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	<id>https://chemwiki.ch.ic.ac.uk/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Ysl115</id>
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	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615769</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615769"/>
		<updated>2017-05-05T17:04:30Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
[[File:MEshishi.PNG]]&lt;br /&gt;
[[File:dynamicsshuishui.PNG]]&lt;br /&gt;
&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:1ni.PNG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:2wo.PNG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:3ta.PNG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:4nimen.PNG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:5women.PNG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
The transition position is when HF has a distance of 1.81 and HH has a distance of 0.745.&lt;br /&gt;
[[File:woahahah.PNG]]&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
Activation energy (form HF and F)= 0.6kJ/mol&lt;br /&gt;
Activation energy (form F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; )=30.6 kJ/mol&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
The amount of translatinoal and virational energy will affect whether the reaction can be reactive or not.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615768</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615768"/>
		<updated>2017-05-05T17:01:25Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
[[File:MEshishi.PNG]]&lt;br /&gt;
[[File:dynamicsshuishui.PNG]]&lt;br /&gt;
&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:1ni.PNG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:2wo.PNG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:3ta.PNG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:4nimen.PNG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:5women.PNG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
The transition position is when HF has a distance of 1.81 and HH has a distance of 0.745.&lt;br /&gt;
[[File:woahahah.PNG]]&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
Activation energy (form HF and F)= 0.6kJ/mol&lt;br /&gt;
Activation energy (form F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; )=30.6 kJ/mol&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Woahahah.PNG&amp;diff=615760</id>
		<title>File:Woahahah.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Woahahah.PNG&amp;diff=615760"/>
		<updated>2017-05-05T16:57:39Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615759</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615759"/>
		<updated>2017-05-05T16:57:20Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
[[File:MEshishi.PNG]]&lt;br /&gt;
[[File:dynamicsshuishui.PNG]]&lt;br /&gt;
&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:1ni.PNG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:2wo.PNG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:3ta.PNG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:4nimen.PNG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:5women.PNG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
The transition position is when HF has a distance of 1.81 and HH has a distance of 0.745.&lt;br /&gt;
[[File:woahahah.PNG]]&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615758</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615758"/>
		<updated>2017-05-05T16:56:29Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
[[File:MEshishi.PNG]]&lt;br /&gt;
[[File:dynamicsshuishui.PNG]]&lt;br /&gt;
&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:1ni.PNG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:2wo.PNG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:3ta.PNG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:4nimen.PNG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:5women.PNG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
The transition position is when HF has a distance of 1.81 and HH has a distance of 0.745.&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:5women.PNG&amp;diff=615738</id>
		<title>File:5women.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:5women.PNG&amp;diff=615738"/>
		<updated>2017-05-05T16:52:03Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:4nimen.PNG&amp;diff=615735</id>
		<title>File:4nimen.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:4nimen.PNG&amp;diff=615735"/>
		<updated>2017-05-05T16:51:45Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:3ta.PNG&amp;diff=615731</id>
		<title>File:3ta.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:3ta.PNG&amp;diff=615731"/>
		<updated>2017-05-05T16:51:28Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:2wo.PNG&amp;diff=615728</id>
		<title>File:2wo.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:2wo.PNG&amp;diff=615728"/>
		<updated>2017-05-05T16:51:12Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:1ni.PNG&amp;diff=615723</id>
		<title>File:1ni.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:1ni.PNG&amp;diff=615723"/>
		<updated>2017-05-05T16:50:52Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615722</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615722"/>
		<updated>2017-05-05T16:50:15Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
[[File:MEshishi.PNG]]&lt;br /&gt;
[[File:dynamicsshuishui.PNG]]&lt;br /&gt;
&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:1ni.PNG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:2wo.PNG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:3ta.PNG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:4nimen.PNG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:5women.PNG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
 The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dynamicsshuishui.PNG&amp;diff=615721</id>
		<title>File:Dynamicsshuishui.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dynamicsshuishui.PNG&amp;diff=615721"/>
		<updated>2017-05-05T16:49:42Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MEshishi.PNG&amp;diff=615718</id>
		<title>File:MEshishi.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MEshishi.PNG&amp;diff=615718"/>
		<updated>2017-05-05T16:48:40Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615714</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615714"/>
		<updated>2017-05-05T16:48:08Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
[[File:MEshishi.PNG]]&lt;br /&gt;
[[File:dynamics.PNG]]&lt;br /&gt;
&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:1ni.PNG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:2wo.PNG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:3ta.PNG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:4nimen.PNG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:5women.PNG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
 The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615711</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615711"/>
		<updated>2017-05-05T16:47:27Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
[[File:ME.PNG]]&lt;br /&gt;
[[File:dynamics.PNG]]&lt;br /&gt;
&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:1ni.PNG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:2wo.PNG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:3ta.PNG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:4nimen.PNG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:5women.PNG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
 The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MEP.PNG&amp;diff=615696</id>
		<title>File:MEP.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MEP.PNG&amp;diff=615696"/>
		<updated>2017-05-05T16:44:06Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615692</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615692"/>
		<updated>2017-05-05T16:43:34Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
[[File:MEP.PNG]]&lt;br /&gt;
[[File:dynamics.PNG]]&lt;br /&gt;
&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:1.PNG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:2.PNG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:3.PNG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:4.PNG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:5.PNG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
 The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615682</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615682"/>
		<updated>2017-05-05T16:40:25Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 1 ST3515.JPG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 2 ST3515.JPG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 3 ST3515.JPG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 4 ST3515.JPG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 5 ST3515.JPG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
 The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615678</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615678"/>
		<updated>2017-05-05T16:38:47Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 1 ST3515.JPG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 2 ST3515.JPG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 3 ST3515.JPG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 4 ST3515.JPG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 5 ST3515.JPG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theory===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
 The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615676</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615676"/>
		<updated>2017-05-05T16:37:27Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 1 ST3515.JPG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 2 ST3515.JPG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 3 ST3515.JPG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 4 ST3515.JPG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 5 ST3515.JPG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theorʏ===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
 The reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; to form HF and H. The reaction will be exothermic, because the energy results from bond forming and breaking. In this reaction, H-H bond are being broken which needs to absorb energy and H-F bonds are being formed which will release energy. Since H-F is a stronger bond than H-H, thus energy will be given out which means this reaction is exothermic.&lt;br /&gt;
The reaction of HF and H to form  F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;. The reaction will be endothermic, because more energy are absorbed than that being released.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Po.PNG&amp;diff=615642</id>
		<title>File:Po.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Po.PNG&amp;diff=615642"/>
		<updated>2017-05-05T16:25:48Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615637</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615637"/>
		<updated>2017-05-05T16:25:19Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
[[File:po.PNG]]&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 1 ST3515.JPG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 2 ST3515.JPG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 3 ST3515.JPG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 4 ST3515.JPG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 5 ST3515.JPG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theorʏ===&lt;br /&gt;
The transition state theory assumes that there is a quasi-equilibrium between reactants and transition state, and when it reaches the equilibrium, the system will form product. But as it is shown in the example above, this is not necessary the case as indicated in the 4th example that the system has passed through the activation barrier but it bounces back to the reactants channel to reproduce the reactants and the reaction wasn&#039;t successful.&lt;br /&gt;
&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Reaction of F and H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;===&lt;br /&gt;
 The reaction of &lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615569</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615569"/>
		<updated>2017-05-05T16:09:31Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive or unreactive trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 1 ST3515.JPG|256px]] || -1.25 || -2.5 || Reactive || Products are formed since the system can overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 2 ST3515.JPG|256px]] || -1.50 || -2.0 || Unreactive|| The system don&#039;t have enough energy to overcome the activation barrier and the reactants stay as reactants after they reach the transition structure.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 3 ST3515.JPG|256px]] || -1.50 || -2.5 || Reactive || The system have enough translational and vibrational energy to overcome the barrier to proceed to the product channel to form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 4 ST3515.JPG|256px]] || -2.50 || -5.0 || Unreactive || This is barrier re crossing as the system first had enough energy to pass through the barrier but at the end it bounce back to the reactant channel to reform reactants.&lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 5 ST3515.JPG|256px]] || -2.50 || -5.2 || Reactive || This is also barrier re-crossing, but in this system, it has been able to have enough energy to rebounce at the reactants channel to proceed to product channel to form products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theorʏ===&lt;br /&gt;
The transitino state theory assumes that there is a quasi-equilibrium between reactants and transition state. But as it shown in the example above &lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615527</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615527"/>
		<updated>2017-05-05T15:54:06Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Reactive and unreactive trajectories&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive Trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 1 ST3515.JPG|256px]] || -1.25 || -2.5 || Yes || This trajectory forms products as there is the correct combination of vibrational and translational motion for the system to overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 2 ST3515.JPG|256px]] || -1.50 || -2.0 || No || The system approaches the transition structure however does not have sufficient energy to overcome the activation barrier. Products are not formed and the reactants move away from each other after approaching the transition structure. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 3 ST3515.JPG|256px]] || -1.50 || -2.5 || Yes || Increasing the translational energy gives the system sufficient energy to overcome the activation barrier and form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 4 ST3515.JPG|256px]] || -2.50 || -5.0 || No || The system is able to overcome the activation barrier to form products however reverses back and crosses the barrier again (barrier re-crossing) to reform the reactants. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 5 ST3515.JPG|256px]] || -2.50 || -5.2 || Yes || Barrier re-crossing also occurs for this trajectory. However increasing the translational energy causes it to cross the barrier twice and form the products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theorʏ===&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615521</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615521"/>
		<updated>2017-05-05T15:53:07Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from the transition state region===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is expected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;br /&gt;
&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
MEP shows the direction of the reaction. For example, the reaction will be forming product if the trajectory of MEP is going towards the direction of the product. The reaction is not forming product if the trajectory is proceeding towards reactants. On MEP, it doesn&#039;t show the change in potential energy whereas it will be shown on dynamics plot. &lt;br /&gt;
&lt;br /&gt;
===Reactive and unreactive trajectories ===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Table showing how vibrational and translational energies affect a trajectory&lt;br /&gt;
! Surface Plot !! p&amp;lt;sub&amp;gt;1&amp;lt;/sub&amp;gt; !! p&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; !! Reactive Trajectory? !! Description &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 1 ST3515.JPG|256px]] || -1.25 || -2.5 || Yes || This trajectory forms products as there is the correct combination of vibrational and translational motion for the system to overcome the activation barrier. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 2 ST3515.JPG|256px]] || -1.50 || -2.0 || No || The system approaches the transition structure however does not have sufficient energy to overcome the activation barrier. Products are not formed and the reactants move away from each other after approaching the transition structure. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 3 ST3515.JPG|256px]] || -1.50 || -2.5 || Yes || Increasing the translational energy gives the system sufficient energy to overcome the activation barrier and form products. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 4 ST3515.JPG|256px]] || -2.50 || -5.0 || No || The system is able to overcome the activation barrier to form products however reverses back and crosses the barrier again (barrier re-crossing) to reform the reactants. &lt;br /&gt;
|-&lt;br /&gt;
|[[File:Reactive Trajectory 5 ST3515.JPG|256px]] || -2.50 || -5.2 || Yes || Barrier re-crossing also occurs for this trajectory. However increasing the translational energy causes it to cross the barrier twice and form the products. &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===Assumptions of Transition State Theorʏ===&lt;br /&gt;
== EXERCISE 2: F - H - H system ==&lt;br /&gt;
===Locate the transition state===&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
[[File:Transition State Dynamics 2 ST3515.JPG]]&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615458</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=615458"/>
		<updated>2017-05-05T15:38:59Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H2 system ==&lt;br /&gt;
===Dynamics from Transition State===&lt;br /&gt;
===Transition State Position===&lt;br /&gt;
===MEP and Dynamics===&lt;br /&gt;
===Transition State Theory===&lt;br /&gt;
== F-H-H System ==&lt;br /&gt;
===Transtion State Position===&lt;br /&gt;
===Activation Energy===&lt;br /&gt;
===Reaction Dynamics===&lt;br /&gt;
===Transition State Position and Distribution of Energy===&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
r ts.PNG&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&#039;&#039;&#039;r&amp;lt;sub&amp;gt;ts=0.91 A&amp;lt;/sub&amp;gt;&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is exoected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=613659</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=613659"/>
		<updated>2017-05-04T15:56:35Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; system ==&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
r ts.PNG&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&#039;&#039;&#039;r&amp;lt;sub&amp;gt;ts=0.91 A&amp;lt;/sub&amp;gt;&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is exoected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.And the distance AC will be double of that of AB or BC which is the sum of AB and BC.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=613538</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=613538"/>
		<updated>2017-05-04T14:58:10Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; system ==&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;gallery&amp;gt;&lt;br /&gt;
r ts.PNG&lt;br /&gt;
&amp;lt;/gallery&amp;gt;&#039;&#039;&#039;r&amp;lt;sub&amp;gt;ts=0.91 A&amp;lt;/sub&amp;gt;&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
At this value of r, the system will reach a transition structure which is the maximum point on the minimum energy path. The transition state position is when &#039;&#039;&#039;r&amp;lt;sub&amp;gt;1 =&amp;lt;/sub&amp;gt;&#039;&#039;&#039; &#039;&#039;&#039;r&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&#039;&#039;&#039; so it is exoected that on the internuclear distances vs time plot will show that the distances of AB and BC will be the same in the time frame.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=613460</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=613460"/>
		<updated>2017-05-04T14:18:26Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* EXERCISE 1: H + H2 system */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; system ==&lt;br /&gt;
The transition structure is the maximum on the minimum energy path whereas the minimum is at the minimum point on the path. At a minimum and a transition structure, the total gradient of the potential energy surface is 0. On the potential energy surface diagram, the transition structure will be the saddle point which is the local maximum on the path which will have a negative value for the second derivative. Meanwhile, the minimum will be the local minimum on the path which has a positive value for the second derivative. The transition structure will be indicated by negative curvature whereas as the minimum has positive curvature.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=612838</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=612838"/>
		<updated>2017-05-02T15:56:28Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== EXERCISE 1: H + H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; system ==&lt;br /&gt;
Question 1:&lt;br /&gt;
&lt;br /&gt;
Question 2:What value does the total gradient of the potential energy surface have at a minimum and at a transition structure? Briefly explain how minima and transition structures can be distinguished using the curvature of the potential energy surface.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=612642</id>
		<title>Yukilamys010</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Yukilamys010&amp;diff=612642"/>
		<updated>2017-05-02T14:51:33Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: Created page with &amp;quot;What value does the total gradient of the potential energy surface have at a minimum and at a transition structure? Briefly explain how minima and transition structures can be...&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;What value does the total gradient of the potential energy surface have at a minimum and at a transition structure? Briefly explain how minima and transition structures can be distinguished using the curvature of the potential energy surface.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=549068</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=549068"/>
		<updated>2016-03-04T15:31:41Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Reaction energy */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is one mode expected according to the 3N-5 rule.&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
The energy of the haber process is shown as below.&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Calculation on another molecule ==&lt;br /&gt;
&lt;br /&gt;
=== HCl ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of HCl ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of HCl&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || HCl&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -460.80077875 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00005211 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;infV&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-Cl =1.28599 Å, HCl is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000090     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000090     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000139     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000197     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of HCl ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLHCLOPT.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;HCl&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLHCLOPT.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: YSLHCLCAP.PNG]]&lt;br /&gt;
&lt;br /&gt;
The charge of H is 0.284 and that of Cl is -0.284. The charge of Cl is expected of be more positive compare to that of H because Cl is more electronegative than H.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548993</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548993"/>
		<updated>2016-03-04T15:21:00Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Display vibration and atomic charges */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is one mode expected according to the 3N-5 rule.&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Calculation on another molecule ==&lt;br /&gt;
&lt;br /&gt;
=== HCl ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of HCl ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of HCl&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || HCl&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -460.80077875 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00005211 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;infV&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-Cl =1.28599 Å, HCl is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000090     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000090     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000139     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000197     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of HCl ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLHCLOPT.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;HCl&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLHCLOPT.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: YSLHCLCAP.PNG]]&lt;br /&gt;
&lt;br /&gt;
The charge of H is 0.284 and that of Cl is -0.284. The charge of Cl is expected of be more positive compare to that of H because Cl is more electronegative than H.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548980</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548980"/>
		<updated>2016-03-04T15:19:39Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Display vibration and atomic charges */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Calculation on another molecule ==&lt;br /&gt;
&lt;br /&gt;
=== HCl ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of HCl ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of HCl&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || HCl&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -460.80077875 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00005211 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;infV&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-Cl =1.28599 Å, HCl is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000090     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000090     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000139     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000197     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of HCl ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLHCLOPT.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;HCl&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLHCLOPT.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: YSLHCLCAP.PNG]]&lt;br /&gt;
&lt;br /&gt;
The charge of H is 0.284 and that of Cl is -0.284. The charge of Cl is expected of be more positive compare to that of H because Cl is more electronegative than H.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548935</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548935"/>
		<updated>2016-03-04T15:11:51Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Optimisation file of HCl */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Calculation on another molecule ==&lt;br /&gt;
&lt;br /&gt;
=== HCl ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of HCl ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of HCl&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || HCl&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -460.80077875 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00005211 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;infV&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-Cl =1.28599 Å, HCl is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000090     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000090     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000139     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000197     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of HCl ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLHCLOPT.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;HCl&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLHCLOPT.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: YSLHCLCAP.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548885</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548885"/>
		<updated>2016-03-04T15:04:51Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Summary of HCl */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Calculation on another molecule ==&lt;br /&gt;
&lt;br /&gt;
=== HCl ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of HCl ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of HCl&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || HCl&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -460.80077875 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00005211 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;infV&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-Cl =1.28599 Å, HCl is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000090     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000090     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000139     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000197     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of HCl ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLHCLOPT.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;HCl&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: YSLHCLCAP.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:YSLHCLCAP.PNG&amp;diff=548865</id>
		<title>File:YSLHCLCAP.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:YSLHCLCAP.PNG&amp;diff=548865"/>
		<updated>2016-03-04T15:01:21Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548861</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548861"/>
		<updated>2016-03-04T15:01:02Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Calculation on another molecule ==&lt;br /&gt;
&lt;br /&gt;
=== HCl ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of HCl ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of HCl&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || HCl&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -460.80077875 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00005211 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-Cl =1.28599 Å, HCl is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000090     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000090     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000139     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000197     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of HCl ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLHCLOPT.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;HCl&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: YSLHCLCAP.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:YSLHCLOPT.LOG&amp;diff=548838</id>
		<title>File:YSLHCLOPT.LOG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:YSLHCLOPT.LOG&amp;diff=548838"/>
		<updated>2016-03-04T14:58:04Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: Ysl115 uploaded a new version of File:YSLHCLOPT.LOG&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548827</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548827"/>
		<updated>2016-03-04T14:55:53Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Calculation on another molecule ==&lt;br /&gt;
&lt;br /&gt;
=== HCl ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of HCl ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of HCl&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || HCl&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -460.80077875 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00005211 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-Cl =1.28599 Å, HCl is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000090     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000090     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000139     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000197     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of HCl ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLHCLOPT.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;HCl&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:YSLHCLOPT.LOG&amp;diff=548822</id>
		<title>File:YSLHCLOPT.LOG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:YSLHCLOPT.LOG&amp;diff=548822"/>
		<updated>2016-03-04T14:55:03Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548820</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548820"/>
		<updated>2016-03-04T14:54:28Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Calculation on another molecule ==&lt;br /&gt;
&lt;br /&gt;
=== HCl ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of HCl ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of HCl&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || HCl&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -460.80077875 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00005211 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-Cl =1.28599 Å, HCl is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000090     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000090     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000139     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000197     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of HCl ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;HCl&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548752</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548752"/>
		<updated>2016-03-04T14:42:52Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Calculation on another molecule ==&lt;br /&gt;
&lt;br /&gt;
=== HCl ===&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548727</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548727"/>
		<updated>2016-03-04T14:38:38Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Molecular orbitals of Cl2 */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548651</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548651"/>
		<updated>2016-03-04T14:24:44Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Bond length and bond angle of Cl2 */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174 Å, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO which will form a sig. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548646</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548646"/>
		<updated>2016-03-04T14:24:24Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Bond length and bond angle */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279 Å, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO which will form a sig. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548645</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548645"/>
		<updated>2016-03-04T14:23:58Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Bond length and bond angle */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550 Å, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO which will form a sig. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548633</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548633"/>
		<updated>2016-03-04T14:21:51Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Summary of Cl2 */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO which will form a sig. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548626</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548626"/>
		<updated>2016-03-04T14:21:07Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Summary of H2 */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || Dinfh&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO which will form a sig. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548601</id>
		<title>Rep:Mod:XYZ1379</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:XYZ1379&amp;diff=548601"/>
		<updated>2016-03-04T14:13:13Z</updated>

		<summary type="html">&lt;p&gt;Ysl115: /* Display Vibrations and atomic charges */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Project molecule ==&lt;br /&gt;
&lt;br /&gt;
=== NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -56.55776873 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000485 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || C&amp;lt;sub&amp;gt;3V&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N-H =1.01798 Å. Optimized H-N-H bond angle =105.741 degrees.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000004     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000004     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000072     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000035     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file of NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:yslNH3.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;NH3&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;yslNH3.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display Vibrations and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: Ysldvcapture.PNG]]&lt;br /&gt;
&lt;br /&gt;
6 modes are expected from 3N-6 rule.&lt;br /&gt;
&lt;br /&gt;
Mode 2&amp;amp;3 and mode 5&amp;amp;6 are degenerate .&lt;br /&gt;
&lt;br /&gt;
Mode 1&amp;amp;2&amp;amp;3 are &#039;bending&#039; vibrations, mode 4&amp;amp;5&amp;amp;6 are &#039;bond stretch&#039; vibrations.&lt;br /&gt;
Number 4 is the highly symmetric one because the point group doesn&#039;t change. &lt;br /&gt;
&lt;br /&gt;
Mode 1 has the umbrella mode.&lt;br /&gt;
&lt;br /&gt;
Two bands will be expected for ammonia in the spectrum. Because the infrared intensity of mode 4&amp;amp;5&amp;amp;6 are too small to be seen and mode 2&amp;amp;3 are degenerate therefore only two bands will be expected.&lt;br /&gt;
&lt;br /&gt;
The charge on hydrogen is expected to be positive and the charge of nitrogen is expected to be negative because nitrogen is more electronegative than hydrogen. The charge on hydrogen is 0.375 and that on nitrogen is -1.125.&lt;br /&gt;
&lt;br /&gt;
=== N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -109.52412868 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000060 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || D&amp;lt;sub&amp;gt;infh&amp;lt;/sub&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance N≡N =1.10550, N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
          Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000001     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000001     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000000     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimisation file of N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLN2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;N2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLN2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslN2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
=== H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -1.17853936 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00000017 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || Dinfh&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance H-H =0.74279, H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000000     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000000     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000000     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000001     0.001200     YES&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLH2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;H2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLH2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslh2capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no change in the electronegativity in H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero.&lt;br /&gt;
&lt;br /&gt;
== Reaction energy ==&lt;br /&gt;
&lt;br /&gt;
E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)= -56.55776873 au&lt;br /&gt;
&lt;br /&gt;
2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)=-113.11553746 au&lt;br /&gt;
&lt;br /&gt;
E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-109.52412868 au&lt;br /&gt;
&lt;br /&gt;
E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-1.17853936 au&lt;br /&gt;
&lt;br /&gt;
3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)=-3.53561808 au&lt;br /&gt;
&lt;br /&gt;
ΔE=2*E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)-[E(N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)+3*E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)]=-0.05579146 au =-146.480478 kJ/mol&lt;br /&gt;
&lt;br /&gt;
The ammonia product is more stable because energy is released during the process since the sign of the energy change is negative.&lt;br /&gt;
&lt;br /&gt;
== Molecule of own choice ==&lt;br /&gt;
&lt;br /&gt;
=== Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;  ===&lt;br /&gt;
&lt;br /&gt;
==== Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Summary of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Molecule || Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|Calculation Method || RB3LYP&lt;br /&gt;
|-&lt;br /&gt;
|Basic Set || 6-31G(d,p)&lt;br /&gt;
|-&lt;br /&gt;
|Final Energy E(RB3LYP) || -920.34987886 au&lt;br /&gt;
|-&lt;br /&gt;
|RMS Gradient || 0.00002511 au&lt;br /&gt;
|-&lt;br /&gt;
|Point Group || Dinfh&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==== Bond length and bond angle of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
Optimized bond distance Cl-Cl =2.04174, Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is linear.&lt;br /&gt;
&lt;br /&gt;
==== Final set of force and displacement ====&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
         Item               Value     Threshold  Converged?&lt;br /&gt;
 Maximum Force            0.000043     0.000450     YES&lt;br /&gt;
 RMS     Force            0.000043     0.000300     YES&lt;br /&gt;
 Maximum Displacement     0.000121     0.001800     YES&lt;br /&gt;
 RMS     Displacement     0.000172     0.001200     YES&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Optimization file ====&lt;br /&gt;
&lt;br /&gt;
The optimization file is linked to [[Media:YSLCL2OPTIMISATION.LOG| here]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt;&lt;br /&gt;
  &amp;lt;title&amp;gt;Cl2&amp;lt;/title&amp;gt;&lt;br /&gt;
  &amp;lt;color&amp;gt;black&amp;lt;/color&amp;gt;&lt;br /&gt;
  &amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
  &amp;lt;uploadedFileContents&amp;gt;YSLCL2OPTIMISATION.LOG&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==== Display vibration and atomic charges ====&lt;br /&gt;
&lt;br /&gt;
[[File: yslcl2Capture.PNG]]&lt;br /&gt;
&lt;br /&gt;
There is no difference in the electronegativity between Cl and Cl in Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, therefore the charge is excepted to be zero. Since Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; is a linear molecule, therefore 3N-5 mode i expected which means only one mode is expected. And there is no change in dipole moment which means no band will be expected in the spectrum.&lt;br /&gt;
&lt;br /&gt;
==== Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; ====&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Molecular orbitals of Cl&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl211capture.PNG|350px]] MO#11 || This molecular orbital is formed from two 3s atomic orbitals overlapping giving an occupied bonding MO. This MO will form a sigma bond since the orbitals are on the same line with bond axis. This MO is low in energy.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl213capture.PNG|350px]] MO#13 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an occupied bonding MO which will give rise to a sigma bond. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl214.PNG|350px]] MO#14 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed from this occupied bonding MO. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl216capture.PNG|350px]] MO#16 || This is an occupied anti-bonding molecular orbital formed from two 3p&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; atomic orbitals. A pi bond will be formed. This MO is in the HOMO/LUMO region.&lt;br /&gt;
|-&lt;br /&gt;
|[[File: yslcl218capture.PNG|350px]] MO#18 || This molecular orbital is formed from two 3p&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; atomic orbitals. This is an unoccupied anti-bonding MO which will form a sig. This is the LUMO since it is the unoccupied MO with the lowest energy.&lt;br /&gt;
|}&lt;/div&gt;</summary>
		<author><name>Ysl115</name></author>
	</entry>
</feed>