MRD:pp4717

2019-05-16T13:59:26Z

Pp4717:

2nd year computational labs

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 transition state is generated from making a skew plot to form coordinates q1 and q2. The coordinates q1 and q2 are then differentiated and the minimum of one curve is the maximum of the other. The point at which the minimum and maximum converge is 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 transition state position was 0.9075 Ǎ

[[File:TSpp4717.PNG]]

The Internuclear Distances vs Time plot shows two straight lines corresponding to the bonds A-C and B-C which helped to identify the transition state. There are no fluctuations of the distance with time of the bonds in the transition state because they have no potential energy.

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

MEP does not consider the momentum that the molecule already has, only the momentum that was defined in the initial conditions in the first step. In the dynamic trajectory, the residual momentum is considered which is why there are vibrations present and the point at which the potential energy is zero occurs at a larger distance.
{| class="wikitable"
!p1
!p2
!E(total)
!Reactive?
!Description of the dynamics
!Illustration of trajectory
|-
|<nowiki>-1.25</nowiki>
|<nowiki>-2.5</nowiki>
|<nowiki>-99.119</nowiki>
|yes
|Central proton is transferred from A to B.
|[[File:pp47171.png]]
|-
|<nowiki>-1.5</nowiki>
|<nowiki>-2.0</nowiki>
|<nowiki>-100.619</nowiki>
|no
|Central proton is not transferred.
|[[File:pp47172.png]]
|-
|<nowiki>-1.5</nowiki>
|<nowiki>-2.5</nowiki>
|<nowiki>-99.119</nowiki>
|yes
|Central proton is transferred from A to B.
|[[File:pp47173.png]]
|-
|<nowiki>-2.5</nowiki>
|<nowiki>-5.0</nowiki>
|<nowiki>-85.119</nowiki>
|no
|Central proton continuously moves from A to B.
|[[File:pp47174.png]]
|-
|<nowiki>-2.5</nowiki>
|<nowiki>-5.2</nowiki>
|<nowiki>-83.579</nowiki>
|yes
|Central proton is initially attached to A, then B to A.
|[[File:pp47175.png]]
|}
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 is an exothermic reaction; this shows that the bond strength is strong.

H + HF is endothermic; this shows that the bond strength is weak.

Locate the approximate position of the transition state.

[[File:TS pp01333427.PNG]]

[[File:Ts01333428.PNG]]

The transition state is located at 1.83 Ǎ.

Report the activation energy for both reactions.

For the F + H2 reaction:

[[File:ActivationenergyFHH pp01333428.png]]

The activation energy for the F + H2 reaction = 29.474 KCal/mol

For the H + HF reaction:

[[File:TS201333428.png]]

Activation energy = 0.009 KCal/mol

File:TS201333428.png

2019-05-16T13:57:27Z

Pp4717:

MRD:pp4717

2019-05-16T13:29:29Z

Pp4717:

2nd year computational labs

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 transition state is generated from making a skew plot to form coordinates q1 and q2. The coordinates q1 and q2 are then differentiated and the minimum of one curve is the maximum of the other. The point at which the minimum and maximum converge is 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 transition state position was 0.9075 Ǎ

[[File:TSpp4717.PNG]]

The Internuclear Distances vs Time plot shows two straight lines corresponding to the bonds A-C and B-C which helped to identify the transition state. There are no fluctuations of the distance with time of the bonds in the transition state because they have no potential energy.

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

MEP does not consider the momentum that the molecule already has, only the momentum that was defined in the initial conditions in the first step. In the dynamic trajectory, the residual momentum is considered which is why there are vibrations present and the point at which the potential energy is zero occurs at a larger distance.
{| class="wikitable"
!p1
!p2
!E(total)
!Reactive?
!Description of the dynamics
!Illustration of trajectory
|-
|<nowiki>-1.25</nowiki>
|<nowiki>-2.5</nowiki>
|<nowiki>-99.119</nowiki>
|yes
|Central proton is transferred from A to B.
|[[File:pp47171.png]]
|-
|<nowiki>-1.5</nowiki>
|<nowiki>-2.0</nowiki>
|<nowiki>-100.619</nowiki>
|no
|Central proton is not transferred.
|[[File:pp47172.png]]
|-
|<nowiki>-1.5</nowiki>
|<nowiki>-2.5</nowiki>
|<nowiki>-99.119</nowiki>
|yes
|Central proton is transferred from A to B.
|[[File:pp47173.png]]
|-
|<nowiki>-2.5</nowiki>
|<nowiki>-5.0</nowiki>
|<nowiki>-85.119</nowiki>
|no
|Central proton continuously moves from A to B.
|[[File:pp47174.png]]
|-
|<nowiki>-2.5</nowiki>
|<nowiki>-5.2</nowiki>
|<nowiki>-83.579</nowiki>
|yes
|Central proton is initially attached to A, then B to A.
|[[File:pp47175.png]]
|}
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 is an exothermic reaction; this shows that the bond strength is strong.

H + HF is endothermic; this shows that the bond strength is weak.

Locate the approximate position of the transition state.

[[File:TS pp01333427.PNG]]

[[File:Ts01333428.PNG]]

The transition state is located at 1.83 Ǎ.

Report the activation energy for both reactions.

[[File:ActivationenergyFHH pp01333428.png]]

The activation energy for the F + H2 reaction = 29.474 KCal/mol

2019-05-16T13:14:31Z

Pp4717:

MRD:pp4717

2019-05-16T13:10:37Z

2019-05-16T12:45:28Z

Pp4717: Pp4717 uploaded a new version of File:Pp47171.png

MRD:pp4717

2019-05-16T12:42:21Z

Pp4717:

2nd year computational labs

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 transition state is generated from making a skew plot to form coordinates q1 and q2. The coordinates q1 and q2 are then differentiated and the minimum of one curve is the maximum of the other. The point at which the minimum and maximum converge is 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 transition state position was 0.9075 Ǎ

[[File:TSpp4717.PNG]]

The Internuclear Distances vs Time plot shows two straight lines corresponding to the bonds A-C and B-C which helped to identify the transition state. There are no fluctuations of the distance with time of the bonds in the transition state because they have no potential energy.

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

MEP does not consider the momentum that the molecule already has, only the momentum that was defined in the initial conditions in the first step. In the dynamic trajectory, the residual momentum is considered which is why there are vibrations present and the point at which the potential energy is zero occurs at a larger distance.
{| class="wikitable"
!p1
!p2
!E(total)
!Reactive?
!Description of the dynamics
!Illustration of trajectory
|-
|<nowiki>-1.25</nowiki>
|<nowiki>-2.5</nowiki>
|<nowiki>-99.119</nowiki>
|yes
|Central proton is transferred from A to B.
|[[File:pp47171.PNG]]
|-
|<nowiki>-1.5</nowiki>
|<nowiki>-2.0</nowiki>
|<nowiki>-100.619</nowiki>
|no
|Central proton is not transferred.
|
|-
|<nowiki>-1.5</nowiki>
|<nowiki>-2.5</nowiki>
|<nowiki>-99.119</nowiki>
|yes
|Central proton is transferred from A to B.
|
|-
|<nowiki>-2.5</nowiki>
|<nowiki>-5.0</nowiki>
|<nowiki>-85.119</nowiki>
|no
|Central proton continuously moves from A to B.
|
|-
|<nowiki>-2.5</nowiki>
|<nowiki>-5.2</nowiki>
|<nowiki>-83.579</nowiki>
|yes
|Central proton is initially attached to A, then B to A.
|
|}
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?

Locate the approximate position of the transition state.

F + H2 is an exothermic reaction; this shows that the bond strength is strong.

H + HF is endothermic; this shows that the bond strength is weak.

MRD:pp4717

2019-05-14T19:51:57Z

Pp4717:

2nd year computational labs

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 transition state is generated from making a skew plot to form coordinates q1 and q2. The coordinates q1 and q2 are then differentiated and the minimum of one curve is the maximum of the other. The point at which the minimum and maximum converge is 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 transition state position was 0.9075 Ǎ

[[File:TSpp4717.PNG]]

The Internuclear Distances vs Time plot shows two straight lines corresponding to the bonds A-C and B-C which helped to identify the transition state. There are no fluctuations of the distance with time of the bonds in the transition state because they have no potential energy.

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

MEP does not consider the momentum that the molecule already has, only the momentum that was defined in the initial conditions in the first step. In the dynamic trajectory, the residual momentum is considered which is why there are vibrations present and the point at which the potential energy is zero occurs at a larger distance.
{| class="wikitable"
!p1
!p2
!E(total)
!Reactive?
!Description of the dynamics
!Illustration of trajectory
|-
|<nowiki>-1.25</nowiki>
|<nowiki>-2.5</nowiki>
|<nowiki>-99.119</nowiki>
|yes
|Central proton is transferred from A to B.
|<nowiki>-1.5</nowiki>
|-
|<nowiki>-1.5</nowiki>
|<nowiki>-2.0</nowiki>
|<nowiki>-100.619</nowiki>
|no
|Central proton is not transferred.
|
|-
|<nowiki>-1.5</nowiki>
|<nowiki>-2.5</nowiki>
|<nowiki>-99.119</nowiki>
|yes
|Central proton is transferred from A to B.
|
|-
|<nowiki>-2.5</nowiki>
|<nowiki>-5.0</nowiki>
|<nowiki>-85.119</nowiki>
|no
|Central proton continuously moves from A to B.
|
|-
|<nowiki>-2.5</nowiki>
|<nowiki>-5.2</nowiki>
|<nowiki>-83.579</nowiki>
|yes
|Central proton is initially attached to A, then B to A.
|
|}
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?

Locate the approximate position of the transition state.

F + H2 is an exothermic reaction; this shows that the bond strength is strong.

H + HF is endothermic; this shows that the bond strength is weak.

CP3MD

2019-05-14T19:10:25Z

2019-05-10T15:40:37Z

Pp4717:

BH3 

Calculation method: RB3LYP

Basis set: 3-21G

Final energy in atomic units (a.u): -26.46226

[[File:bh3_opt.png|260px]]

<pre>

Item Value Threshold Converged?
Maximum Force 0.000220 0.000450 YES
RMS Force 0.000106 0.000300 YES
Maximum Displacement 0.000940 0.001800 YES
RMS Displacement 0.000447 0.001200 YES
Predicted change in Energy=-1.672478D-07
Optimization completed.
-- Stationary point found.
</pre>

Calculation method: RB3LYP

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

Final energy in atomic units (a.u): -26.61532

[[File:bh3_631_sum.png|260px]]

<pre>

Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000061 0.001800 YES
RMS Displacement 0.000038 0.001200 YES
Predicted change in Energy=-1.069047D-09
Optimization completed.
-- Stationary point found.
</pre>

 Frequency analysis: 

[[File:bh3_freq.png|260px]]

<pre>

Low frequencies --- -0.2263 -0.1037 -0.0054 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731

</pre>
{| class="wikitable"
!
!Vibration
!Intensity
!Symmetry
!IR active
!Type of vibration
|-
|1
|1164
|92
|
|
|
|-
|2
|1214
|14
|
|
|
|-
|3
|1214
|14
|
|
|
|-
|4
|2580
|0
|
|
|
|-
|5
|2713
|126
|
|
|
|-
|6
|2713
|126
|
|
|
|}
<pre>
</pre>

 IR Spectrum 

[[File:IRspec.png|550px]]

There are less than 6 peaks seen in the IR spectrum because 1 peak is not IR active and there are are 2 sets of degenerate frequencies which thus show up as the same peak in the spectrum.

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PRIYA BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

 MO diagram of BH3 

There are no significant differences in the LCAOs and the computed MOs; this shows the usefulness of the qualititative MO diagram.

[[File:MO.png|600px]]

 NH3 

Calculation method: RB3LYP

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

[[File:nh3_631g.png|260px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000060 0.000450 YES
RMS Force 0.000040 0.000300 YES
Maximum Displacement 0.000369 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.259212D-08
Optimization completed.
-- Stationary point found.

</pre>

 Frequency analysis: 

[[File:amm_freq.png|260px]]

<pre>
Low frequencies --- -32.4128 -32.3999 -11.4544 -0.0032 0.0078 0.0521
Low frequencies --- 1088.7642 1694.0248 1694.0252
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PRIYA NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

 NH3BH3 

Calculation method: RB3LYP

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

[[File:nh3bh3.png|260px]]

<pre>

Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.001017 0.001800 YES
RMS Displacement 0.000224 0.001200 YES
Predicted change in Energy=-1.131227D-07
Optimization completed.
-- Stationary point found.
</pre>

 Frequency analysis: 

[[File:nh3_bh3freq.png|260px]]

<pre>
Low frequencies --- -0.0172 -0.0141 -0.0074 100.7930 100.7958 165.6168
Low frequencies --- 421.7202 601.9051 685.5876
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PRIYA NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

 Energy Calculation 

E(NH3) = -56.55777 a.u

E(BH3) = -26.61532 a.u

E(NH3BH3) = -83.22415 a.u

Enthalpy change for the reaction = -83.22145 -(-56.55777+ -26.61532) = -0.05106 a.u
= -134 kjmol-1

 NI3 

Calculation method: RB3LYP

Basis set: GEN

[[File:ni3.png|260px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000114 0.000450 YES
RMS Force 0.000079 0.000300 YES
Maximum Displacement 0.000735 0.001800 YES
RMS Displacement 0.000543 0.001200 YES
Predicted change in Energy=-1.081659D-07
Optimization completed.
-- Stationary point found.
</pre>

 Frequency analysis: 

[[File:ni3_pp.PNG]]

<pre>
Low frequencies --- -12.7242 -12.7182 -6.3942 -0.0039 0.0189 0.0623
Low frequencies --- 101.0680 101.0688 147.4487
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PRIYA NI3 MIXEDPP FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

Optimised N-I bond length: 2.18368

=== Ionic Liquids: Designer Solvents ===

 N(CH3)4 optimisation: 

Calculation method: RB3LYP

Basis set: 6-31 (d,p)

[[File:Nch3.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000132 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.001021 0.001800 YES
RMS Displacement 0.000301 0.001200 YES
Predicted change in Energy=-2.883750D-07
Optimization completed.
-- Stationary point found.
</pre>

 Frequency analysis: 

[[File:Nch3 freq.PNG]]

<pre>
Low frequencies --- -0.0013 -0.0013 -0.0009 32.7135 32.7135 32.7135
Low frequencies --- 213.0784 313.6512 313.6512
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PRIYA NCH34 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

 P(CH3)4 optimisation: 

Calculation method: RB3LYP

Basis set: 6-31 (d,p)

[[File:P(ch3).PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000663 0.001800 YES
RMS Displacement 0.000249 0.001200 YES
Predicted change in Energy=-5.209118D-08
Optimization completed.
-- Stationary point found.
</pre>

 Frequency analysis: 

[[File:P(ch3) freq.PNG]]

<pre>
Low frequencies --- 0.0010 0.0012 0.0015 50.3813 50.3813 50.3813
Low frequencies --- 185.7545 210.8019 210.8019
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>PRIYA PH3NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

 NBO Charge distribution: 

[[File:N(ch3)4nbo.PNG|700px]] [[File:P(ch3)4nbo.PNG|700px]]

The NBO charge analysis of N(CH3)4 and P(CH3)4 are differemt because they show a postive charge subsided on the phosphorus atom but a negative charge on the nitrogen atom.

The traditional description of the positive charge on the nitrogen centre in the molecule N(CH3)4 is flawed by the NBO analysis. The NBO analysis shows a negative charge on the nitrogen atom and positive charges on the hydrogen atoms. In reality however the charges are not localised; they are distributed around the whole molecule.

[[File:LCAOS.PNG]]