File:Exe2 Q5 3.png

2020-05-22T17:09:14Z

Xs2218:

File:Exe2 Q5 2.png

2020-05-22T17:00:54Z

Xs2218:

File:Exe2 Q5 1.png

2020-05-22T16:57:25Z

Xs2218:

MRD:xs2218

2020-05-22T13:06:19Z

Xs2218: /* Q5 */

==Molecular Reaction Dynamic Lab==
===Exercise1: H + H2 system===

====Q1====
On a potential energy surface diagram, the transition state is mathematically defined as a first-order saddle point, ∂V('''ri''')/∂V('''ri''')/∂'''ri'''=0.
The transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish from the local minimum on the PES, the first-order saddle point is at a minimum in all directions except for one and the trajectories near the transition state roll towards reactants or products. See the surface plot below, the TS is at a saddle point.
[[File:Q1_xs2218.png|thumb|center|Surface plot of transition state.]]

====Q2====
My best estimate of rtsis 90.775pm, it is when the force along AB and BC is 0 KJ.mol-1.pm-1. The atoms are not bonded at TS
The internuclear distance vs time plot shows 2 straight lines illustrating that when the atoms are at the transition state, the internuclear distance does not change, no such oscillating behavior where the 2 lines are wavy when not at TS.
[[File:Exe1 Q2.png|thumb|center|internuclear distance vs time plot at TS|350px]]

====Q3====
As shown from the surface plots below, two different calculation types give different trajectories. The MEP shows the minimal energy path that any point on the path is at energy minimum in all directions perpendicular to the path which passes through at least one saddle point. Looking at the plots from the same angle, the dynamic surface plot gives a wavy line coming out of the BC distance axis whereas the MEP surface plot gives a relatively straight line within the BC distance axis.
[[File:Exe1_Q3_mep_xs2218.png|thumb|left|Surface plot of MEP calculation type.|350px]]
[[File:Exe1_Q3_dynamics_xs2218.png|thumb|center|Surface plot of dynamics calculation type.|350px]]

====Q4====
{| class="wikitable" border="1"
|+ Table 1 rAB=74pm, rBC=200pm
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || yes || AB are bonded at first until B bonds with C and A moves away, prodct BC formed || [[File:table1_row1.png|150px]] ||
|-
| -3.1 || -4.1 || -420.077 || No || AB is always bonded, no product formed || [[File:table1_row2.png|150px]] ||
|-
| -3.1 || -5.1 || -413.977 || yes || AB are bonded at first until B is bonded with C and A moves away, prodct BC formed || [[File:table1_row3.png|150px]] ||
|-
| -5.1 || -10.1 || -357.277 || No || AB are bonded at first until B bonds with C, but eventually B is back to bonded with A, C moves away, no product BC formed || [[File:table1_row4.png|150px]] ||
|-
| -5.1 || -10.6 || -349.477 || yes || AB are bonded at first until C approaches and B bonds with C, then B bonds with A again, eventually, B bonds with C and forms a product BC, A moves away|| [[File:table1_row5.png|150px]] ||
|}

In conclusion, trajectories starting with the same positions but with higher values of momenta would not always be reactive, although the total energy is getting more positive, therefore, the hypothesis is not supported

====Q5====
The Transition State Theory assumes that Rcl is that all trajectories with a KE greater than the activation energy will be reactive, however, our experimental has suggested that this is not true.
Transition state theory is based on classical mechanics, Quasi-equilibrium basically covers that if the atoms did not have enough energy to collide to form the TS, the reaction would not be feasible. However, in quantum mechanics, as long as the barrier has a finite amount of energy, the atoms can still tunnel across the barrier which means that the reaction could still be feasible even if the atoms do not collide enough energy to cross the energy barrier.
Quantum tunneling is minimal in TS theory, if quantum tunneling was present, the reaction rate would increase.
In transition state theory, it assumes that the step from TS to products is the rate-determining step, but in reality, it might not be true, the reaction rate would. be decreased

===Exercise2: F-H-H system===

====Q1====
F + H2 is exothermic, whereas HF + H is endothermic.

H-H bond strength is weaker than the H-F bond. The energy absorbed to break the F-F bond is smaller than the energy needed to make the new bond H-F, the excess energy is then released as heat, so the reaction is exothermic. However, for HF + H, more energy is needed to break the H-F bond than to make the F-F bond, overall, energy is being absorbed rather than released, so the reaction is endothermic.

====Q2====
The approximate position of transition state: rAB=181.1 pm, rBC=74.488pm
The forces along AB and BC at this position are both 0. According to Hammond Postulate, an exothermic reaction has an early TS, whereas an endothermic reaction has a late TS, therefore, one of the eigenvalues at TS is positive, another one is negative. In this case, the Hessian eigenvalues are -0.002 and +0.332.
As shown in the surface plot below, now it is at a saddle point which confirms the atoms are at the transition state.
[[File:Q7_xs2218_new.png|thumb|center|Surface Plot of transition state.]]

====Q3====
The transition state energy is reported as -433.981 kJ.mol-1.
A plot of energy vs time is plotted at TS as shown below.
[[File:Exe2_Q3_TSenergy.png|thumb|center|Energy vs Time plot at TS for F-H-H system.]]

For the exothermic reaction F + H2, the initial state energy is -435.059 kJ.mol-1. Activation energy can then be calculated as 1.08 kJ.mol-1.
[[File:Exe2_Q3_exoenergy.png|thumb|center|Energy vs Time plot at initial state for exothermic rxn.]]

For the endothermic reaction HF + H, the initial state energy is -560.700 kJ.mol-1. Activation energy for this reaction is 126.02 kJ.mol-1.
[[File:Exe2_Q3_endoenergy.png|thumb|center|Energy vs Time plot at initial state for endothermic rxn.]]

By locating a structure neighboring the TS, the plot of Energy vs time shows that the energy dropping clearly.
[[File:Exe2_Q3_endoenergy_new.png|thumb|center|Energy vs Time plot at the neighboring structure of transition state for endothermic rxn.]]

(The plot of the neighboring structure of TS for exothermic reaction is not shown because the difference is too small to be spotted.)

====Q4====
The release of reaction energy is basically a release of vibrational kinetic energy converted from potential energy. A contour plot of a reactive trajectory is shown below to illustrate.
[[File:Exe2_Q4_xs2218.png|thumb|center|A contour plot of a reactive trajectory in a F-H-H system.]]

An experimental method to confirm it is IR spectrometry. IR absorption would have stronger overtones that measuring the transition from the first to second state, while IR emission measures the transition from the first to the ground state.

====Q5====
In general, vibrational energy is better than promoting endothermic reactions than exothermic reactions, whereas translational energy is better than promoting exothermic reactions than endothermic reactions.
When having translational energy, the atoms would bounce onto the potential wall and bounce back, when having vibrational energy, the atoms fall down the reaction channel and overcome the reaction barrier, forming the product.

===References===
1. R. J. Silbey, R. A. Alberty, M. G. Bawendi Physical Chemistry, 4th ed, John Wiley & Sons, 2005.
2. J. I. Steinfeld, J. S. Francisco, W. L. Hase Chemical Kinetic and Dynamics 2nd ed., Prentice-Hall, 1998, chapter 10
3. K. J. Laidler Chemical Kinetics 3rd ed., Harper-Collins, 1987, chapter 4
4. M. J. Pilling, P. W. Seakins Reaction Kinetics, 2nd ed., OUP, 1995, chapter 4
5.Atkins, de Paula, Keeler, Physical Chemistry, 11th ed
6. I. N. Levine, Physical Chemistry, McGraw-Hill, 4th ed

MRD:xs2218

2020-05-22T12:26:17Z

Xs2218: /* Q4 */

File:Exe2 Q4 xs2218.png

2020-05-22T12:25:03Z

Xs2218:

MRD:xs2218

2020-05-22T12:20:40Z

Xs2218: /* Q3 */

==Molecular Reaction Dynamic Lab==
===Exercise1: H + H2 system===

====Q1====
On a potential energy surface diagram, the transition state is mathematically defined as a first-order saddle point, ∂V('''ri''')/∂V('''ri''')/∂'''ri'''=0.
The transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish from the local minimum on the PES, the first-order saddle point is at a minimum in all directions except for one and the trajectories near the transition state roll towards reactants or products. See the surface plot below, the TS is at a saddle point.
[[File:Q1_xs2218.png|thumb|center|Surface plot of transition state.]]

====Q2====
My best estimate of rtsis 90.775pm, it is when the force along AB and BC is 0 KJ.mol-1.pm-1. The atoms are not bonded at TS
The internuclear distance vs time plot shows 2 straight lines illustrating that when the atoms are at the transition state, the internuclear distance does not change, no such oscillating behavior where the 2 lines are wavy when not at TS.
[[File:Exe1 Q2.png|thumb|center|internuclear distance vs time plot at TS|350px]]

====Q3====
As shown from the surface plots below, two different calculation types give different trajectories. The MEP shows the minimal energy path that any point on the path is at energy minimum in all directions perpendicular to the path which passes through at least one saddle point. Looking at the plots from the same angle, the dynamic surface plot gives a wavy line coming out of the BC distance axis whereas the MEP surface plot gives a relatively straight line within the BC distance axis.
[[File:Exe1_Q3_mep_xs2218.png|thumb|left|Surface plot of MEP calculation type.|350px]]
[[File:Exe1_Q3_dynamics_xs2218.png|thumb|center|Surface plot of dynamics calculation type.|350px]]

====Q4====
{| class="wikitable" border="1"
|+ Table 1 rAB=74pm, rBC=200pm
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || yes || AB are bonded at first until B bonds with C and A moves away, prodct BC formed || [[File:table1_row1.png|150px]] ||
|-
| -3.1 || -4.1 || -420.077 || No || AB is always bonded, no product formed || [[File:table1_row2.png|150px]] ||
|-
| -3.1 || -5.1 || -413.977 || yes || AB are bonded at first until B is bonded with C and A moves away, prodct BC formed || [[File:table1_row3.png|150px]] ||
|-
| -5.1 || -10.1 || -357.277 || No || AB are bonded at first until B bonds with C, but eventually B is back to bonded with A, C moves away, no product BC formed || [[File:table1_row4.png|150px]] ||
|-
| -5.1 || -10.6 || -349.477 || yes || AB are bonded at first until C approaches and B bonds with C, then B bonds with A again, eventually, B bonds with C and forms a product BC, A moves away|| [[File:table1_row5.png|150px]] ||
|}

In conclusion, trajectories starting with the same positions but with higher values of momenta would not always be reactive, although the total energy is getting more positive, therefore, the hypothesis is not supported

====Q5====
The Transition State Theory assumes that Rcl is that all trajectories with a KE greater than the activation energy will be reactive, however, our experimental has suggested that this is not true.
Transition state theory is based on classical mechanics, Quasi-equilibrium basically covers that if the atoms did not have enough energy to collide to form the TS, the reaction would not be feasible. However, in quantum mechanics, as long as the barrier has a finite amount of energy, the atoms can still tunnel across the barrier which means that the reaction could still be feasible even if the atoms do not collide enough energy to cross the energy barrier.
Quantum tunneling is minimal in TS theory, if quantum tunneling was present, the reaction rate would increase.
In transition state theory, it assumes that the step from TS to products is the rate-determining step, but in reality, it might not be true, the reaction rate would. be decreased

===Exercise2: F-H-H system===

====Q1====
F + H2 is exothermic, whereas HF + H is endothermic.

H-H bond strength is weaker than the H-F bond. The energy absorbed to break the F-F bond is smaller than the energy needed to make the new bond H-F, the excess energy is then released as heat, so the reaction is exothermic. However, for HF + H, more energy is needed to break the H-F bond than to make the F-F bond, overall, energy is being absorbed rather than released, so the reaction is endothermic.

====Q2====
The approximate position of transition state: rAB=181.1 pm, rBC=74.488pm
The forces along AB and BC at this position are both 0. According to Hammond Postulate, an exothermic reaction has an early TS, whereas an endothermic reaction has a late TS, therefore, one of the eigenvalues at TS is positive, another one is negative. In this case, the Hessian eigenvalues are -0.002 and +0.332.
As shown in the surface plot below, now it is at a saddle point which confirms the atoms are at the transition state.
[[File:Q7_xs2218_new.png|thumb|center|Surface Plot of transition state.]]

====Q3====
The transition state energy is reported as -433.981 kJ.mol-1.
A plot of energy vs time is plotted at TS as shown below.
[[File:Exe2_Q3_TSenergy.png|thumb|center|Energy vs Time plot at TS for F-H-H system.]]

For the exothermic reaction F + H2, the initial state energy is -435.059 kJ.mol-1. Activation energy can then be calculated as 1.08 kJ.mol-1.
[[File:Exe2_Q3_exoenergy.png|thumb|center|Energy vs Time plot at initial state for exothermic rxn.]]

For the endothermic reaction HF + H, the initial state energy is -560.700 kJ.mol-1. Activation energy for this reaction is 126.02 kJ.mol-1.
[[File:Exe2_Q3_endoenergy.png|thumb|center|Energy vs Time plot at initial state for endothermic rxn.]]

By locating a structure neighboring the TS, the plot of Energy vs time shows that the energy dropping clearly.
[[File:Exe2_Q3_endoenergy_new.png|thumb|center|Energy vs Time plot at the neighboring structure of transition state for endothermic rxn.]]

(The plot of the neighboring structure of TS for exothermic reaction is not shown because the difference is too small to be spotted.)

====Q4====
The release of reaction energy is basically a release of vibrational kinetic energy converted from potential energy. An experimental method to confirm it is IR spectrometry. IR absorption would have stronger overtones that measuring the transition from the first to second state, while IR emission measures the transition from the first to the ground state.

====Q5====

MRD:xs2218

2020-05-22T11:06:48Z

Xs2218: /* Q5 */

MRD:xs2218

2020-05-22T10:37:31Z

Xs2218: /* Q3 */

==Molecular Reaction Dynamic Lab==
===Exercise1: H + H2 system===

====Q1====
On a potential energy surface diagram, the transition state is mathematically defined as a first-order saddle point, ∂V('''ri''')/∂V('''ri''')/∂'''ri'''=0.
The transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish from the local minimum on the PES, the first-order saddle point is at a minimum in all directions except for one and the trajectories near the transition state roll towards reactants or products. See the surface plot below, the TS is at a saddle point.
[[File:Q1_xs2218.png|thumb|center|Surface plot of transition state.]]

====Q2====
My best estimate of rtsis 90.775pm, it is when the force along AB and BC is 0 KJ.mol-1.pm-1. The atoms are not bonded at TS
The internuclear distance vs time plot shows 2 straight lines illustrating that when the atoms are at the transition state, the internuclear distance does not change, no such oscillating behavior where the 2 lines are wavy when not at TS.
[[File:Exe1 Q2.png|thumb|center|internuclear distance vs time plot at TS|350px]]

====Q3====
As shown from the surface plots below, two different calculation types give different trajectories. The MEP shows the minimal energy path that any point on the path is at energy minimum in all directions perpendicular to the path which passes through at least one saddle point. Looking at the plots from the same angle, the dynamic surface plot gives a wavy line coming out of the BC distance axis whereas the MEP surface plot gives a relatively straight line within the BC distance axis.
[[File:Exe1_Q3_mep_xs2218.png|thumb|left|Surface plot of MEP calculation type.|350px]]
[[File:Exe1_Q3_dynamics_xs2218.png|thumb|center|Surface plot of dynamics calculation type.|350px]]

====Q4====
{| class="wikitable" border="1"
|+ Table 1 rAB=74pm, rBC=200pm
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || yes || AB are bonded at first until B bonds with C and A moves away, prodct BC formed || [[File:table1_row1.png|150px]] ||
|-
| -3.1 || -4.1 || -420.077 || No || AB is always bonded, no product formed || [[File:table1_row2.png|150px]] ||
|-
| -3.1 || -5.1 || -413.977 || yes || AB are bonded at first until B is bonded with C and A moves away, prodct BC formed || [[File:table1_row3.png|150px]] ||
|-
| -5.1 || -10.1 || -357.277 || No || AB are bonded at first until B bonds with C, but eventually B is back to bonded with A, C moves away, no product BC formed || [[File:table1_row4.png|150px]] ||
|-
| -5.1 || -10.6 || -349.477 || yes || AB are bonded at first until C approaches and B bonds with C, then B bonds with A again, eventually, B bonds with C and forms a product BC, A moves away|| [[File:table1_row5.png|150px]] ||
|}

In conclusion, trajectories starting with the same positions but with higher values of momenta would not always be reactive, although the total energy is getting more positive, therefore, the hypothesis is not supported

====Q5====
The Transition State Theory assumes that Rcl is that all trajectories with a KE greater than the activation energy will be reactive, however, our experimental has suggested that this is not true.
Transition state theory is based on classical mechanics that the formation of the product from the TS is the rate determining step, if the atoms did not have enough energy to collide to form the TS, the reaction would not be feasible. However, in quantum mechanics, as long as the barrier has a finite amount of energy, the atoms can still tunnel across the barrier which means that the reaction could still be feasible even if the atoms do not collide enough energy to cross the energy barrier. Taking account of this, the experimental reaction rate would be smaller than the TST predictions.
Quantum tunneling is minimal in TS theory, if quantum tunneling was present, the reaction rate would increase.

===Exercise2: F-H-H system===

====Q1====
F + H2 is exothermic, whereas HF + H is endothermic.

H-H bond strength is weaker than the H-F bond. The energy absorbed to break the F-F bond is smaller than the energy needed to make the new bond H-F, the excess energy is then released as heat, so the reaction is exothermic. However, for HF + H, more energy is needed to break the H-F bond than to make the F-F bond, overall, energy is being absorbed rather than released, so the reaction is endothermic.

====Q2====
The approximate position of transition state: rAB=181.1 pm, rBC=74.488pm
The forces along AB and BC at this position are both 0. According to Hammond Postulate, an exothermic reaction has an early TS, whereas an endothermic reaction has a late TS, therefore, one of the eigenvalues at TS is positive, another one is negative. In this case, the Hessian eigenvalues are -0.002 and +0.332.
As shown in the surface plot below, now it is at a saddle point which confirms the atoms are at the transition state.
[[File:Q7_xs2218_new.png|thumb|center|Surface Plot of transition state.]]

====Q3====
The transition state energy is reported as -433.981 kJ.mol-1.
A plot of energy vs time is plotted at TS as shown below.
[[File:Exe2_Q3_TSenergy.png|thumb|center|Energy vs Time plot at TS for F-H-H system.]]

For the exothermic reaction F + H2, the initial state energy is -435.059 kJ.mol-1. Activation energy can then be calculated as 1.08 kJ.mol-1.
[[File:Exe2_Q3_exoenergy.png|thumb|center|Energy vs Time plot at initial state for exothermic rxn.]]

For the endothermic reaction HF + H, the initial state energy is -560.700 kJ.mol-1. Activation energy for this reaction is 126.02 kJ.mol-1.
[[File:Exe2_Q3_endoenergy.png|thumb|center|Energy vs Time plot at initial state for endothermic rxn.]]

By locating a structure neighboring the TS, the plot of Energy vs time shows that the energy dropping clearly.
[[File:Exe2_Q3_endoenergy_new.png|thumb|center|Energy vs Time plot at the neighboring structure of transition state for endothermic rxn.]]

(The plot of the neighboring structure of TS for exothermic reaction is not shown because the difference is too small to be spotted.)

MRD:xs2218

==Molecular Reaction Dynamic Lab==
===Exercise 1 H + H2 system===

====Q1====
On a potential energy surface diagram, the transition state is mathematically defined as a first-order saddle point, ∂V('''ri''')/∂V('''ri''')/∂'''ri'''=0.
The transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish from the local minimum on the PES, the first-order saddle point is at a minimum in all directions except for one and the trajectories near the transition state roll towards reactants or products. See the surface plot below, the TS is at a saddle point.
[[File:Q1_xs2218.png|thumb|center|Surface plot of transition state.]]

====Q2====
My best estimate of rtsis 90.775pm, it is when the force along AB and BC is 0 KJ.mol-1.pm-1.
The internuclear distance vs time plot shows 2 straight lines illustrating that when the atoms are at the transition state, the internuclear distance does not change, no such oscillating behavior where the 2 lines are wavy when not at TS.
[[File:Exe1 Q2.png|thumb|center|internuclear distance vs time plot at TS|350px]]

====Q3====
As shown from the surface plots below, two different calculation types give different trajectories. Looking at the plots from the same angle, the dynamic surface plot gives a wavy line coming out of the BC distance axis whereas the MEP surface plot gives a relatively straight line within the BC distance axis.
[[File:Exe1_Q3_mep_xs2218.png|thumb|left|Surface plot of MEP calculation type.|350px]]
[[File:Exe1_Q3_dynamics_xs2218.png|thumb|center|Surface plot of dynamics calculation type.|350px]]

====Q4====
{| class="wikitable" border="1"
|+ Table 1 rAB=74pm, rBC=200pm
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || yes || AB are bonded at first until B bonds with C and A moves away, prodct BC formed || [[File:table1_row1.png|150px]] ||
|-
| -3.1 || -4.1 || -420.077 || No || AB is always bonded, no product formed || [[File:table1_row2.png|150px]] ||
|-
| -3.1 || -5.1 || -413.977 || yes || AB are bonded at first until B is bonded with C and A moves away, prodct BC formed || [[File:table1_row3.png|150px]] ||
|-
| -5.1 || -10.1 || -357.277 || No || AB are bonded at first until B bonds with C, but eventually B is back to bonded with A, C moves away, no product BC formed || [[File:table1_row4.png|150px]] ||
|-
| -5.1 || -10.6 || -349.477 || yes || AB are bonded at first until C approaches and B bonds with C, then B bonds with A again, eventually, B bonds with C and forms a product BC, A moves away|| [[File:table1_row5.png|150px]] ||
|}

In conclusion, trajectories starting with the same positions but with higher values of momenta would not always be reactive, although the total energy is getting more positive, therefore, the hypothesis is not supported

====Q5====
The Transition State Theory assumes that Rcl is that all trajectories with a KE greater than the activation energy will be reactive, however, our experimental has suggested that this is not true.

===Exercise2: F-H-H system===

====Q6====
F + H2 is exothermic, whereas HF + H is endothermic.

H-H bond strength is weaker than the H-F bond. The energy absorbed to break the F-F bond is smaller than the energy needed to make the new bond H-F, the excess energy is then released as heat, so the reaction is exothermic. However, for HF + H, more energy is needed to break the H-F bond than to make the F-F bond, overall, energy is being absorbed rather than released, so the reaction is endothermic.

====Q7====
The approximate position of transition state: rAB=377 pm, rBC=74pm
As shown in the surface plot below, now it is at a saddle point which confirms the atoms are at the transition state.
[[File:Q7_xs2218.png|thumb|center|Surface Plot of transition state.]]

====Q8====

MRD:xs2218

2020-05-20T12:13:17Z

2020-05-20T10:35:52Z

Xs2218: /* Q5 */

==Molecular Reaction Dynamic Lab==
===Exercise 1 H + H2 system===

====Q1====
On a potential energy surface diagram, the transition state is mathematically defined as a first-order saddle point, ∂V(ri)/∂ri=0.
The transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish from the local minimum on the PES, the first-order saddle point is at a minimum in all directions except for one and the trajectories near the transition state roll towards reactants or products.

====Q2====
My best estimate of rtsis 90.775pm, it is when the force along AB and BC is 0 KJ.mol-1.pm-1.
The internuclear distance vs time plot shows 2 straight lines illustrating that when the atoms are at the transition state, the internuclear distance does not change, no such oscillating behavior where the 2 lines are wavy when not at TS.
[[File:Exe1 Q2.png|thumb|center|internuclear distance vs time plot at TS|350px]]

====Q3====
As shown from the surface plots below, two different calculation types give different trajectories. Looking at the plots from the same angle, the dynamic surface plot gives a wavy line coming out of the BC distance axis whereas the MEP surface plot gives a relatively straight line within the BC distance axis.
[[File:Exe1_Q3_mep_xs2218.png|thumb|left|Surface plot of MEP calculation type.|350px]]
[[File:Exe1_Q3_dynamics_xs2218.png|thumb|center|Surface plot of dynamics calculation type.|350px]]

====Q4====
{| class="wikitable" border="1"
|+ Table 1 rAB=74pm, rBC=200pm
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || yes || AB are bonded at first until B bonds with C and A moves away, prodct BC formed || [[File:table1_row1.png|150px]] ||
|-
| -3.1 || -4.1 || -420.077 || No || AB is always bonded, no product formed || [[File:table1_row2.png|150px]] ||
|-
| -3.1 || -5.1 || -413.977 || yes || AB are bonded at first until B is bonded with C and A moves away, prodct BC formed || [[File:table1_row3.png|150px]] ||
|-
| -5.1 || -10.1 || -357.277 || No || AB are bonded at first until B bonds with C, but eventually B is back to bonded with A, C moves away, no product BC formed || [[File:table1_row4.png|150px]] ||
|-
| -5.1 || -10.6 || -349.477 || yes || AB are bonded at first until C approaches and B bonds with C, then B bonds with A again, eventually, B bonds with C and forms a product BC, A moves away|| [[File:table1_row5.png|150px]] ||
|}

In conclusion, trajectories starting with the same positions but with higher values of momenta would not always be reactive, although the total energy is getting more positive, therefore, the hypothesis is not supported

====Q5====
The Transition State Theory assumes that Rcl is that all trajectories with a KE greater than the activation energy will be reactive, however, our experimental has suggested that this is not true.

====Q6====
F + H2 is exothermic, whereas HF + H is endothermic.
F-F bond is a weak covalent bond, H-F is a strong bond. The energy absorbed to break the F-F bond is smaller than the energy needed to make the new bond H-F, the excess energy is then released as heat, so the reaction is exothermic. However, for HF + H, more energy is needed to break the H-F bond than to make the F-F bond, overall, energy is being absorbed rather than released, so the reaction is endothermic.

MRD:xs2218

2020-05-20T08:55:04Z

Xs2218: /* Q5 */

==Molecular Reaction Dynamic Lab==
===Exercise 1 H + H2 system===

====Q1====
On a potential energy surface diagram, the transition state is mathematically defined as a first-order saddle point, ∂V(ri)/∂ri=0.
The transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish from the local minimum on the PES, the first-order saddle point is at a minimum in all directions except for one and the trajectories near the transition state roll towards reactants or products.

====Q2====
My best estimate of rtsis 90.775pm, it is when the force along AB and BC is 0 KJ.mol-1.pm-1.
The internuclear distance vs time plot shows 2 straight lines illustrating that when the atoms are at the transition state, the internuclear distance does not change, no such oscillating behavior where the 2 lines are wavy when not at TS.
[[File:Exe1 Q2.png|thumb|center|internuclear distance vs time plot at TS|350px]]

====Q3====
As shown from the surface plots below, two different calculation types give different trajectories. Looking at the plots from the same angle, the dynamic surface plot gives a wavy line coming out of the BC distance axis whereas the MEP surface plot gives a relatively straight line within the BC distance axis.
[[File:Exe1_Q3_mep_xs2218.png|thumb|left|Surface plot of MEP calculation type.|350px]]
[[File:Exe1_Q3_dynamics_xs2218.png|thumb|center|Surface plot of dynamics calculation type.|350px]]

====Q4====
{| class="wikitable" border="1"
|+ Table 1 rAB=74pm, rBC=200pm
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || yes || AB are bonded at first until B bonds with C and A moves away, prodct BC formed || [[File:table1_row1.png|150px]] ||
|-
| -3.1 || -4.1 || -420.077 || No || AB is always bonded, no product formed || [[File:table1_row2.png|150px]] ||
|-
| -3.1 || -5.1 || -413.977 || yes || AB are bonded at first until B is bonded with C and A moves away, prodct BC formed || [[File:table1_row3.png|150px]] ||
|-
| -5.1 || -10.1 || -357.277 || No || AB are bonded at first until B bonds with C, but eventually B is back to bonded with A, C moves away, no product BC formed || [[File:table1_row4.png|150px]] ||
|-
| -5.1 || -10.6 || -349.477 || yes || AB are bonded at first until C approaches and B bonds with C, then B bonds with A again, eventually, B bonds with C and forms a product BC, A moves away|| [[File:table1_row5.png|150px]] ||
|}

In conclusion, trajectories starting with the same positions but with higher values of momenta would not always be reactive, although the total energy is getting more positive, therefore, the hypothesis is not supported

====Q5====
The Transition State Theory assumes that Rcl is that all trajectories with a KE greater than the activation energy will be reactive, however, our experimental has suggested that this is not true.

====Q5====

MRD:xs2218

2020-05-20T08:07:34Z

Xs2218: /* Q4 */

==Molecular Reaction Dynamic Lab==
===Exercise 1 H + H2 system===

====Q1====
On a potential energy surface diagram, the transition state is mathematically defined as a first-order saddle point, ∂V(ri)/∂ri=0.
The transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish from the local minimum on the PES, the first-order saddle point is at a minimum in all directions except for one and the trajectories near the transition state roll towards reactants or products.

====Q2====
My best estimate of rtsis 90.775pm, it is when the force along AB and BC is 0 KJ.mol-1.pm-1.
The internuclear distance vs time plot shows 2 straight lines illustrating that when the atoms are at the transition state, the internuclear distance does not change, no such oscillating behavior where the 2 lines are wavy when not at TS.
[[File:Exe1 Q2.png|thumb|center|internuclear distance vs time plot at TS|350px]]

====Q3====
As shown from the surface plots below, two different calculation types give different trajectories. Looking at the plots from the same angle, the dynamic surface plot gives a wavy line coming out of the BC distance axis whereas the MEP surface plot gives a relatively straight line within the BC distance axis.
[[File:Exe1_Q3_mep_xs2218.png|thumb|left|Surface plot of MEP calculation type.|350px]]
[[File:Exe1_Q3_dynamics_xs2218.png|thumb|center|Surface plot of dynamics calculation type.|350px]]

====Q4====
{| class="wikitable" border="1"
|+ Table 1 rAB=74pm, rBC=200pm
! p1/ g.mol-1.pm.fs-1 !! p2/ g.mol-1.pm.fs-1 !! Etot !! Reactive? !! Description of the dynamics !! Illustration of the trajectory
|-
| -2.56 || -5.1 || -414.280 || yes || AB are bonded at first until B bonds with C and A moves away, prodct BC formed || [[File:table1_row1.png|150px]] ||
|-
| -3.1 || -4.1 || -420.077 || No || AB is always bonded, no product formed || [[File:table1_row2.png|150px]] ||
|-
| -3.1 || -5.1 || -413.977 || yes || AB are bonded at first until B is bonded with C and A moves away, prodct BC formed || [[File:table1_row3.png|150px]] ||
|-
| -5.1 || -10.1 || -357.277 || No || AB are bonded at first until B bonds with C, but eventually B is back to bonded with A, C moves away, no product BC formed || [[File:table1_row4.png|150px]] ||
|-
| -5.1 || -10.6 || -349.477 || yes || AB are bonded at first until C approaches and B bonds with C, then B bonds with A again, eventually, B bonds with C and forms a product BC, A moves away|| [[File:table1_row5.png|150px]] ||
|}

In conclusion, trajectories starting with the same positions but with higher values of momenta would not always be reactive, although the total energy is getting more positive, therefore, the hypothesis is not supported

====Q5====

====Q5====

MRD:xs2218

2020-05-19T17:44:51Z

2020-05-19T16:39:07Z

Xs2218: /* Q3 */

==Molecular Reaction Dynamic Lab==
===Exercise 1 H + H2 system===

====Q1====
On a potential energy surface diagram, the transition state is mathematically defined as a first-order saddle point, ∂V(ri)/∂ri=0.
The transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish from the local minimum on the PES, the first-order saddle point is at a minimum in all directions except for one and the trajectories near the transition state roll towards reactants or products.

====Q2====
My best estimate of rtsis 90.775pm, it is when the force along AB and BC is 0 KJ.mol-1.pm-1.
The internuclear distance vs time plot shows 2 straight lines illustrating that when the atoms are at the transition state, the internuclear distance does not change, no such oscillating behavior where the 2 lines are wavy when not at TS.
[[File:Exe1 Q2.png|thumb|center|internuclear distance vs time plot at TS|350px]]

====Q3====
As shown from the surface plots below, two different calculation types give different trajectories. Looking at the plots from the same angle, the dynamic surface plot gives a wavy line coming out of the BC distance axis whereas the MEP surface plot gives a relatively straight line within the BC distance axis.
[[File:Exe1_Q3_mep_xs2218.png|thumb|left|Surface plot of MEP calculation type.|350px]]
[[File:Exe1_Q3_dynamics_xs2218.png|thumb|center|Surface plot of dynamics calculation type.|350px]]

====Q4====

File:Exe1 Q3 dynamics xs2218.png

2020-05-19T16:20:26Z

Xs2218:

File:Exe1 Q3 mep xs2218.png

2020-05-19T16:19:40Z

Xs2218:

MRD:xs2218

2020-05-19T16:17:29Z

Xs2218: /* Q2 */

==Molecular Reaction Dynamic Lab==
===Exercise 1 H + H2 system===

====Q1====
On a potential energy surface diagram, the transition state is mathematically defined as a first-order saddle point, ∂V(ri)/∂ri=0.
The transition state is defined as the maximum on the minimum energy path linking reactants and the products. To distinguish from the local minimum on the PES, the first-order saddle point is at a minimum in all directions except for one and the trajectories near the transition state roll towards reactants or products.

====Q2====
My best estimate of rtsis 90.775pm, it is when the force along AB and BC is 0 KJ.mol-1.pm-1.
The internuclear distance vs time plot shows 2 straight lines illustrating that when the atoms are at the transition state, the internuclear distance does not change, no such oscillating behavior where the 2 lines are wavy when not at TS.
[[File:Exe1 Q2.png|thumb|center|internuclear distance vs time plot at TS|350px]]

====Q3====