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MRD:00940575

2020-05-22T23:10:56Z

Jhc14: /* Molecular Reaction Dynamics Write-up */

== '''Molecular Reaction Dynamics Write-up''' ==

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

The energy as a function of the positons of atoms needs to be worked out first. The first order derivative of this gives stationary points. These points correspond to the physically stable reactant and product, and transition state. The transition state is defined by the saddle point on a potential energy surface diagram. This point has the highest energy on the reaction pathway line, so it can be distinguished easily from other stationary points.

''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.''<gallery>
File:00940575_1.png
</gallery><gallery>
File:00940575_2.png
</gallery>At rab and rbc = 90. both bonds has an oscillation that superimpose on each other as they have the same length. Many values of r was put in until the value converged to a flat line with no oscillation that showed that rts= 90.76 pm <gallery>
[[File:00940575_1]]
</gallery>

''Comment on how the mep and the trajectory you just calculated differ.''<gallery>
File:00940575_mep_1.png
</gallery><gallery>
File:00940575_mep_2.png
</gallery><gallery>
File:00940575_p.png
</gallery>In the previous trajectory, rab and rbc was 90.76pm, but when rbc was chaged to 91.76 pm, it increases and rab decreases and asymptotes to a rab=74.04743. Momentum for ab asymptotes too.

''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?''

rbc =74 pm , rab = 200 pm
{| 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>-414.28</nowiki>
|reactive
|rab and rbc has crossed once at the transition state. r ab is oscillating and rbc is increasing so it has reacted.
|<gallery>
File:00940575 31.png
</gallery>
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-4.1</nowiki>
|<nowiki>-420.08</nowiki>
|unreactive
|rab and rbc does not cross, as the momentum was not enough to overcome the barrier it does not react
|<gallery>
File:00940575 32.png
</gallery>
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-413.97</nowiki>
|reactive
|rab and rbc has crossed once at the transition state. r ab is oscillating and rbc is increasing so it has reacted.
|<gallery>
File:00940575 33.png
</gallery>
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.1</nowiki>
|<nowiki>-357.26</nowiki>
|unreactive
|rab and rbc has crossed twice . rab is smaller than rbc for a short while, this means p2 was too large so even the energy was enough to overcome the barrier, the transition state was not formed.
|<gallery>
File:00940575 34.png
</gallery>
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.6</nowiki>
|<nowiki>-349.47</nowiki>
|reactive
|rab and rbc has crossed three times. The saddle point where the transition state is formed is when they meet for the third time.
|<gallery>
File:00940575 35.png
</gallery>
|}

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

The transition state theory uses the surface that intersects with the saddle point. This overestimates the rate of reaction.

File:00940575 1.png

2020-05-22T23:09:45Z

Jhc14: Jhc14 uploaded a new version of File:00940575 1.png

MRD:00940575

2020-05-22T23:00:04Z

Jhc14:

== '''Molecular Reaction Dynamics Write-up''' ==

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

The energy as a function of the positons of atoms needs to be worked out first. The first order derivative of this gives stationary points. These points correspond to the physically stable reactant and product, and transition state. The transition state is defined by the saddle point on a potential energy surface diagram. This point has the highest energy on the reaction pathway line, so it can be distinguished easily from other stationary points.

''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.''<gallery>
File:00940575_1
</gallery><gallery>
File:00940575_2
</gallery>At rab and rbc = 90. both bonds has an oscillation that superimpose on each other as they have the same length. Many values of r was put in until the value converged to a flat line with no oscillation that showed that rts= 90.76 pm <gallery>
[[File:00940575_1]]
</gallery>

''Comment on how the mep and the trajectory you just calculated differ.''<gallery>
File:00940575_mep_1
</gallery><gallery>
File:00940575_mep_2
</gallery><gallery>
File:00940575_p
</gallery>In the previous trajectory, rab and rbc was 90.76pm, but when rbc was chaged to 91.76 pm, it increases and rab decreases and asymptotes to a rab=74.04743. Momentum for ab asymptotes too.

''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?''

rbc =74 pm , rab = 200 pm
{| 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>-414.28</nowiki>
|reactive
|rab and rbc has crossed once at the transition state. r ab is oscillating and rbc is increasing so it has reacted.
|<gallery>
File:00940575 31.png
</gallery>
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-4.1</nowiki>
|<nowiki>-420.08</nowiki>
|unreactive
|rab and rbc does not cross, as the momentum was not enough to overcome the barrier it does not react
|<gallery>
File:00940575 32.png
</gallery>
|-
|<nowiki>-3.1</nowiki>
|<nowiki>-5.1</nowiki>
|<nowiki>-413.97</nowiki>
|reactive
|rab and rbc has crossed once at the transition state. r ab is oscillating and rbc is increasing so it has reacted.
|<gallery>
File:00940575 33.png
</gallery>
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.1</nowiki>
|<nowiki>-357.26</nowiki>
|unreactive
|rab and rbc has crossed twice . rab is smaller than rbc for a short while, this means p2 was too large so even the energy was enough to overcome the barrier, the transition state was not formed.
|<gallery>
File:00940575 34.png
</gallery>
|-
|<nowiki>-5.1</nowiki>
|<nowiki>-10.6</nowiki>
|<nowiki>-349.47</nowiki>
|reactive
|rab and rbc has crossed three times. The saddle point where the transition state is formed is when they meet for the third time.
|<gallery>
File:00940575 35.png
</gallery>
|}

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

The transition state theory uses the surface that intersects with the saddle point. This overestimates the rate of reaction.

File:00940575 35.png

2020-05-22T22:55:06Z

Jhc14:

File:00940575 34.png

2020-05-22T22:54:51Z

Jhc14:

File:00940575 33.png

2020-05-22T22:54:30Z

Jhc14:

File:00940575 32.png

2020-05-22T22:54:16Z

Jhc14:

File:00940575 31.png

2020-05-22T22:53:58Z

Jhc14:

File:00940575 p.png

2020-05-22T22:25:48Z

Jhc14:

File:00940575 mep 2.png

2020-05-22T22:25:32Z

Jhc14:

File:00940575 mep 1.png

2020-05-22T22:25:13Z

Jhc14: Jhc14 uploaded a new version of File:00940575 mep 1.png

File:00940575 2.png

2020-05-22T22:24:52Z

Jhc14: Jhc14 uploaded a new version of File:00940575 2.png

File:00940575 1.png

2020-05-22T22:24:01Z

Jhc14: Jhc14 uploaded a new version of File:00940575 1.png

File:00940575 1.png

2020-05-22T22:23:39Z

Jhc14: Jhc14 uploaded a new version of File:00940575 1.png

MRD:00940575

2020-05-22T22:23:16Z

Jhc14:

MRD:00940575

2020-05-22T21:53:41Z

Jhc14: /* Molecular Reaction Dynamics Write-up */

MRD:00940575

2020-05-22T21:48:21Z

Jhc14: /* Molecular Reaction Dynamics Write-up */

File:00940575 mep 1.png

2020-05-22T21:46:09Z

Jhc14:

File:00940575 2.png

2020-05-22T21:45:48Z

Jhc14:

MRD:00940575

2020-05-22T21:45:18Z

Jhc14: /* Molecular Reaction Dynamics Write-up */

MRD:00940575

2020-05-22T21:12:44Z

Jhc14:

MRD:00940575

2020-05-22T21:11:27Z

Jhc14: /* Exercise 1 */

File:00940575 1.png

2020-05-22T21:08:46Z

Jhc14: Jhc14 uploaded a new version of File:00940575 1.png

File:00940575 1.png

2020-05-22T21:07:04Z

Jhc14:

MRD:00940575

2020-05-22T21:05:41Z

Jhc14: /* Exercise 1 */

MRD:00940575

2020-05-22T21:04:24Z

Jhc14:

== '''Molecular Reaction Dynamics Write-up''' ==

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

The energy as a function of the positons of atoms needs to be worked out first. The first order derivative of this gives stationary points. These points correspond to the physically stable reactant and product, and transition state. The transition state is defined by the saddle point on a potential energy surface diagram. This point has the highest energy on the reaction pathway line, so it can be distinguished easily from other stationary points.

''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.''

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

''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?''

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

MRD:00940575

2020-05-22T16:58:43Z

Jhc14: /* Molecular Reaction Dynamics Write up */

== '''Molecular Reaction Dynamics Write-up''' ==
Exercise 1

MRD:00940575

2020-05-22T16:57:01Z

Jhc14: Created page with " == '''Molecular Reaction Dynamics Write up''' =="

== '''Molecular Reaction Dynamics Write up''' ==