<?xml version="1.0"?>
<feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en">
	<id>https://chemwiki.ch.ic.ac.uk/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Dhk3517</id>
	<title>ChemWiki - User contributions [en]</title>
	<link rel="self" type="application/atom+xml" href="https://chemwiki.ch.ic.ac.uk/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Dhk3517"/>
	<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/wiki/Special:Contributions/Dhk3517"/>
	<updated>2026-05-30T15:56:21Z</updated>
	<subtitle>User contributions</subtitle>
	<generator>MediaWiki 1.43.0</generator>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783997</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783997"/>
		<updated>2019-05-17T16:43:35Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: /* References */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
The main assumptions of the transition state theory is that the reactants have energies which are Boltzmann distributed and that once it reaches the transition state, it will not collapse back to the state of the reactants.&amp;lt;ref name=&amp;quot;theory&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The transition state theory predictions would match the values for conditions 1 to 3 in the question above as they either form products from the reactants directly or do not breakdown from the state of reactants. However, for conditions 4 and 5, the reactants passes the transition state but goes back to the reactant stage at least once which does not agree with the assumption of the transition state theory and hence the experimental values may not follow the predictions.&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that vibrational energy is more efficient for a reaction with a late transition state while translational energy is better at promoting a reaction with an early transition state.&amp;lt;ref name=&amp;quot;rule&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==References==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;theory&amp;quot;&amp;gt;Atkins, P., de Paula, J., Elements of Physical Chemistry, 5th ed.; Oxford University Press, 2009.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;rule&amp;quot;&amp;gt;J. Phys. Chem. Lett. 2012,  3, 23, 3416-3419&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783995</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783995"/>
		<updated>2019-05-17T16:42:42Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: /* 10.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. */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
The main assumptions of the transition state theory is that the reactants have energies which are Boltzmann distributed and that once it reaches the transition state, it will not collapse back to the state of the reactants.&amp;lt;ref name=&amp;quot;theory&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The transition state theory predictions would match the values for conditions 1 to 3 in the question above as they either form products from the reactants directly or do not breakdown from the state of reactants. However, for conditions 4 and 5, the reactants passes the transition state but goes back to the reactant stage at least once which does not agree with the assumption of the transition state theory and hence the experimental values may not follow the predictions.&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that vibrational energy is more efficient for a reaction with a late transition state while translational energy is better at promoting a reaction with an early transition state.&amp;lt;ref name=&amp;quot;rule&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==References==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;theory&amp;quot;&amp;gt;Atkins, P., de Paula, J., Elements of Physical Chemistry, 5th ed.; Oxford University Press, 2009.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783994</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783994"/>
		<updated>2019-05-17T16:41:54Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: /* 10.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. */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
The main assumptions of the transition state theory is that the reactants have energies which are Boltzmann distributed and that once it reaches the transition state, it will not collapse back to the state of the reactants.&amp;lt;ref name=&amp;quot;theory&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The transition state theory predictions would match the values for conditions 1 to 3 in the question above as they either form products from the reactants directly or do not breakdown from the state of reactants. However, for conditions 4 and 5, the reactants passes the transition state but goes back to the reactant stage at least once which does not agree with the assumption of the transition state theory and hence the experimental values may not follow the predictions.&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that vibrational energy is more efficient for a reaction with a late transition state while translational energy is better at promoting a reaction with an early transition state.&lt;br /&gt;
&lt;br /&gt;
==References==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;theory&amp;quot;&amp;gt;Atkins, P., de Paula, J., Elements of Physical Chemistry, 5th ed.; Oxford University Press, 2009.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783984</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783984"/>
		<updated>2019-05-17T16:35:04Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
The main assumptions of the transition state theory is that the reactants have energies which are Boltzmann distributed and that once it reaches the transition state, it will not collapse back to the state of the reactants.&amp;lt;ref name=&amp;quot;theory&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The transition state theory predictions would match the values for conditions 1 to 3 in the question above as they either form products from the reactants directly or do not breakdown from the state of reactants. However, for conditions 4 and 5, the reactants passes the transition state but goes back to the reactant stage at least once which does not agree with the assumption of the transition state theory and hence the experimental values may not follow the predictions.&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==References==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;theory&amp;quot;&amp;gt;Atkins, P., de Paula, J., Elements of Physical Chemistry, 5th ed.; Oxford University Press, 2009.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783965</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783965"/>
		<updated>2019-05-17T16:28:49Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
The main assumptions of the transition state theory is that the reactants have energies which are Boltzmann distributed and that once it reaches the transition state, it will not collapse back to the state of the reactants.&lt;br /&gt;
The transition state theory predictions would match the values for conditions 1 to 3 in the question above as they either form products from the reactants directly or do not breakdown from the state of reactants. However, for conditions 4 and 5, the reactants passes the transition state but goes back to the reactant stage at least once which does not agree with the assumption of the transition state theory and hence the experimental values may not follow the predictions.&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783951</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783951"/>
		<updated>2019-05-17T16:23:07Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: /* 5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values? */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
The main assumptions of the transition state theory is that the reactants have energies which are Boltzmann distributed and that once it reaches the transition state, it will not collapse back to the state of the reactants.&amp;lt;ref name=&amp;quot;theory&amp;quot; /&amp;gt;&amp;lt;references&amp;gt;&lt;br /&gt;
The transition state theory predictions would match the values for conditions 1 to 3 in the question above as they either form products from the reactants directly or do not breakdown from the state of reactants. However, for conditions 4 and 5, the reactants passes the transition state but goes back to the reactant stage at least once which does not agree with the assumption of the transition state theory and hence the experimental values may not follow the predictions.&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;br /&gt;
&lt;br /&gt;
==References===&lt;br /&gt;
&amp;lt;ref name=&amp;quot;theory&amp;quot;&amp;gt;Atkins, P., de Paula, J., Elements of Physical Chemistry, 5th ed.; Oxford University Press, 2009.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783944</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783944"/>
		<updated>2019-05-17T16:22:15Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: /* 5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values? */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
The main assumptions of the transition state theory is that the reactants have energies which are Boltzmann distributed and that once it reaches the transition state, it will not collapse back to the state of the reactants.&amp;lt;ref name=&amp;quot;theory&amp;quot; /&amp;gt;&amp;lt;references&amp;gt;&lt;br /&gt;
The transition state theory predictions would match the values for conditions 1 to 3 in the question above as they either form products from the reactants directly or do not breakdown from the state of reactants. However, for conditions 4 and 5, the reactants passes the transition state but goes back to the reactant stage at least once which does not agree with the assumption of the transition state theory and hence the experimental values may not follow the predictions.&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;br /&gt;
&lt;br /&gt;
==References===&lt;br /&gt;
Atkins, P., de Paula, J., Elements of Physical Chemistry, 5th ed.; Oxford University Press, 2009.&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783900</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783900"/>
		<updated>2019-05-17T16:14:01Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
The main assumptions of the transition state theory is that the reactants have energies which are Boltzmann distributed and that once it reaches the transition state, it will not collapse back to the state of the reactants. &lt;br /&gt;
The transition state theory predictions would match the values for conditions 1 to 3 in the question above as they either form products from the reactants directly or do not breakdown from the state of reactants. However, for conditions 4 and 5, the reactants passes the transition state but goes back to the reactant stage at least once which does not agree with the assumption of the transition state theory and hence the experimental values may not follow the predictions.&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;br /&gt;
&lt;br /&gt;
==References===&lt;br /&gt;
Atkins, P., de Paula, J., Elements of Physical Chemistry, 5th ed.; Oxford University Press, 2009.&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783889</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783889"/>
		<updated>2019-05-17T16:12:48Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: /* 5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values? */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
The main assumptions of the transition state theory is that the reactants have energies which are Boltzmann distributed and that once it reaches the transition state, it will not collapse back to the state of the reactants. &lt;br /&gt;
The transition state theory predictions would match the values for conditions 1 to 3 in the question above as they either form products from the reactants directly or do not breakdown from the state of reactants. However, for conditions 4 and 5, the reactants passes the transition state but goes back to the reactant stage at least once which does not agree with the assumption of the transition state theory and hence the experimental values may not follow the predictions.&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783835</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783835"/>
		<updated>2019-05-17T16:03:00Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Exercise 1==&lt;br /&gt;
&lt;br /&gt;
===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?===&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
===2. 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.===&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===3. Comment on how the mep and the trajectory you just calculated differ.===&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===4. 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?===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
===5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?===&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Exercise 2==&lt;br /&gt;
===6. 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?===&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===7. Locate the approximate position of the transition state.===&lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===8. Report the activation energy for both reactions.===&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===9.  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.===&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
===10.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.===&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783762</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783762"/>
		<updated>2019-05-17T15:55:11Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
[[File:Reactive_H2.png|thumb|left|Reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:Energy_reactive.png|thumb|left|Energy vs time of reactive H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Energy_reactive.png&amp;diff=783740</id>
		<title>File:Energy reactive.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Energy_reactive.png&amp;diff=783740"/>
		<updated>2019-05-17T15:53:47Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Reactive_H2.png&amp;diff=783724</id>
		<title>File:Reactive H2.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Reactive_H2.png&amp;diff=783724"/>
		<updated>2019-05-17T15:52:49Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783723</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783723"/>
		<updated>2019-05-17T15:52:19Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. The horizontal lines also suggest that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
[[File:TS_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
[[File:AE_H2.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
[[File:AE_HF.png|thumb|left|HF+H]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:AE_HF.png&amp;diff=783709</id>
		<title>File:AE HF.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:AE_HF.png&amp;diff=783709"/>
		<updated>2019-05-17T15:50:24Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:AE_H2.png&amp;diff=783707</id>
		<title>File:AE H2.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:AE_H2.png&amp;diff=783707"/>
		<updated>2019-05-17T15:50:12Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:TS_H2.png&amp;diff=783654</id>
		<title>File:TS H2.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:TS_H2.png&amp;diff=783654"/>
		<updated>2019-05-17T15:45:10Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783645</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783645"/>
		<updated>2019-05-17T15:44:26Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
[[File:H2exo.png|thumb|left|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;+F]]&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
All lines are horizontal in the internuclear distance vs time graph. This is because the atoms are not oscillating at this point, or in other words, that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:H2exo.png&amp;diff=783608</id>
		<title>File:H2exo.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:H2exo.png&amp;diff=783608"/>
		<updated>2019-05-17T15:41:06Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783593</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783593"/>
		<updated>2019-05-17T15:39:39Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:Firstset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|[[File:2ndset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|[[File:3rdset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|[[File:4thset.png]]&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|[[File:5thset.png]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
All lines are horizontal in the internuclear distance vs time graph. This is because the atoms are not oscillating at this point, or in other words, that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:5thset.png&amp;diff=783585</id>
		<title>File:5thset.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:5thset.png&amp;diff=783585"/>
		<updated>2019-05-17T15:39:15Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:4thset.png&amp;diff=783581</id>
		<title>File:4thset.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:4thset.png&amp;diff=783581"/>
		<updated>2019-05-17T15:38:49Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:3rdset.png&amp;diff=783572</id>
		<title>File:3rdset.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:3rdset.png&amp;diff=783572"/>
		<updated>2019-05-17T15:37:53Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:2ndset.png&amp;diff=783552</id>
		<title>File:2ndset.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:2ndset.png&amp;diff=783552"/>
		<updated>2019-05-17T15:36:26Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Firstset.png&amp;diff=783515</id>
		<title>File:Firstset.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Firstset.png&amp;diff=783515"/>
		<updated>2019-05-17T15:33:17Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783498</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783498"/>
		<updated>2019-05-17T15:31:24Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg|thumb|left|Internuclear distance vs time graph for transition state]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
[[File:Cont_dy.png|thumb|left|Dynamic]]&lt;br /&gt;
[[File:Cont_mep.png|thumb|left|MEP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
All lines are horizontal in the internuclear distance vs time graph. This is because the atoms are not oscillating at this point, or in other words, that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Cont_mep.png&amp;diff=783448</id>
		<title>File:Cont mep.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Cont_mep.png&amp;diff=783448"/>
		<updated>2019-05-17T15:24:05Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783433</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783433"/>
		<updated>2019-05-17T15:22:03Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
[[File:Transistion.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
All lines are horizontal in the internuclear distance vs time graph. This is because the atoms are not oscillating at this point, or in other words, that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Cont_dy.png&amp;diff=783432</id>
		<title>File:Cont dy.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Cont_dy.png&amp;diff=783432"/>
		<updated>2019-05-17T15:21:55Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Transistion.jpeg&amp;diff=783404</id>
		<title>File:Transistion.jpeg</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Transistion.jpeg&amp;diff=783404"/>
		<updated>2019-05-17T15:15:47Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783402</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783402"/>
		<updated>2019-05-17T15:13:58Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
As seen in the graphs, H2 + F is exothermic and HF + H is endothermic. HF has a stronger bond than H2 due to the electronegativity difference between H and F which contributes to the ionic interaction of the molecule. Hence, energy is needed to break this bond while energy is released when making this bond.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
AB 1.8A&lt;br /&gt;
BC 0.74A &lt;br /&gt;
All lines are horizontal in the internuclear distance vs time graph. This is because the atoms are not oscillating at this point, or in other words, that the atoms are not &amp;quot;rolling into&amp;quot; the side of products or reactants at which point is said to be the transition state.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is reactive when AB distance is 1.8A, momentum is -0.5 and BC distance is 0.74A and momentum is 0.555. In the energy vs time curve, the energy conservation is shown as when the potential energy is at its maximum, the kinetic energy is at its minimum and when the kinetic energy is at its maximum, the potential energy is at its minimum and the total energy of the system does not change.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Polanyi&#039;s empirical rules state that&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783389</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783389"/>
		<updated>2019-05-17T14:22:55Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Dynamic considers the residual momentum the molecules have while MEP only considers the momentum the molecules would have that exact moment or position without any residual momentum. &#039;&#039;&#039;This explains why the path of the dynamic is curly while MEP is straight; dynamic state has momentum which leads to vibrations causing contractions and elongations of bonds while MEP does not have this quality. Also, the dynamic ranges further than MEP due to the residual momentum dynamic state has.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is exothermic&lt;br /&gt;
&lt;br /&gt;
HF + H is enothermic&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
AB 1.8A H2+F&lt;br /&gt;
BC 0.74A &lt;br /&gt;
&lt;br /&gt;
HF + H&lt;br /&gt;
AB 2.132 &lt;br /&gt;
BC 0.92&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 reactive&lt;br /&gt;
AB 1.8A -0.5&lt;br /&gt;
BC 0.74A 0.555&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
HF reactive &lt;br /&gt;
AB 0.74A -0.5&lt;br /&gt;
BC 1.8A -0.2&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783378</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783378"/>
		<updated>2019-05-17T14:05:46Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
&lt;br /&gt;
The reactant and product are the same molecule so the transition state resembles the reactant as much as it does the product. Therefore, according to the Hammond postulate, it is neither an early or late transition state which explains that the transition state has equal bond lengths between the three hydrogen atoms. The transition state is where the molecules are not vibrating, hence the horizontal lines in the internuclear distances vs time graph. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is exothermic&lt;br /&gt;
&lt;br /&gt;
HF + H is enothermic&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039;&lt;br /&gt;
AB 1.8A H2+F&lt;br /&gt;
BC 0.74A &lt;br /&gt;
&lt;br /&gt;
HF + H&lt;br /&gt;
AB 2.132 &lt;br /&gt;
BC 0.92&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 reactive&lt;br /&gt;
AB 1.8A -0.5&lt;br /&gt;
BC 0.74A 0.555&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
HF reactive &lt;br /&gt;
AB 0.74A -0.5&lt;br /&gt;
BC 1.8A -0.2&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783358</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=783358"/>
		<updated>2019-05-17T13:45:38Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate the potential energy curve to get the minimum energy curve (black line on the surface diagram), differentiate again (i.e. differentiate the minimum energy curve) and equate to zero to find where the gradient is zero (either maximum or minimum point), differentiate the third time and substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum. Hence, that point is the transition state. Another way if to differentiate the potential energy curve with respect to Q1 and Q2. Equate both differential equations to zero to find where the gradient is zero for both. Q1 would have a minimum point while Q2 has a maximum point. The intersection of Q1&#039;s min and Q2&#039;s max is the transition state.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is exothermic&lt;br /&gt;
&lt;br /&gt;
HF + H is enothermic&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039;&lt;br /&gt;
AB 1.8A H2+F&lt;br /&gt;
BC 0.74A &lt;br /&gt;
&lt;br /&gt;
HF + H&lt;br /&gt;
AB 2.132 &lt;br /&gt;
BC 0.92&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 reactive&lt;br /&gt;
AB 1.8A -0.5&lt;br /&gt;
BC 0.74A 0.555&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
HF reactive &lt;br /&gt;
AB 0.74A -0.5&lt;br /&gt;
BC 1.8A -0.2&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=780914</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=780914"/>
		<updated>2019-05-16T14:31:02Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
Differentiate potential wrt q1 and q2. the intersection of q1&#039;s min and q2&#039;s max is the transition state.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is exothermic&lt;br /&gt;
&lt;br /&gt;
HF + H is enothermic&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039;&lt;br /&gt;
AB 1.8A H2+F&lt;br /&gt;
BC 0.74A &lt;br /&gt;
&lt;br /&gt;
HF + H&lt;br /&gt;
AB 2.132 &lt;br /&gt;
BC 0.92&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 132.579 - 132.974&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 reactive&lt;br /&gt;
AB 1.8A -0.5&lt;br /&gt;
BC 0.74A 0.555&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
HF reactive &lt;br /&gt;
AB 0.74A -0.5&lt;br /&gt;
BC 1.8A -0.2&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=780878</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=780878"/>
		<updated>2019-05-16T14:25:14Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
Differentiate potential wrt q1 and q2. the intersection of q1&#039;s min and q2&#039;s max is the transition state.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is exothermic&lt;br /&gt;
&lt;br /&gt;
HF + H is enothermic&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039;&lt;br /&gt;
AB 1.8A H2+F&lt;br /&gt;
BC 0.74A &lt;br /&gt;
&lt;br /&gt;
HF + H&lt;br /&gt;
AB 2.132 &lt;br /&gt;
BC 0.92&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 104.9 - 131.4&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 reactive&lt;br /&gt;
AB 1.8A -0.5&lt;br /&gt;
BC 0.74A 0.555&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;10.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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
HF reactive &lt;br /&gt;
AB 0.74A 2&lt;br /&gt;
BC 1.8A -0.1&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=780635</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=780635"/>
		<updated>2019-05-16T13:56:10Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
Differentiate potential wrt q1 and q2. the intersection of q1&#039;s min and q2&#039;s max is the transition state.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is exothermic&lt;br /&gt;
&lt;br /&gt;
HF + H is enothermic&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039;&lt;br /&gt;
AB 1.8A H2+F&lt;br /&gt;
BC 0.74A &lt;br /&gt;
&lt;br /&gt;
HF + H&lt;br /&gt;
AB 2.132 &lt;br /&gt;
BC 0.92&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;8. Report the activation energy for both reactions.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
energy vs time &lt;br /&gt;
step size 10000&lt;br /&gt;
&lt;br /&gt;
H2 103.8 - 131.9 &lt;br /&gt;
&lt;br /&gt;
HF 104.9 - 131.4&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;9.  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.&#039;&#039;&#039;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778784</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778784"/>
		<updated>2019-05-14T19:57:21Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
Differentiate potential wrt q1 and q2. the intersection of q1&#039;s min and q2&#039;s max is the transition state.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
H2 + F is exothermic&lt;br /&gt;
&lt;br /&gt;
HF + H is enothermic&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;7. Locate the approximate position of the transition state.&#039;&#039;&#039;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778764</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778764"/>
		<updated>2019-05-14T19:22:36Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
Differentiate potential wrt q1 and q2. the intersection of q1&#039;s min and q2&#039;s max is the transition state.  &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;6. 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?&#039;&#039;&#039;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778727</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778727"/>
		<updated>2019-05-14T18:59:20Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is initially bonded to C then B bounces between A and C. In the end, B is bonded to A.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Reactants have energies which are Boltzmann distributed&lt;br /&gt;
Once it reaches the transition state, it will not go back to the state of the reactants&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778693</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778693"/>
		<updated>2019-05-14T18:37:44Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B bounces between A and C.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From the table, we can see how the reactivity is related to the total energy. The total energy must be of certain balance so that the BC bond can be broken and AB bond can be formed and stable enough to go back to BC.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;5. State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?&#039;&#039;&#039;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778691</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778691"/>
		<updated>2019-05-14T18:33:09Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-99.018&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-100.456&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is bonded to C and the molecule BC comes close to A but not  close enough for proton transfer and distance between those increase again.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-98.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|B is transferred from C to A slowly and it stays with A.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-84.956&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B is transferred to A then bounces away from it twice, goes back to A and bounces three times.&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-83.416&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|No&lt;br /&gt;
|B bounces between A and C.&lt;br /&gt;
|&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778317</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778317"/>
		<updated>2019-05-14T16:07:28Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-103.869&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|Yes&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778304</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778304"/>
		<updated>2019-05-14T16:04:15Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!p1&lt;br /&gt;
!p2&lt;br /&gt;
!Etot&lt;br /&gt;
!Reactive?&lt;br /&gt;
!Description of the dynamics&lt;br /&gt;
!Illustration of the trajectory&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.25&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-1.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.0&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-2.5&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-5.2&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778289</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=778289"/>
		<updated>2019-05-14T16:02:20Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;4. 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?&#039;&#039;&#039;&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=777840</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=777840"/>
		<updated>2019-05-14T15:14:01Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
equal bond lengths as it is neither an early or late transition state. It is a same molecule so the transition state resembles the reactant as much as it does the product. hammond postulate.&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.90774249783929994&lt;br /&gt;
more precise&lt;br /&gt;
the one above is just an estimate&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=777785</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=777785"/>
		<updated>2019-05-14T15:09:21Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;3. Comment on how the mep and the trajectory you just calculated differ.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.90774249783929994&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=777700</id>
		<title>MRD:dhk3517</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:dhk3517&amp;diff=777700"/>
		<updated>2019-05-14T14:59:01Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: Created page with &amp;quot;&amp;#039;&amp;#039;&amp;#039;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 fr...&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&#039;&#039;&#039;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?&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Differentiate potential energy to get the minimum energy curve, differentiate again and equate to zero to find where the gradient is zero (either maximum or minimum), differentiate the third time substitute coordinates found from the second derivative, if it is negative it proves that the point found is a maximum.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;2. 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.&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
0.9075 Å&lt;br /&gt;
insert image here&lt;br /&gt;
it is where the molecules are not vibrating, hence the horizontal lines. This is because the potential energy of the molecules are zero and hence do not have any energy for vibrations.&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Group5_sodiumalginate&amp;diff=718246</id>
		<title>Group5 sodiumalginate</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Group5_sodiumalginate&amp;diff=718246"/>
		<updated>2018-05-17T10:46:14Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: /*  */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Synthesis of Calcium alginate ==&lt;br /&gt;
=== Permeability Test ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Paste: 50g containing 2% w/w sodium alginate &lt;br /&gt;
&lt;br /&gt;
2. Calcium chloride: 10% w/v aq. calcium chloride &lt;br /&gt;
&lt;br /&gt;
2. Membrane thickness: 0.4mm&lt;br /&gt;
&lt;br /&gt;
3. Temperature: room temperature &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Calculations&amp;gt; ====&lt;br /&gt;
P = 240 x Δm / A &lt;br /&gt;
&lt;br /&gt;
Δm: mg/h &lt;br /&gt;
&lt;br /&gt;
A: cm&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; (10cm&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Results&amp;gt; ====&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Without additive&lt;br /&gt;
! Trial !! Initial mass /g !! Final mass / g !! Change in mass /g (Δm) !! Time take / mins !! Permeability &lt;br /&gt;
|-&lt;br /&gt;
| 1 || 63.11 || 59.71 || 3.4 || 20 || 244 800&lt;br /&gt;
|-&lt;br /&gt;
| 2 || 57.13 || 56.49 || 0.64 || 50 || 18432&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ With 0.05g chitosan &lt;br /&gt;
! Trial !! Initial mass /g !! Final mass / g !! Change in mass /g (Δm) !! Time take / mins !! Permeability &lt;br /&gt;
|-&lt;br /&gt;
| 1 || 61.24 || 60.53 || 0.71 || 120 || 8520&lt;br /&gt;
|-&lt;br /&gt;
| 2 || 58.75 || 52.74 || 6.01 || 1352 || 6401&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Alginate hydrolysis and calcium titration ==&lt;br /&gt;
=== Hydrolysis ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Temperature: Room temperature&lt;br /&gt;
&lt;br /&gt;
2. Time for hydrolysis: 30 minutes &lt;br /&gt;
&lt;br /&gt;
3. Amount of chitosan used: 0.05g &lt;br /&gt;
&lt;br /&gt;
4. Volume of 2M Hydrochloric acid used: 25ml&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Titration ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Amount of calcium alginate: 5g&lt;br /&gt;
&lt;br /&gt;
2. Volume of calcium chloride: 25ml&lt;br /&gt;
&lt;br /&gt;
3. Amount of buffer: 10 drops &lt;br /&gt;
&lt;br /&gt;
4. Amount of indicator: 0.15g &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Color change&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Initial: Pinkish red&lt;br /&gt;
&lt;br /&gt;
End point: Blue &lt;br /&gt;
&lt;br /&gt;
Past end point: Orange-ish pink &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Results&amp;gt; ====&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Titration results&lt;br /&gt;
!  Condition !! Volume of EDTA used for 1st trial / ml !! 2nd trial / ml !! 3rd trial / ml !! Average volume used / ml !! Amount of Calcium Chloride remaining &lt;br /&gt;
|-&lt;br /&gt;
| Hydrolyzed with 0.05g chitosan  || 7.7 || 7.3 || 6.3 || 7.1 ||&lt;br /&gt;
|-&lt;br /&gt;
| Non-hydrolyzed with 0.05g chitosan || 9.5 || 8.5 || 8.7 || 8.9 ||&lt;br /&gt;
|-&lt;br /&gt;
| Hydrolyzed without additive || 6.8 || 8 || 6.2 || 7 || &lt;br /&gt;
|-&lt;br /&gt;
| Non-hydrolyzed without additive || 6.2 || 7.3 || 4.7 || 6.1 || &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Extension ==&lt;br /&gt;
=== Tea bag replacements ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Sodium alginate used: 1g&lt;br /&gt;
&lt;br /&gt;
2. Amount of tea: 1g&lt;br /&gt;
&lt;br /&gt;
3. Volume of water: 250ml&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Results&lt;br /&gt;
! Composition of paste !! Result !! Reason&lt;br /&gt;
|-&lt;br /&gt;
| 0.1g Chitosan || Not permeable enough || &lt;br /&gt;
|-&lt;br /&gt;
| 0.05g Chitosan + 0.05g Sodium hexametaphosphate || Broke ||&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=== Temperature stability ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Temperature: 100°C&lt;br /&gt;
&lt;br /&gt;
2. Time left in hot water: 2 minutes&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Results&amp;gt; ====&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Results for temperature stability test&lt;br /&gt;
! Composition of paste !! Initial mass (g) !! Final mass (g) !! Mass change (g) !! Final mass/Initial mass&lt;br /&gt;
|-&lt;br /&gt;
| 0.05g Chitosan || 0.38 || 0.22 || 0.16 || 0.5789&lt;br /&gt;
|-&lt;br /&gt;
| 0.05g Chitosan(2) || 0.17 || 0.11 || 0.06 || 0.6471&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Group5_sodiumalginate&amp;diff=718244</id>
		<title>Group5 sodiumalginate</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Group5_sodiumalginate&amp;diff=718244"/>
		<updated>2018-05-17T10:45:53Z</updated>

		<summary type="html">&lt;p&gt;Dhk3517: /* Temperature stability */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Synthesis of Calcium alginate ==&lt;br /&gt;
=== Permeability Test ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Paste: 50g containing 2% w/w sodium alginate &lt;br /&gt;
&lt;br /&gt;
2. Calcium chloride: 10% w/v aq. calcium chloride &lt;br /&gt;
&lt;br /&gt;
2. Membrane thickness: 0.4mm&lt;br /&gt;
&lt;br /&gt;
3. Temperature: room temperature &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Calculations&amp;gt; ====&lt;br /&gt;
P = 240 x Δm / A &lt;br /&gt;
&lt;br /&gt;
Δm: mg/h &lt;br /&gt;
&lt;br /&gt;
A: cm&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; (10cm&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Results&amp;gt; ====&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Without additive&lt;br /&gt;
! Trial !! Initial mass /g !! Final mass / g !! Change in mass /g (Δm) !! Time take / mins !! Permeability &lt;br /&gt;
|-&lt;br /&gt;
| 1 || 63.11 || 59.71 || 3.4 || 20 || 244 800&lt;br /&gt;
|-&lt;br /&gt;
| 2 || 57.13 || 56.49 || 0.64 || 50 || 18432&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ With 0.05g chitosan &lt;br /&gt;
! Trial !! Initial mass /g !! Final mass / g !! Change in mass /g (Δm) !! Time take / mins !! Permeability &lt;br /&gt;
|-&lt;br /&gt;
| 1 || 61.24 || 60.53 || 0.71 || 120 || 8520&lt;br /&gt;
|-&lt;br /&gt;
| 2 || 58.75 || 52.74 || 6.01 || 1352 || 6401&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Alginate hydrolysis and calcium titration ==&lt;br /&gt;
=== Hydrolysis ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Temperature: Room temperature&lt;br /&gt;
&lt;br /&gt;
2. Time for hydrolysis: 30 minutes &lt;br /&gt;
&lt;br /&gt;
3. Amount of chitosan used: 0.05g &lt;br /&gt;
&lt;br /&gt;
4. Volume of 2M Hydrochloric acid used: 25ml&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Titration ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Amount of calcium alginate: 5g&lt;br /&gt;
&lt;br /&gt;
2. Volume of calcium chloride: 25ml&lt;br /&gt;
&lt;br /&gt;
3. Amount of buffer: 10 drops &lt;br /&gt;
&lt;br /&gt;
4. Amount of indicator: 0.15g &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Color change&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Initial: Pinkish red&lt;br /&gt;
&lt;br /&gt;
End point: Blue &lt;br /&gt;
&lt;br /&gt;
Past end point: Orange-ish pink &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Results&amp;gt; ====&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Titration results&lt;br /&gt;
!  Condition !! Volume of EDTA used for 1st trial / ml !! 2nd trial / ml !! 3rd trial / ml !! Average volume used / ml !! Amount of Calcium Chloride remaining &lt;br /&gt;
|-&lt;br /&gt;
| Hydrolyzed with 0.05g chitosan  || 7.7 || 7.3 || 6.3 || 7.1 ||&lt;br /&gt;
|-&lt;br /&gt;
| Non-hydrolyzed with 0.05g chitosan || 9.5 || 8.5 || 8.7 || 8.9 ||&lt;br /&gt;
|-&lt;br /&gt;
| Hydrolyzed without additive || 6.8 || 8 || 6.2 || 7 || &lt;br /&gt;
|-&lt;br /&gt;
| Non-hydrolyzed without additive || 6.2 || 7.3 || 4.7 || 6.1 || &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Extension ==&lt;br /&gt;
=== Tea bag replacements ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Sodium alginate used: 1g&lt;br /&gt;
&lt;br /&gt;
2. Amount of tea: 1g&lt;br /&gt;
&lt;br /&gt;
3. Volume of water: 250ml&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Results&lt;br /&gt;
! Composition of paste !! Result !! Reason&lt;br /&gt;
|-&lt;br /&gt;
| 0.1g Chitosan || Not permeable enough || &lt;br /&gt;
|-&lt;br /&gt;
| 0.05g Chitosan + 0.05g Sodium hexametaphosphate || Broke ||&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
=== Temperature stability ===&lt;br /&gt;
==== &amp;lt;Controls&amp;gt; ====&lt;br /&gt;
1. Temperature: 100°C&lt;br /&gt;
&lt;br /&gt;
2. Time left in hot water: 2 minutes&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;Results&amp;gt; ====&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Results&lt;br /&gt;
! Composition of paste !! Initial mass (g) !! Final mass (g) !! Mass change (g) !! Final mass/Initial mass&lt;br /&gt;
|-&lt;br /&gt;
| 0.05g Chitosan || 0.38 || 0.22 || 0.16 || 0.5789&lt;br /&gt;
|-&lt;br /&gt;
| 0.05g Chitosan(2) || 0.17 || 0.11 || 0.06 || 0.6471&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Dhk3517</name></author>
	</entry>
</feed>