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	<id>https://chemwiki.ch.ic.ac.uk/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Lh106</id>
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	<updated>2026-05-16T21:11:38Z</updated>
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	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=36541</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=36541"/>
		<updated>2009-01-12T09:59:45Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Project: Diels Alder Reaction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Chair Conformation ==&lt;br /&gt;
The transition state was optimised using two different methods. The first was to use the HF method and 3-21G base set but to optimise to a Berny transition state. This took a few attempts to work as the two parts to the transition state had to be correctly orientated but a transition state was finally optimised. This gave a negative wavelength, as expected for a transition state, at -817.987cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; which is very close to the -818cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;  expected.&lt;br /&gt;
[[Image:IRfortransitionsstate.JPG]]&lt;br /&gt;
&lt;br /&gt;
The other method was to freeze the distance between the atoms that will bond during the reaction. This gave the same molecule as in the first method but the bonds were limited to 2.2A as was determined when setting the distance. This method was then used again to optimise the bonds that had previously been frozen at 2.2A. This optimisation gave bond lengths of 1.55A and 4.36A between the atoms that were expected to bond.&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Boat Conformation ==&lt;br /&gt;
The boat conformation was optimised using a different method- the QST2 method. The reactant and product were made in Gaussian and numbered accordingly. The two molecules were altered to give the boat form. This took a few attempts for the QST2 calculation to run because the geometry of the molecules had to be correct. This gave an imaginary frequency at -154.81cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimised Structures ==&lt;br /&gt;
Boat Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Qstusepic.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Chair Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtsusepic.mol‎&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
The IRC for these structures was run, with Gaussian calculating the force constants at every point so that the minimum geometry would be reached. The chair IRC gave a movement between the terminal carbons, this was a small movement. The boat IRC gave a greater movement, this gave a rotation between the two halves of the molecule- the two fragments that were originally created.&lt;br /&gt;
&lt;br /&gt;
== Activation Energies ==&lt;br /&gt;
&lt;br /&gt;
FreqChk was used to calculate the activation energy at 298.15K. For the chair conformation this eneryg was 83.288 KCal/mol and for the boat form:87.661 KCal/mol. It was predicted that the chair form should give a lower activation energy than the boat form, although the activation energies should be a lot lower, although this was taken at 0K and so will explain the difference.&lt;br /&gt;
&lt;br /&gt;
== Project: Diels Alder Reaction ==&lt;br /&gt;
&#039;&#039;&#039;Cis butadiene&#039;&#039;&#039;&lt;br /&gt;
Cis butadiene was created in Gaussian and optimised using the AM! semi-empirical method.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Ethylene+Cis Butadiene Transition Structure&#039;&#039;&#039;&lt;br /&gt;
[[Image:Dielsalderpic.JPG]]&lt;br /&gt;
The frozen coordinate method was used to analyse the transition structure of this reaction. This took many attempts as the molecule shapes and the calculation coding had to be exact to obtain a result. The HOMO and LUMO were visualised as follows&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;HOMO&#039;&#039;&#039;[[Image:Dielsalderhomo.JPG]]&lt;br /&gt;
&#039;&#039;&#039;LUMO&#039;&#039;&#039;[[Image:Dielsalderlumo.JPG]]&lt;br /&gt;
Here, the LUMO is symmetric and the HOMO antisymmetric. The bond lengths were found to be: for C-C: 152.356pm and for C=C: 132.412 pm These bond lengths are usually 154pm and 134pm&amp;lt;ref&amp;gt;http://books.google.co.uk/books?id=aOij0MVjsy0C&amp;amp;pg=PA124&amp;amp;dq=C-C+bond+length, Lets Review: Chemistry, the Physical Setting, Albert S Tarendash, 2001&amp;lt;/ref&amp;gt; respectively, so the bond lengths in this transition structure are a bit shorter than expected. The Van Der Waals radius of a carbon atom is 1.7A.&lt;br /&gt;
&lt;br /&gt;
The transition frequency was found at -89.0787. The bonding is not synchronous, as vibration is only occuring at one of the bond making ends of the cis-butadiene. If both bonds were to be made at the same time, the transition state would show two vibrations- one at each end of the cis-butadiene (as two bonds are made in the final product). The orbitals used in this reaction are the HOMO and the LUMO as shown below.&lt;br /&gt;
[[Image:Dielsalderorbitalpic.JPG]].&lt;br /&gt;
&lt;br /&gt;
The reaction between cyclohexa-1,3-diene and maleic anhydride proved more difficult to model in Gaussian. The frozen coordinate method and the transition state method (setting the calculation to calculate for a transition state) led to errors multiple times.&lt;br /&gt;
For the exo form, the calculation (using the frozen coordinate method) ran to completion once given the following molecular orbitals but I do not believe this is the true transition state.&amp;lt;ref&amp;gt;{{DOI|10042/to-1554}}&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
HOMO[[Image:HOMOmaleic.JPG]]&lt;br /&gt;
LUMO[[Image:LUMOmaleic.JPG]]&lt;br /&gt;
&lt;br /&gt;
This model did give a transition vibration frequency at -4.3 representing the two molecule s rocking from side to side. This is quite high for a transition state frequency. Also, the molecular orbitals suggest that the HOMO is carried solely by the cyclohexa-1,3-diene and the LUMO solely represents the maleic anhydride. If this was a transition state, then I would expect some interaction between the two. That is unless it is a very early transition state as that would give a molecules similar to the reactants.&lt;br /&gt;
&lt;br /&gt;
The endo form gave a more satisfactory result (after many attempts). This gave 4 transition frequencies, at -223.9, -143.4, -115.2 and -25.66. These represented the vibrations as follows:&lt;br /&gt;
-223&lt;br /&gt;
[[Image:-223.JPG]]&lt;br /&gt;
-143&lt;br /&gt;
[[Image:-143.JPG]]&lt;br /&gt;
-115&lt;br /&gt;
[[Image:-115.JPG]]&lt;br /&gt;
-25 was a rocking motion similar to that in the exo form.&lt;br /&gt;
&lt;br /&gt;
For the exo form, the energy was -0.18447 whereas the endo form had an energy of -0.17979 making it slightly lower in energy and therefore more stable. This follows with the idea that the exo form is more strained because of the maleic anhydride fragment being closer to the bridging carbons which could give an interaction. This is also supported by the secondary orbital overlap as this occurs most for the endo form.&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:-115.JPG&amp;diff=36539</id>
		<title>File:-115.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:-115.JPG&amp;diff=36539"/>
		<updated>2009-01-12T09:51:38Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:-143.JPG&amp;diff=36538</id>
		<title>File:-143.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:-143.JPG&amp;diff=36538"/>
		<updated>2009-01-12T09:51:04Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:-223.JPG&amp;diff=36537</id>
		<title>File:-223.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:-223.JPG&amp;diff=36537"/>
		<updated>2009-01-12T09:50:39Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:LUMOmaleic.JPG&amp;diff=36535</id>
		<title>File:LUMOmaleic.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:LUMOmaleic.JPG&amp;diff=36535"/>
		<updated>2009-01-12T09:29:33Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:HOMOmaleic.JPG&amp;diff=36534</id>
		<title>File:HOMOmaleic.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:HOMOmaleic.JPG&amp;diff=36534"/>
		<updated>2009-01-12T09:28:18Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalderorbitalpic.JPG&amp;diff=36533</id>
		<title>File:Dielsalderorbitalpic.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalderorbitalpic.JPG&amp;diff=36533"/>
		<updated>2009-01-12T09:21:32Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=36478</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=36478"/>
		<updated>2009-01-10T19:38:56Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Project: Diels Alder Reaction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Chair Conformation ==&lt;br /&gt;
The transition state was optimised using two different methods. The first was to use the HF method and 3-21G base set but to optimise to a Berny transition state. This took a few attempts to work as the two parts to the transition state had to be correctly orientated but a transition state was finally optimised. This gave a negative wavelength, as expected for a transition state, at -817.987cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; which is very close to the -818cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;  expected.&lt;br /&gt;
[[Image:IRfortransitionsstate.JPG]]&lt;br /&gt;
&lt;br /&gt;
The other method was to freeze the distance between the atoms that will bond during the reaction. This gave the same molecule as in the first method but the bonds were limited to 2.2A as was determined when setting the distance. This method was then used again to optimise the bonds that had previously been frozen at 2.2A. This optimisation gave bond lengths of 1.55A and 4.36A between the atoms that were expected to bond.&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Boat Conformation ==&lt;br /&gt;
The boat conformation was optimised using a different method- the QST2 method. The reactant and product were made in Gaussian and numbered accordingly. The two molecules were altered to give the boat form. This took a few attempts for the QST2 calculation to run because the geometry of the molecules had to be correct. This gave an imaginary frequency at -154.81cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimised Structures ==&lt;br /&gt;
Boat Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Qstusepic.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Chair Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtsusepic.mol‎&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
The IRC for these structures was run, with Gaussian calculating the force constants at every point so that the minimum geometry would be reached. The chair IRC gave a movement between the terminal carbons, this was a small movement. The boat IRC gave a greater movement, this gave a rotation between the two halves of the molecule- the two fragments that were originally created.&lt;br /&gt;
&lt;br /&gt;
== Activation Energies ==&lt;br /&gt;
&lt;br /&gt;
FreqChk was used to calculate the activation energy at 298.15K. For the chair conformation this eneryg was 83.288 KCal/mol and for the boat form:87.661 KCal/mol. It was predicted that the chair form should give a lower activation energy than the boat form, although the activation energies should be a lot lower, although this was taken at 0K and so will explain the difference.&lt;br /&gt;
&lt;br /&gt;
== Project: Diels Alder Reaction ==&lt;br /&gt;
&#039;&#039;&#039;Cis butadiene&#039;&#039;&#039;&lt;br /&gt;
Cis butadiene was created in Gaussian and optimised using the AM! semi-empirical method.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Ethylene+Cis Butadiene Transition Structure&#039;&#039;&#039;&lt;br /&gt;
[[Image:Dielsalderpic.JPG]]&lt;br /&gt;
The frozen coordinate method was used to analyse the transition structure of this reaction. This took many attempts as the molecule shapes and the calculation coding had to be exact to obtain a result. The HOMO and LUMO were visualised as follows&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;HOMO&#039;&#039;&#039;[[Image:Dielsalderhomo.JPG]]&lt;br /&gt;
&#039;&#039;&#039;LUMO&#039;&#039;&#039;[[Image:Dielsalderlumo.JPG]]&lt;br /&gt;
Here, the LUMO is symmetric and the HOMO antisymmetric. The bond lengths were found to be: for C-C: 152.356pm and for C=C: 132.412 pm These bond lengths are usually 154pm and 134pm&amp;lt;ref=http://books.google.co.uk/books?id=aOij0MVjsy0C&amp;amp;pg=PA124&amp;amp;dq=C-C+bond+length&amp;gt;Lets Review: Chemistry, the Physical Setting, Albert S Tarendash, 2001&amp;lt;/ref&amp;gt; respectively, so the bond lengths in this transition structure are a bit shorter than expected. The Van Der Waals radius of a carbon atom is 1.7A.&lt;br /&gt;
&lt;br /&gt;
The transition frequency was found at -89.0787. The bonding is not synchronous, as vibration is only occuring at one of the bond making ends of the cis-butadiene. If both bonds were to be made at the same time, the transition state would show two vibrations- one at each end of the cis-butadiene (as two bonds are made in the final product). The orbitals used in this reaction are the HOMO and the LUMO as shown below.&lt;br /&gt;
[[Image:Dielsalderorbitalpic.JPG]]&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalderpic.JPG&amp;diff=36467</id>
		<title>File:Dielsalderpic.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalderpic.JPG&amp;diff=36467"/>
		<updated>2009-01-10T16:56:36Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=36458</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=36458"/>
		<updated>2009-01-10T16:19:05Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Chair Conformation ==&lt;br /&gt;
The transition state was optimised using two different methods. The first was to use the HF method and 3-21G base set but to optimise to a Berny transition state. This took a few attempts to work as the two parts to the transition state had to be correctly orientated but a transition state was finally optimised. This gave a negative wavelength, as expected for a transition state, at -817.987cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; which is very close to the -818cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;  expected.&lt;br /&gt;
[[Image:IRfortransitionsstate.JPG]]&lt;br /&gt;
&lt;br /&gt;
The other method was to freeze the distance between the atoms that will bond during the reaction. This gave the same molecule as in the first method but the bonds were limited to 2.2A as was determined when setting the distance. This method was then used again to optimise the bonds that had previously been frozen at 2.2A. This optimisation gave bond lengths of 1.55A and 4.36A between the atoms that were expected to bond.&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Boat Conformation ==&lt;br /&gt;
The boat conformation was optimised using a different method- the QST2 method. The reactant and product were made in Gaussian and numbered accordingly. The two molecules were altered to give the boat form. This took a few attempts for the QST2 calculation to run because the geometry of the molecules had to be correct. This gave an imaginary frequency at -154.81cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimised Structures ==&lt;br /&gt;
Boat Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Qstusepic.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Chair Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtsusepic.mol‎&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
The IRC for these structures was run, with Gaussian calculating the force constants at every point so that the minimum geometry would be reached. The chair IRC gave a movement between the terminal carbons, this was a small movement. The boat IRC gave a greater movement, this gave a rotation between the two halves of the molecule- the two fragments that were originally created.&lt;br /&gt;
&lt;br /&gt;
== Activation Energies ==&lt;br /&gt;
&lt;br /&gt;
FreqChk was used to calculate the activation energy at 298.15K. For the chair conformation this eneryg was 83.288 KCal/mol and for the boat form:87.661 KCal/mol. It was predicted that the chair form should give a lower activation energy than the boat form, although the activation energies should be a lot lower, although this was taken at 0K and so will explain the difference.&lt;br /&gt;
&lt;br /&gt;
== Project: Diels Alder Reaction ==&lt;br /&gt;
&#039;&#039;&#039;Cis butadiene&#039;&#039;&#039;&lt;br /&gt;
Cis butadiene was created in Gaussian and optimised using the AM! semi-empirical method.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Ethylene+Cis Butadiene Transition Structure&#039;&#039;&#039;&lt;br /&gt;
The frozen coordinate method was used to analyse the transition structure of this reaction. This took many attempts as the molecule shapes and the calculation coding had to be exact to obtain a result. The HOMO and LUMO were visualised as follows&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;HOMO&#039;&#039;&#039;[[Image:Dielsalderhomo.JPG]]&lt;br /&gt;
&#039;&#039;&#039;LUMO&#039;&#039;&#039;[[Image:Dielsalderlumo.JPG]]&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalderlumo.JPG&amp;diff=36457</id>
		<title>File:Dielsalderlumo.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalderlumo.JPG&amp;diff=36457"/>
		<updated>2009-01-10T16:18:28Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalderhomo.JPG&amp;diff=36456</id>
		<title>File:Dielsalderhomo.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalderhomo.JPG&amp;diff=36456"/>
		<updated>2009-01-10T16:15:14Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35707</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35707"/>
		<updated>2008-12-19T15:58:12Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Activation Energies */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Chair Conformation ==&lt;br /&gt;
The transition state was optimised using two different methods. The first was to use the HF method and 3-21G base set but to optimise to a Berny transition state. This took a few attempts to work as the two parts to the transition state had to be correctly orientated but a transition state was finally optimised. This gave a negative wavelength, as expected for a transition state, at -817.987cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; which is very close to the -818cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;  expected.&lt;br /&gt;
[[Image:IRfortransitionsstate.JPG]]&lt;br /&gt;
&lt;br /&gt;
The other method was to freeze the distance between the atoms that will bond during the reaction. This gave the same molecule as in the first method but the bonds were limited to 2.2A as was determined when setting the distance. This method was then used again to optimise the bonds that had previously been frozen at 2.2A. This optimisation gave bond lengths of 1.55A and 4.36A between the atoms that were expected to bond.&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Boat Conformation ==&lt;br /&gt;
The boat conformation was optimised using a different method- the QST2 method. The reactant and product were made in Gaussian and numbered accordingly. The two molecules were altered to give the boat form. This took a few attempts for the QST2 calculation to run because the geometry of the molecules had to be correct. This gave an imaginary frequency at -154.81cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimised Structures ==&lt;br /&gt;
Boat Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Qstusepic.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Chair Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtsusepic.mol‎&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
The IRC for these structures was run, with Gaussian calculating the force constants at every point so that the minimum geometry would be reached. The chair IRC gave a movement between the terminal carbons, this was a small movement. The boat IRC gave a greater movement, this gave a rotation between the two halves of the molecule- the two fragments that were originally created.&lt;br /&gt;
&lt;br /&gt;
== Activation Energies ==&lt;br /&gt;
&lt;br /&gt;
FreqChk was used to calculate the activation energy at 298.15K. For the chair conformation this eneryg was 83.288 KCal/mol and for the boat form:87.661 KCal/mol. It was predicted that the chair form should give a lower activation energy than the boat form, although the activation energies should be a lot lower, although this was taken at 0K and so will explain the difference.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Diels Alder ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Dielsalder2.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Dielsalder1.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalder1.mol&amp;diff=35706</id>
		<title>File:Dielsalder1.mol</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalder1.mol&amp;diff=35706"/>
		<updated>2008-12-19T15:57:21Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalder2.mol&amp;diff=35705</id>
		<title>File:Dielsalder2.mol</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Dielsalder2.mol&amp;diff=35705"/>
		<updated>2008-12-19T15:56:45Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35365</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35365"/>
		<updated>2008-12-18T15:33:12Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Optimised Structures */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Chair Conformation ==&lt;br /&gt;
The transition state was optimised using two different methods. The first was to use the HF method and 3-21G base set but to optimise to a Berny transition state. This took a few attempts to work as the two parts to the transition state had to be correctly orientated but a transition state was finally optimised. This gave a negative wavelength, as expected for a transition state, at -817.987cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; which is very close to the -818cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;  expected.&lt;br /&gt;
[[Image:IRfortransitionsstate.JPG]]&lt;br /&gt;
&lt;br /&gt;
The other method was to freeze the distance between the atoms that will bond during the reaction. This gave the same molecule as in the first method but the bonds were limited to 2.2A as was determined when setting the distance. This method was then used again to optimise the bonds that had previously been frozen at 2.2A. This optimisation gave bond lengths of 1.55A and 4.36A between the atoms that were expected to bond.&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Boat Conformation ==&lt;br /&gt;
The boat conformation was optimised using a different method- the QST2 method. The reactant and product were made in Gaussian and numbered accordingly. The two molecules were altered to give the boat form. This took a few attempts for the QST2 calculation to run because the geometry of the molecules had to be correct. This gave an imaginary frequency at -154.81cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimised Structures ==&lt;br /&gt;
Boat Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Qstusepic.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Chair Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtsusepic.mol‎&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
The IRC for these structures was run, with Gaussian calculating the force constants at every point so that the minimum geometry would be reached. The chair IRC gave a movement between the terminal carbons, this was a small movement. The boat IRC gave a greater movement, this gave a rotation between the two halves of the molecule- the two fragments that were originally created.&lt;br /&gt;
&lt;br /&gt;
== Activation Energies ==&lt;br /&gt;
&lt;br /&gt;
FreqChk was used to calculate the activation energy at 298.15K. For the chair conformation this eneryg was 83.288 KCal/mol and for the boat form:87.661 KCal/mol. It was predicted that the chair form should give a lower activation energy than the boat form, although the activation energies should be a lot lower, although this was taken at 0K and so will explain the difference.&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35352</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35352"/>
		<updated>2008-12-18T15:15:12Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens as shown by the pink arrows below.&lt;br /&gt;
[[Image:Stag_eclipcompare.gif]]&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base. The N→B bond is quite low in energy- 17.58Kcalmol&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&amp;lt;ref&amp;gt;http://www.springerlink.com/content/h16940520664k3g9/fulltext.pdf G Leroy, M Sana and C Wilante, Theoretica Chimica Acta, 1993, 85, 155 &amp;lt;/ref&amp;gt;  but the molecule is still more stable than ethane, which has a bond energy of 80kcal&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
&lt;br /&gt;
This gives an energy of 1.911007 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt; au for the staggered form and 1.912835 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt; au for the eclipsed isomer.&lt;br /&gt;
&lt;br /&gt;
This would suggest that the reaction to create NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; is not favoured as it gives a positive energy. But this was a very small energy and so should still afford product. This also supports the ease of obtaining hydrogen from the molecule as the NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; would prefer to release its hydrogen.&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 Debye and 5.9916 Debye calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&amp;lt;br&amp;gt;[[Image:Bh3nh3net.JPG]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35349</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35349"/>
		<updated>2008-12-18T15:12:08Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Optimising To a Transition State- Boat Conformation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Chair Conformation ==&lt;br /&gt;
The transition state was optimised using two different methods. The first was to use the HF method and 3-21G base set but to optimise to a Berny transition state. This took a few attempts to work as the two parts to the transition state had to be correctly orientated but a transition state was finally optimised. This gave a negative wavelength, as expected for a transition state, at -817.987cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; which is very close to the -818cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;  expected.&lt;br /&gt;
[[Image:IRfortransitionsstate.JPG]]&lt;br /&gt;
&lt;br /&gt;
The other method was to freeze the distance between the atoms that will bond during the reaction. This gave the same molecule as in the first method but the bonds were limited to 2.2A as was determined when setting the distance. This method was then used again to optimise the bonds that had previously been frozen at 2.2A. This optimisation gave bond lengths of 1.55A and 4.36A between the atoms that were expected to bond.&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Boat Conformation ==&lt;br /&gt;
The boat conformation was optimised using a different method- the QST2 method. The reactant and product were made in Gaussian and numbered accordingly. The two molecules were altered to give the boat form. This took a few attempts for the QST2 calculation to run because the geometry of the molecules had to be correct. This gave an imaginary frequency at -154.81cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimised Structures ==&lt;br /&gt;
Boat Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Qstusepic.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Chair Structure&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtsusepic.mol‎&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Chairtsusepic.mol&amp;diff=35348</id>
		<title>File:Chairtsusepic.mol</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Chairtsusepic.mol&amp;diff=35348"/>
		<updated>2008-12-18T15:11:41Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Qstusepic.mol&amp;diff=35346</id>
		<title>File:Qstusepic.mol</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Qstusepic.mol&amp;diff=35346"/>
		<updated>2008-12-18T15:10:06Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35344</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35344"/>
		<updated>2008-12-18T15:06:35Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Optimising To a Transition State- Boat Conformation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Chair Conformation ==&lt;br /&gt;
The transition state was optimised using two different methods. The first was to use the HF method and 3-21G base set but to optimise to a Berny transition state. This took a few attempts to work as the two parts to the transition state had to be correctly orientated but a transition state was finally optimised. This gave a negative wavelength, as expected for a transition state, at -817.987cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; which is very close to the -818cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;  expected.&lt;br /&gt;
[[Image:IRfortransitionsstate.JPG]]&lt;br /&gt;
&lt;br /&gt;
The other method was to freeze the distance between the atoms that will bond during the reaction. This gave the same molecule as in the first method but the bonds were limited to 2.2A as was determined when setting the distance. This method was then used again to optimise the bonds that had previously been frozen at 2.2A. This optimisation gave bond lengths of 1.55A and 4.36A between the atoms that were expected to bond.&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Boat Conformation ==&lt;br /&gt;
The boat conformation was optimised using a different method- the QST2 method. The reactant and product were made in Gaussian and numbered accordingly. The two molecules were altered to give the boat form. This took a few attempts for the QST2 calculation to run because the geometry of the molecules had to be correct. This gave an imaginary frequency at -154.81cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35342</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35342"/>
		<updated>2008-12-18T15:01:17Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Optimising To a Transition State */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Chair Conformation ==&lt;br /&gt;
The transition state was optimised using two different methods. The first was to use the HF method and 3-21G base set but to optimise to a Berny transition state. This took a few attempts to work as the two parts to the transition state had to be correctly orientated but a transition state was finally optimised. This gave a negative wavelength, as expected for a transition state, at -817.987cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; which is very close to the -818cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;  expected.&lt;br /&gt;
[[Image:IRfortransitionsstate.JPG]]&lt;br /&gt;
&lt;br /&gt;
The other method was to freeze the distance between the atoms that will bond during the reaction. This gave the same molecule as in the first method but the bonds were limited to 2.2A as was determined when setting the distance. This method was then used again to optimise the bonds that had previously been frozen at 2.2A. This optimisation gave bond lengths of 1.55A and 4.36A between the atoms that were expected to bond.&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State- Boat Conformation ==&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35327</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35327"/>
		<updated>2008-12-18T14:46:57Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Optimising To a Transition State */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State ==&lt;br /&gt;
The transition state was optimised using two different methods. The first was to use the HF method and 3-21G base set but to optimise to a Berny transition state. This took a few attempts to work as the two parts to the transition state had to be correctly orientated but a transition state was finally optimised. This gave a negative wavelength, as expected for a transition state, at -817.987cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; which is very close to the -818cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;  expected.&lt;br /&gt;
[[Image:IRfortransitionsstate.JPG]]&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:IRfortransitionsstate.JPG&amp;diff=35325</id>
		<title>File:IRfortransitionsstate.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:IRfortransitionsstate.JPG&amp;diff=35325"/>
		<updated>2008-12-18T14:46:47Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35313</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35313"/>
		<updated>2008-12-18T14:37:38Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Optimisation of Chair and Boat Forms */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State ==&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;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35312</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35312"/>
		<updated>2008-12-18T14:37:12Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Optimisation of Chair and Boat Forms */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&amp;lt;br&amp;gt;&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments. This transition state was then optimised using two different methods&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State ==&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;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35311</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35311"/>
		<updated>2008-12-18T14:36:44Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Optimisation of Chair and Boat Forms */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;br /&gt;
The Cope rearrangement reaction was investigate to find whether it proceeds via a cis or boat transition state.&lt;br /&gt;
[[Image:Coperearrangement.gif]]&lt;br /&gt;
The &amp;quot;guessed&amp;quot; transition state was created using two allyl fragments. This transition state was then optimised using two different methods:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimising To a Transition State ==&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;Transition state&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chairtransitionpic.mol&lt;br /&gt;
&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Chairtransitionpic.mol&amp;diff=35310</id>
		<title>File:Chairtransitionpic.mol</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Chairtransitionpic.mol&amp;diff=35310"/>
		<updated>2008-12-18T14:35:52Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Coperearrangement.gif&amp;diff=35309</id>
		<title>File:Coperearrangement.gif</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Coperearrangement.gif&amp;diff=35309"/>
		<updated>2008-12-18T14:26:42Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35307</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35307"/>
		<updated>2008-12-18T14:22:45Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Module 3- The Transition State */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As can be seen in the model, the geometry has changed between the theory sets, the Ci structure is a stretched out anti form whereas the molecule after B3LYP/6-31G treatment looks more like a ring.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Optimisation of Chair and Boat Forms ==&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35298</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35298"/>
		<updated>2008-12-18T14:07:47Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Module 3- The Transition State */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35297</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35297"/>
		<updated>2008-12-18T14:07:24Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Module 3- The Transition State */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&lt;br /&gt;
&amp;lt;jmol&amp;gt;&amp;lt;jmolApplet&amp;gt; &lt;br /&gt;
&amp;lt;title&amp;gt;Ci Conformer&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Ciuse.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &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;Chair 631-G&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Ciuse.mol&amp;diff=35296</id>
		<title>File:Ciuse.mol</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Ciuse.mol&amp;diff=35296"/>
		<updated>2008-12-18T14:07:17Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35295</id>
		<title>Rep:Mod:lh106module3</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module3&amp;diff=35295"/>
		<updated>2008-12-18T14:00:34Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Module 3- The Transition State */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Module 3- The Transition State ==&lt;br /&gt;
Different configurations of 1,5-hexadiene were optimised to find which would be the most stable for the Cope Rearrangement.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Anti&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69153035&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C2&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same geometry/symmetry and roughly same energy as anti 1.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;Gauche&#039;&#039;&#039;&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Energy, au&lt;br /&gt;
| -231.69266122&lt;br /&gt;
|-&lt;br /&gt;
| Point group, Debye&lt;br /&gt;
| C1&lt;br /&gt;
|-&lt;br /&gt;
| colspan=&amp;quot;2&amp;quot; | Same energy as Gauche 3 but the point group and geometry of Gauche 4&lt;br /&gt;
|}&lt;br /&gt;
The lowest energy conformer should be the conformer with the least strain. The Gauche form had a lower energy than the anti form and so I predict the lowest energy conformer will be a Gauche type conformer.The lowest conformation should be that where the the double bonds (of higher electron density) were furthest away from each other.&lt;br /&gt;
&lt;br /&gt;
The C&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt; anti 2 conformation was created and optimised using HF method with 3-21G basis set. The Ci conformation gave a total energy of -231.692535 au which is in between the values obtained for the Anti and Gauche forms.&lt;br /&gt;
The Ci structure was then optimised with the B3LYP method and  6-31G base set- a higher level of theory. This gave a slightly different looking molecule. &lt;br /&gt;
&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;BCl&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;&amp;lt;/title&amp;gt;&amp;lt;color&amp;gt;white&amp;lt;/color&amp;gt;&lt;br /&gt;
&amp;lt;size&amp;gt;200&amp;lt;/size&amp;gt;&lt;br /&gt;
&amp;lt;script&amp;gt;zoom 80; cpk -25;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&amp;lt;/script&amp;gt;&lt;br /&gt;
&amp;lt;uploadedFileContents&amp;gt;Chair631g.mol&amp;lt;/uploadedFileContents&amp;gt;&lt;br /&gt;
&amp;lt;/jmolApplet&amp;gt;&amp;lt;/jmol&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Chair631g.mol&amp;diff=35294</id>
		<title>File:Chair631g.mol</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Chair631g.mol&amp;diff=35294"/>
		<updated>2008-12-18T13:59:35Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35105</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35105"/>
		<updated>2008-12-17T22:51:26Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Melting Point */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens as shown by the pink arrows below.&lt;br /&gt;
[[Image:Stag_eclipcompare.gif]]&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base. The N→B bond is quite low in energy- 17.58Kcalmol&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&amp;lt;ref&amp;gt;http://www.springerlink.com/content/h16940520664k3g9/fulltext.pdf G Leroy, M Sana and C Wilante, Theoretica Chimica Acta, 1993, 85, 155 &amp;lt;/ref&amp;gt;  but the molecule is still more stable than ethane, which has a bond energy of 80kcal&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
&lt;br /&gt;
This gives an energy of 1.911007 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt; au for the staggered form and 1.912835 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt; au for the eclipsed isomer.&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 Debye and 5.9916 Debye calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&amp;lt;br&amp;gt;[[Image:Bh3nh3net.JPG]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35104</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35104"/>
		<updated>2008-12-17T22:50:22Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens as shown by the pink arrows below.&lt;br /&gt;
[[Image:Stag_eclipcompare.gif]]&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base. The N→B bond is quite low in energy- 17.58Kcalmol&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&amp;lt;ref&amp;gt;http://www.springerlink.com/content/h16940520664k3g9/fulltext.pdf G Leroy, M Sana and C Wilante, Theoretica Chimica Acta, 1993, 85, 155 &amp;lt;/ref&amp;gt;  but the molecule is still more stable than ethane, which has a bond energy of 80kcal&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
&lt;br /&gt;
This gives an energy of 1.911007 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt; au for the staggered form and 1.912835 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt; au for the eclipsed isomer.&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 Debye and 5.9916 Debye calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&amp;lt;br&amp;gt;[[Image:Bh3nh3net.JPG]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35103</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35103"/>
		<updated>2008-12-17T22:49:55Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens as shown by the pink arrows below.&lt;br /&gt;
[[Image:Stag_eclipcompare.gif]]&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base. The N→B bond is quite low in energy- 17.58Kcalmol&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&amp;lt;ref&amp;gt;http://www.springerlink.com/content/h16940520664k3g9/fulltext.pdf G Leroy, M Sana and C Wilante, Theoretica Chimica Acta, 1993, 85, 155 &amp;lt;/ref&amp;gt;  but the molecule is still more stable than ethane, which has a bond energy of 80kcal&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of 1.911007 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
 au for the staggered form and 1.912835 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt; au for the eclipsed isomer.&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 Debye and 5.9916 Debye calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&amp;lt;br&amp;gt;[[Image:Bh3nh3net.JPG]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35102</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35102"/>
		<updated>2008-12-17T22:49:32Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens as shown by the pink arrows below.&lt;br /&gt;
[[Image:Stag_eclipcompare.gif]]&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base. The N→B bond is quite low in energy- 17.58Kcalmol&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&amp;lt;ref&amp;gt;http://www.springerlink.com/content/h16940520664k3g9/fulltext.pdf G Leroy, M Sana and C Wilante, Theoretica Chimica Acta, 1993, 85, 155 &amp;lt;/ref&amp;gt;  but the molecule is still more stable than ethane, which has a bond energy of 80kcal&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of 1.911007 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup)&lt;br /&gt;
 au for the staggered form and 1.912835 x 10&amp;lt;sup&amp;gt;-3&amp;lt;/sup)au for the eclipsed isomer.&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 Debye and 5.9916 Debye calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&amp;lt;br&amp;gt;[[Image:Bh3nh3net.JPG]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35101</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35101"/>
		<updated>2008-12-17T22:46:21Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Comparison With Ethane */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens as shown by the pink arrows below.&lt;br /&gt;
[[Image:Stag_eclipcompare.gif]]&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base. The N→B bond is quite low in energy- 17.58Kcalmol&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&amp;lt;ref&amp;gt;http://www.springerlink.com/content/h16940520664k3g9/fulltext.pdf G Leroy, M Sana and C Wilante, Theoretica Chimica Acta, 1993, 85, 155 &amp;lt;/ref&amp;gt;  but the molecule is still more stable than ethane, which has a bond energy of 80kcal&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of +3.842 au for the staggered form and +3.846663 au for the eclipsed isomer. Gibbs free energy can be used to determine whether a reaction occurs .&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 Debye and 5.9916 Debye calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&amp;lt;br&amp;gt;[[Image:Bh3nh3net.JPG]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35098</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35098"/>
		<updated>2008-12-17T22:21:34Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Structure and Stability */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens as shown by the pink arrows below.&lt;br /&gt;
[[Image:Stag_eclipcompare.gif]]&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of +3.842 au for the staggered form and +3.846663 au for the eclipsed isomer. Gibbs free energy can be used to determine whether a reaction occurs .&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 Debye and 5.9916 Debye calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&amp;lt;br&amp;gt;[[Image:Bh3nh3net.JPG]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Stag_eclipcompare.gif&amp;diff=35097</id>
		<title>File:Stag eclipcompare.gif</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Stag_eclipcompare.gif&amp;diff=35097"/>
		<updated>2008-12-17T22:20:53Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35096</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35096"/>
		<updated>2008-12-17T22:20:44Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Melting Point */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of +3.842 au for the staggered form and +3.846663 au for the eclipsed isomer. Gibbs free energy can be used to determine whether a reaction occurs .&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 Debye and 5.9916 Debye calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&amp;lt;br&amp;gt;[[Image:Bh3nh3net.JPG]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35095</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35095"/>
		<updated>2008-12-17T22:19:47Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Melting Point */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of +3.842 au for the staggered form and +3.846663 au for the eclipsed isomer. Gibbs free energy can be used to determine whether a reaction occurs .&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 and 5.9916 calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:[[Image:Bh3nh3net.JPG]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35094</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35094"/>
		<updated>2008-12-17T22:19:27Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Structure and Stability */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small. The staggered formation is lower in energy because of bond-electron repulsions between the hydrogens&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of +3.842 au for the staggered form and +3.846663 au for the eclipsed isomer. Gibbs free energy can be used to determine whether a reaction occurs .&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 and 5.9916 calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Bh3nh3net.JPG&amp;diff=35093</id>
		<title>File:Bh3nh3net.JPG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Bh3nh3net.JPG&amp;diff=35093"/>
		<updated>2008-12-17T22:18:31Z</updated>

		<summary type="html">&lt;p&gt;Lh106: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35092</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35092"/>
		<updated>2008-12-17T21:57:11Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Mini Project- Fuels of The Future */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure and Stability ==&lt;br /&gt;
&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small.&lt;br /&gt;
&lt;br /&gt;
== Comparison With Ethane ==&lt;br /&gt;
&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
Ammonia Borane also bonds differently to ethane. Ethane, having two carbon bonds bonding can covalently bond whereas ammonia borane, having an abnormal valence at the borane has dative bonding with the nitrogen acting as a lewis base.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Reaction To Make NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; and To Afford Hydrogen ==&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of +3.842 au for the staggered form and +3.846663 au for the eclipsed isomer. Gibbs free energy can be used to determine whether a reaction occurs .&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Melting Point ==&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 and 5.9916 calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35086</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35086"/>
		<updated>2008-12-17T21:15:23Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Mini Project- Fuels of The Future */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;Structure and Stability&#039;&#039;&#039;&amp;lt;br&amp;gt;&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small.&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of +3.842 au for the staggered form and +3.846663 au for the eclipsed isomer. Gibbs free energy can be used to determine whether a reaction occurs .&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 and 5.9916 calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Another way to determine why ammonia-borane has a much higher melting point would be to use the CRYSTAL program in DLVisualise as this would be able to calculate the ground state energy&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35085</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35085"/>
		<updated>2008-12-17T21:09:35Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Mini Project- Fuels of The Future */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;Structure and Stability&#039;&#039;&#039;&amp;lt;br&amp;gt;&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small.&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of +3.842 au for the staggered form and +3.846663 au for the eclipsed isomer. Gibbs free energy can be used to determine whether a reaction occurs .&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 and 5.9916 calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&amp;lt;/ref&amp;gt;&lt;br /&gt;
It has been reported that the solid structure of ammonia-borane takes the form shown below:&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35026</id>
		<title>Rep:Mod:lh106module2project</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:lh106module2project&amp;diff=35026"/>
		<updated>2008-12-17T15:54:31Z</updated>

		<summary type="html">&lt;p&gt;Lh106: /* Mini Project- Fuels of The Future */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Mini Project- Fuels of The Future ==&lt;br /&gt;
Hydrogen is being projected as a the new fuel for the future because, unlike fossil fuels, its only product is water. Hydrogen can be used to release energy when it reacts with oxygen. Of course at room temperature hydrogen is a gas and so is difficult to store as it takes up a lot of room. One way to do this would be to increase the pressure of the hydrogen as the amount of space taken up by hydgogen gas would be lowered:&amp;lt;math&amp;gt;V=nrT/P&amp;lt;/math&amp;gt;. Another way would be to change the phase the hydrogen is stored in, that is to store the hydrogen as a liquid or a solid. Obviously as a liquid is going to be easier but would still require too cold a temperature for realistic use of liquid hydrogen (boiling point=-238.4°&amp;lt;ref&amp;gt;http://www.jstor.org/sici?sici=0370-1662(1901)68%3C44%3ATBPOLH%3E2.0.CO%3B2-E&amp;amp;cookieSet=1 The Boiling Point of Liquid Hydrogen, Determined by Hydrogen and Helium Gas Thermometers, James Dewar, Proceedings of the Royal Society of London, Vol. 68, 1901,pg 44&amp;lt;/ref&amp;gt;. There is a way to carry the hydrogen via the use of a solid, even though the hydrogen itself is not solid. That would be to store a substance with a high hydrogen content that would be easy to get to.&lt;br /&gt;
&lt;br /&gt;
One molecule that is being explored for this purpose is NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; because of the large number of hydrogens it contains.&amp;lt;ref&amp;gt;http://www.rsc.org/Publishing/ChemScience/Volume/2008/08/Borane_fuels.asp Borane leadss the way to alternative fuels, Chemical Science&amp;lt;/ref&amp;gt;. It is also meant to be stable at room temperature, and so could be easily stored. Computational methods will be used to explore how stable the molecule is.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;Structure and Stability&#039;&#039;&#039;&amp;lt;br&amp;gt;&lt;br /&gt;
Ammonia Borane could exist as either an eclipsed or staggered form because of rotation around the nitrogen-borane bond- in the same fashion as the isoelectric ethane. The energies of these two forms were compared to find which geometry is taken.I expect the staggered form to be lower in energy as there is less strain between hydrogens as they are further away.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
| Symmetry&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -83.18805550&lt;br /&gt;
| 5.8939&lt;br /&gt;
| C3V&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -83.18425903&lt;br /&gt;
| 5.9916&lt;br /&gt;
| C3V&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The staggered formation does have a lower energy, but the difference between the two is very small.&lt;br /&gt;
As previously mentioned, ammonia borane is isoelectric with ethane and so I woudl expect the two to have similar properties, and similar energies. The energy of staggered and eclipsed ethane was calculated, again using the Gaussian program with a DFT B3LYP method and 3-21G base set to give quite a rough result as it is only being used as a comparison.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| Form&lt;br /&gt;
| Energy, au&lt;br /&gt;
| Dipole Moment, Debye&lt;br /&gt;
|-&lt;br /&gt;
| Staggered&lt;br /&gt;
| -79.80931774 au&lt;br /&gt;
| 0&lt;br /&gt;
|-&lt;br /&gt;
| Eclipsed&lt;br /&gt;
| -79.80451884&lt;br /&gt;
| 0.0001&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; molecules are slightly more stable than the ethane, this suggests that the bonding between nitrogen and borane is stronger than in the organic analogue.&lt;br /&gt;
&lt;br /&gt;
The stability of the different components of the reaction was calculated using Gaussian. This were then compared to see whether the reaction would take place.&lt;br /&gt;
&lt;br /&gt;
{| cellspacing=&amp;quot;0&amp;quot; cellpadding=&amp;quot;0&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
| NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl&lt;br /&gt;
| -517.32723694&lt;br /&gt;
|-&lt;br /&gt;
| NaCl&lt;br /&gt;
| -622.55076536&lt;br /&gt;
|-&lt;br /&gt;
| H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -1.17548239&lt;br /&gt;
|-&lt;br /&gt;
| NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;&lt;br /&gt;
| -190.05019313&lt;br /&gt;
|}&lt;br /&gt;
The overall energy of the reaction can be calculated by taking away the energy of the products from the energy of the reactants, in this case E&amp;lt;sub&amp;gt;total&amp;lt;/sub&amp;gt;=(E(NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;BH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;)+E(NaCl)+E(H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;))-(E(NH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;Cl)+E(NaBH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;))&lt;br /&gt;
This gives an energy of +3.842 au for the staggered form and +3.846663 au for the eclipsed isomer. Gibbs free energy can be used to determine whether a reaction occurs .&lt;br /&gt;
&lt;br /&gt;
Although isoelectric to ethane, ammonia-borane has a much higher melting point. It has been thought that this is done to the polar nature of ammonia-borane, this is supported by the high dipole of 5.8939 and 5.9916 calculated for the staggered and eclipsed ammonia-borane respectively. Ammonia-borane also has a great capacity for hydrogen bonding both between the borane and ammonia ends of the molecule &amp;lt;ref&amp;gt;http://www.rsc.org/ej/CP/2007/b617781f.pdf Ashley C. Stowe, Wendy J. Shaw,* John C. Linehan, Benjamin Schmid and&lt;br /&gt;
Tom Autrey, Physical Chemistry Chemical Physics, 2007, 9, 1831&lt;/div&gt;</summary>
		<author><name>Lh106</name></author>
	</entry>
</feed>