes that whenever the energy is greater than the activation energy a reaction will occur. But the experimental data won't always agree with this as in reality (experimental) the distribution of energy to vibrational etc components is more important.

MRD:ti1918

2020-05-14T13:11:28Z

Ti1918:

[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.|323x323px]]
# The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.
# The best estimate for the transition state position was 0.90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.|centre]]
#The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule. Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.
#[[File:Screenshot 2020-05-12 at 14.16.26.png|thumb|Figure 3 - Reactive and Unreactive Trajectory Table.|centre]] We can conclude that even if the total energy is greater than the activation energy a reaction won't always occur as the translational and rotational also needs to be taken in the correct composition.
# From the results in Figure 3 we can see that the total energy does not always predict the outcome of the interaction. So therefore experimental data will differ from the theoretical as the theoretical assumes that whenever the energy is greater than the activation energy a reaction will occur. But the experimental data won't always agree with this as in reality (experimental) the distribution of energy to vibrational etc components is more important.

MRD:ti1918

2020-05-14T13:07:31Z

Ti1918:

[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.|323x323px]]
# The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.
# The best estimate for the transition state position was 0.90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.|centre]]
#The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule. Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.
#[[File:Screenshot 2020-05-12 at 14.16.26.png|thumb|Figure 3 - Reactive and Unreactive Trajectory Table.|centre]]
# From the results in Figure 3 we can see that the total energy does not always predict the outcome of the interaction. So therefore experimental data will differ from the theoretical as the theoretical assumes that whenever the energy is greater than the activation energy a reaction will occur. But the experimental data won't always agree with this as in reality (experimental) the distribution of energy to vibrational etc components is more important.

MRD:ti1918

2020-05-12T16:54:15Z

Ti1918:

[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.|323x323px]]
# The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.
# The best estimate for the transition state position was 0.90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.|centre]]
#The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule.Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.
#[[File:Screenshot 2020-05-12 at 14.16.26.png|thumb|Figure 3 - Reactive and Unreactive Trajectory Table.|centre]]
# From the results in Figure 3 we can see that the total energy does not always predict the outcome of the interaction. So therefore experimental data will differ from the theoretical as the theoretical assumes that whenever the energy is greater than the activation energy a reaction will occur. But the experimental data won't always agree with this as in reality (experimental) the distribution of energy to vibrational etc components is more important.

MRD:ti1918

2020-05-12T13:29:35Z

Ti1918:

[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.|323x323px]]
# The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.
# The best estimate for the transition state position was 0.90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.|centre]]
#The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule.Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.
#[[File:Screenshot 2020-05-12 at 14.16.26.png|thumb|Figure 3 - Reactive and Unreactive Trajectory Table.|centre]]
# From the results in Figure 3we can see that the total energy does not always predict the outcome of the interaction. So therefore experimental data will differ from the theoretical as the theoretical assumes that whenever the energy is greater than the activation energy a reaction will occur. But the experimental data won't always agree with this as in reality (experimental) the distribution of energy to vibrational etc components is more important.

MRD:ti1918

2020-05-12T13:25:37Z

Ti1918:

MRD:ti1918

2020-05-12T13:20:02Z

Ti1918:

MRD:ti1918

2020-05-12T13:19:36Z

Ti1918:

File:Screenshot 2020-05-12 at 14.16.26.png

2020-05-12T13:17:12Z

Ti1918:

MRD:ti1918

2020-05-12T12:55:56Z

Ti1918:

MRD:ti1918

2020-05-12T12:54:33Z

Ti1918:

[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.|323x323px]]
# The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.
# The best estimate for the transition state position was 0.90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.|centre]]
#The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule.Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.
# {| 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 |- |-2.56 |-5.1 | | | | |- |-3.1 |-4.1 | | | | |- |-3.1 |-5.1 | | | | |- |-5.1 |-10.1 | | | | |- |-5.1 |-10.6 | | | | |}

MRD:ti1918

2020-05-12T12:48:01Z

Ti1918:

# The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.
# The best estimate for the transition state position was 0.90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.
# The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule.Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.
# {| 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 |- |-2.56 |-5.1 | | | | |- |-3.1 |-4.1 | | | | |- |-3.1 |-5.1 | | | | |- |-5.1 |-10.1 | | | | |- |-5.1 |-10.6 | | | | |}
[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.]]
[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.]]

MRD:ti1918

2020-05-12T12:16:28Z

Ti1918:

# The transition state on a potential energy surface diagram is mathematically defined by the derivative ∂V(ri)/∂ri equalling zero. It can be identified by starting trajectories near its approximate location and seeing whether they form products or revert back to reactants; if you change the geometry one way and it forms products and then change it the opposite way and it forms reactants then that is the transition state. It can be distinguished from other local minima as on the surface plot it is the point where all gradients vanish.
# The best estimate for the transition state position was 0.90 pm as the oscillations in Figure 1 were the smallest at this distance. Also, as I change the trajectory so that one atom has a tiny momentum of 0.1, a hydrogen molecule is formed and the other atom leaves the molecule shown in Figure 2.
# The MEP and dynamic plots differ as the MEP plot does not show vibrational energy of the oscillating hydrogen molecule.Furthermore, the MEP plot internuclear distance begins to plateau as the number of steps increases whereas the dynamic plot follows a relatively linear path.
[[File:Transition_State_Internuclear_Distance_Vs_Time.png|thumb|Figure 1 - Internuclear Distance Vs Time Plot of Transition State Estimation.]]
[[File:Transition_State_Trajectory.png|thumb|Figure 2 - Internuclear Distance Vs Time Plot of Transition State Trajectory.]]

MRD:ti1918

2020-05-12T12:07:52Z

Ti1918: