View source for Rep:Kh1015TSEx3RD

==Exercise 3 Results and Discussion.==

'''Note to Reader/Marker:'''
<br>The compartmentalization of the Results and Discussion into 5 parts was based on relevant discussion idea and for convenient navigation during the write-up. Also, the Jmol files in this page could display the relative energies of the MOs but they could not visualize the MOs. In response, the visualized HOMO of each TS was attached next to the Jmol files for viewing purposes.

===Part 1: Parameters from Reaction Profile.===
Figure 4.3 under Methodology section shows the reaction scheme for Exercise 3.

Referring to Table 5.3.2, calculations at PM6 level showed that only the Diels-Alder minor-regio-isomers were non-spontaneous. The Diels-Alder endo-major-regioisomer (referred to as endo product in Table 5.3.1) was calculated to be the kinetic product (based on lowest activation Gibbs-Free Energy equalled to 83.2 kJ mol<sup>-1</sup>) and an associated rate of reaction of 0.0165 s<sup>-1</sup> at 298.15K. The rate constant was calculated using the formula described under Introduction > Part D. The cheletropic product was calculated to be the thermodynamically favourable product (based on the most negative Δ Gibbs-Free Energy equalled to -155 kJ mol<sup>-1</sup>). This prediction could be verified experimentally by doing a kinetic study and analysis of ratio of Diels-Alder (including the regioisomers) and cheletropic products formed at rtp.

{|  class="wikitable" border="0" style='text-align: center style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5.3.1: Summary of Calculated Gibbs-Free Energy of Species in Diels-Alder and Cheletropic Reactions at 298.15 K and 1 atm (PM6 level).
|-
|rowspan="2"|''' '''
|colspan="12"|'''States'''
|-
|'''5,6-dimethylenecyclohexa-1,3-diene'''
|'''Sulfur Dioxide'''
|'''Endo TS'''
|'''Endo Product'''
|'''Exo TS'''
|'''Exo Product'''
|'''TS of Endo-Minor-Regioisomer'''
|'''Endo-Minor-Regioisomer'''
|'''TS of Exo-Minor-Regioisomer'''
|'''Exo-Minor-Regioisomer'''
|'''Cheletropic TS'''
|'''Cheletropic Product'''
|-
|'''Gibbs-Free Energy (kJ mol<sup>-1</sup>)'''
|468
| -313
|238
|57.0
|242
|56.3
|268
|172
|276
|177
|260
| -0.00263
|}

{|  class="wikitable" border="0" style='text-align: center style="margin-left: auto; margin-right: auto; border: none;"
|+ Table 5.3.2: Summary of Calculated Reaction Profile Parameters for Diels-Alder and Cheletropic Reactions at 298.15 K and 1 atm (PM6 level).
|-
|''' '''
|'''Endo-Major-Regioisomer'''
|'''Exo-Major-Regioisomer'''
|'''Endo-Minor-Regioisomer'''
|'''Exo-Minor-Regioisomer'''
|'''Cheletropic'''
|-
|'''Activation Gibbs-Free Energy (kJ mol<sup>-1</sup>)'''
|83.2
|87.2
|113
|121
|106
|-
|'''Δ Gibbs-Free Energy (kJ mol<sup>-1</sup>)'''
| -97.6
| -98.2
|17.7
|22.2
| -155
|-
|'''Predicted Rate of Reaction (x10<sup>-6</sup> s<sup>-1</sup>)'''
|16,500
|3,280
|0.010
|0.004
|1.67
|}

(Nice to see someone investigating the rates of reaction. There are a few more considerations - including which approximations you are using - when attempting to calculate rates. One of them is the shape of the PES, such as the "wideness" of the barrier. However, the thing that happens to break this the most is there is another barrier: the conversion of the endo and exo products, which is lower than all the other barriers! This means that, under kinetic conditions, the endo isn't the major product [[User:Tam10|Tam10]] ([[User talk:Tam10|talk]]) 12:59, 16 March 2018 (UTC))

===Part 2: Comparison of Reaction Profiles on a Standardized Reaction Coordinate.===

Figure 5.3.1 shows the comparison of the Diels-Alder and Cheletropic Reaction Profiles on a Standardized Reaction Coordinate at 298.15 K and 1 atm (PM6 level). In the Standardized Reaction Coordinate, the reactants' coordinates are set to -1, those of TS set to 0 and those of products set to 1. This was done to align the all the reaction states independent of the rate on a common scale such that the relative energetics could be compared between possible reaction paths. 

{|  class="wikitable" border="0" style='text-align: center style="margin-left: auto; margin-right: auto; border: none;"
|-
|[[File:KH1015 Comparison.png|frame|Figure 5.3.1: Comparison of the Diels-Alder and Cheletropic Reaction Profiles on a Standardized Reaction Coordinate at 298.15 K and 1 atm (PM6 level).]]
|}

(Some suggestions: 1) If you normalise to the common point (reactants) then you can read off the activation and reaction energies more easily. 2) The numeric values of the x axis have no real meaning so these axis labels can be removed. 3) Placing the values of the activation and reaction energies on the chart itself will further improve legibility (especially where the endo- and exo- products overlap [[User:Tam10|Tam10]] ([[User talk:Tam10|talk]]) 12:59, 16 March 2018 (UTC))

===Part 3: Rationalizing the Reaction Profile Parameters.===

Xylylene is an unstable compound because it is a system of 8 π electrons (4n anti-aromatic rule). From the IRC of all the reactions examined (excluding Diels-Alder minor-regio-isomers), it was observed that as xylelene reacted with sulfur dioxide, the 6 membered-ring would end up with a stable 6 π electrons system (4π+2 aromatic rule) in the product. This provided a strong thermodynamic driving force for the reaction with sulfur dioxide to proceed.

For all the reactions examined, there was no identifiable secondary orbital contribution from the Gaussview MO visualizations. 

Referring to Figure 5.3.2-5.3.5, the calculated steric interactions were similar for Diels-Alder endo-exo products that react at the same regio-position. Because of similar steric interactions and electronic interactions within each set, the products that reacted at the same position would possess similar activation Gibbs-Free Energy (calculated) as shown in Table 5.3.2. However, when comparing '''between''' the two sets of Diels-Alder regio-isomers, it could be seen that the activation Gibbs-Free Energy for the minor-regio-isomer set was much higher than the other set ({113, 121} against {83.2, 87.2} where each element of the sets is in the form {endo, exo} and reported in kJ mol<sup>-1</sup>). For both sets, the TS formation involved severance of π interactions in the xylylene system. In the major-regio-isomer set, the activation Gibbs-Free Energy was reduced because there was a corresponding formation of favourable aromatic interaction in the 6-membered ring.

Referring to Figure 5.3.2-5.3.3 and 5.3.6, when comparing between the Diels-Alder major regio-isomer set and the cheletropic product, the steric clash (Red being not favourable and Blue being favourable) in the cheletropic TS was calculated to be higher than those in the Diels-Alder major regio-isomer set. This was due to the approach of two orthogonal lone pairs of S atom towards the 5,6-dimethylenecyclohexa-1,3-diene in the chelotropic TS (Orange colour) that was not present in the Diels-Alder reactions. This contributes to the observation that the calculated activation Gibbs-Free Energy of the cheletropic product, 106 kJ mol<sup>-1</sup>, was much higher than those of the endo and exo products, 83.2 and 87.2 <sup>-1</sup> respectively.

{|  class="wikitable" border="0" style='text-align: center style="margin-left: auto; margin-right: auto; border: none;"
|-
|[[File:KH1015 Endo Diels Alder-Ultrafinegrid Fragment TS den.png|thumb|Figure 5.3.2: Non Covalent Interactions in the Transition State During Diels-Alder Endo Product Formation.]]
|[[File:KH1015 Exo Diels Alder-Ultrafinegrid Fragment TS den.png|thumb|Figure 5.3.3: Non Covalent Interactions in the Transition State During Diels-Alder Exo Product Formation.]]
|[[File:KH1015 Var Endo Diels Alder-Ultrafinegrid Fragment TS den.png|thumb|Figure 5.3.4: Non Covalent Interactions in the Transition State During Diels-Alder Endo Minor-Regioisomer Formation.]]
| [[File:KH1015 Var Exo Diels Alder-Ultrafinegrid Fragment TS den.png|thumb|Figure 5.3.5: Non Covalent Interactions in the Transition State During Diels-Alder Exo Minor-Regioisomer Formation.]]
| [[File:KH1015 Isoindene-Ultrafinegrid Fragment TS den.png|thumb|Figure 5.3.6: Non Covalent Interactions in the Transition State During Cheletropic Product Formation.]]
|-
|}

(Nice analysis. It's pretty difficult to get much information about primary interactions with NCI. Perhaps it would be more valuable to get information about the products with NCI [[User:Tam10|Tam10]] ([[User talk:Tam10|talk]]) 12:59, 16 March 2018 (UTC))

===Part 4: IRC.===
====1. Diels-Alder Products.====
=====1.A. Endo Major-Regio-Isomer.=====
Referring to Figure 5.3.7, the IRC calculation at PM6 level showed that the C-O and C-S sigma bonds were formed in an asynchronous fashion in a concerted mechanism, with C-O bond forming earlier than C-S bond, and that the TS had been optimized. 

{|  class="wikitable" border="0" style='text-align: center style="margin-left: auto; margin-right: auto; border: none;"
|-
|[[File:Kh1015 Endo Diels Alder.gif|frame|left|Figure 5.3.7: IRC for Formation of Diels-Alder Endo Product at 298.15 K and 1 atm (PM6 Level).]]
|| [[File:KH1015 Endo Diels Alder IRC Graph.png|thumb|Figure 5.3.8: IRC Graph of Energy against Reaction Coordinate for the formation of Endo Product at 298.15 K and 1 atm (PM6 Method). Click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:KH1015_Endo_Diels_Alder_IRC_Graph_Gradient.png here] for the concurrent RMS Gradient Norm analysis.]]
|-
|<jmol>
 <jmolApplet>
<title>Figure 5.3.9: Jmol of TS of Endo Path.</title>
 <color>white</color>
 <size>400</size>
 <script>frame 14; mo 29; mo nodots nomesh fill translucent; mo titleformat ""</script>
 <uploadedFileContents>KH1015 ENDO DIELS ALDER-ULTRAFINEGRID FRAGMENT TS MO.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|| [[File:KH1015 Endo Diels Alder-TS HOMO Isovalue 0.02 Cube Grid Coarse.png|thumb|Figure 5.3.10: HOMO of the TS of Endo Path (Isovalue=0.02; Cube Grid=Coarse; MO 29).]]
|-
|}

=====1.B. Exo Major-Regio-Isomer.=====
Referring to Figure 5.3.11, the IRC calculation at PM6 level showed that the C-O and C-S sigma bonds were formed in an asynchronous fashion in a concerted mechanism, with C-O bond forming earlier than C-S bond,  and that the TS had been optimized.

{|  class="wikitable" border="0" style='text-align: center style="margin-left: auto; margin-right: auto; border: none;"
|-
|[[File:Kh1015 Exo Diels Alder.gif|frame|left|Figure 5.3.11: IRC for Formation of Diels-Alder Exo Product (PM6 level).]]
|| [[File:KH1015 Exo Diels Alder IRC Graph.png|thumb|Figure 5.3.12: IRC Graph of Energy against Reaction Coordinate for the formation of Exo Product (PM6 Method). Click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:KH1015_Exo_Diels_Alder_IRC_Graph_Gradient.png here]for the concurrent RMS Gradient Norm analysis.]]
|-
|<jmol>
 <jmolApplet>
<title>Figure 5.3.13: HOMO of TS of Exo Path.</title>
 <color>white</color>
 <size>400</size>
 <script>frame 74; mo 29; mo nodots nomesh fill translucent; mo titleformat ""</script>
 <uploadedFileContents>KH1015 EXO DIELS ALDER-ULTRAFINEGRID FRAGMENT TS MO.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|| [[File:KH1015 Exo Diels Alder-TS HOMO.png|thumb|Figure 5.3.14: HOMO of TS of Exo Path (Isovalue=0.02; Cube Grid=Coarse; MO 29).]]
|-
|}

=====2.A. Endo Minor-Regio-Isomer.=====
Referring to Figure 5.3.15, the IRC calculation at PM6 level showed that the C-O and C-S sigma bonds were formed in an asynchronous fashion in a concerted mechanism, with C-O bond forming earlier than C-S bond, and that the TS had been optimized.

{|  class="wikitable" border="0" style='text-align: center style="margin-left: auto; margin-right: auto; border: none;"
|-
|[[File:KH1015 Var Endo Diels Alder.gif|frame|left|Figure 5.3.15: IRC for Formation of Endo Minor-Regioisomer.]]
|| [[File:KH1015 Var Endo Diels Alder IRC Graph.png|thumb|Figure 5.3.16: IRC Graph of Energy against Reaction Coordinate for the formation of Endo Minor-Regioisomer (PM6 Method). Click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:KH1015_Var_Endo_Diels_Alder_IRC_Graph_Gradient.png here] for the concurrent RMS Gradient Norm analysis.]]
|-
|<jmol>
 <jmolApplet>
<title>Figure 5.3.17: HOMO of Endo Minor-Regioisomer Path.</title>
 <color>white</color>
 <size>400</size>
 <script>frame 24; mo 29; mo nodots nomesh fill translucent; mo titleformat ""</script>
 <uploadedFileContents>KH1015 VAR ENDO DIELS ALDER PM6 FRAGMENT TS MO.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|| [[File:KH1015 Var Endo Diels Alder-TS HOMO.png|thumb|Figure 5.3.18: HOMO of TS of Endo Minor-Regioisomer Path (Isovalue=0.02; Cube Grid=Coarse; MO 29).]]
|-
|}

=====2.B. Exo Minor-Regio-Isomer.=====
Referring to Figure 5.3.19, the IRC calculation at PM6 level showed that the C-O and C-S sigma bonds were formed in an asynchronous fashion in a concerted mechanism, with C-O bond forming earlier than C-S bond, and that the TS had been optimized.

{|  class="wikitable" border="0" style='text-align: center style="margin-left: auto; margin-right: auto; border: none;"
|-
|[[File:KH1015 Var Exo Diels Alder.gif|frame|left|Figure 5.3.19: IRC for Formation of Exo Minor-Regioisomer.]]
|| [[File:KH1015 Var Exo Diels Alder IRC Graph.png|thumb|Figure 5.3.20: IRC Graph of Energy against Reaction Coordinate for the formation of Exo Minor-Regioisomer (PM6 Method). Click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:KH1015_Var_Exo_Diels_Alder_IRC_Graph_Gradient.png here] for the concurrent RMS Gradient Norm analysis.]]
|-
|<jmol>
 <jmolApplet>
<title>Figure 5.3.21: HOMO of TS of Exo Minor-Regioisomer Path.</title>
 <color>white</color>
 <size>400</size>
 <script>frame 16; mo 29; mo nodots nomesh fill translucent; mo titleformat ""</script>
 <uploadedFileContents>KH1015 VAR DIELS ALDER PM6 FRAGMENT TS MO.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|| [[File:KH1015 Var Exo Diels Alder-TS HOMO.png|thumb|Figure 5.3.22: HOMO of TS of Exo Minor-Regioisomer Path (Isovalue=0.02; Cube Grid=Coarse; MO 29).]]
|-
|}

====2. Cheletropic  Product.====
Referring to Figure 5.3.23, the IRC calculation at PM6 level showed that the two C-S sigma bonds were formed in a synchronous fashion in a concerted mechanism and that the TS had been optimized.

{|  class="wikitable" border="0" style='text-align: center style="margin-left: auto; margin-right: auto; border: none;"
|-
|[[File:Kh1015 Isoindene.gif|frame|left|Figure 5.3.23: IRC for Formation of Cheletropic Product.]]
|| [[File:KH1015 Isoindene IRC Graph.png|thumb|Figure 5.3.24:  IRC Graph of Energy against Reaction Coordinate for the formation of Cheletropic Product (PM6 Method). Click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:KH1015_Isoindene_IRC_Graph_Gradient.png here] for the concurrent RMS Gradient Norm analysis.]]
|-
|<jmol>
 <jmolApplet>
<title>Figure 5.3.25: HOMO of TS of Cheletropic Path.</title>
 <color>white</color>
 <size>400</size>
 <script>frame 36; mo 29; mo nodots nomesh fill translucent; mo titleformat ""</script>
 <uploadedFileContents>KH1015 ISOINDENE ULTRAFINEGRID FRAGMENT TS MO.LOG</uploadedFileContents>
 </jmolApplet>
</jmol>
|| [[File:KH1015 Isoindene-TS HOMO.png|thumb|Figure 5.3.26: HOMO of TS of Cheletropic Path (Isovalue=0.02; Cube Grid=Coarse; MO 29).]]
|-
|}

===Part 5: Interactive Vibration Animations.===

Figures 5.3.27-5.3.31 show the interactive vibration animations.

<jmol>                                                                                                                                                              //Group all the HTML within "jmol"
    <jmolApplet>
<title>Figure 5.3.27: Interactive Vibration Animation of the Endo TS (PM6 Method).</title>                                                                                                                                               //Initialise the applet
        <uploadedFileContents>KH1015 ENDO DIELS ALDER-ULTRAFINEGRID FRAGMENT TS MO.LOG</uploadedFileContents>                                     
        <script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script>                                     //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
        <name>Endo</name>                                                                                                                       //The name of the applet must be set. This is the name that the controls refer to (the target)
    </jmolApplet>
    <jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>Endo</target>
     </jmolbutton>
     <jmolbutton>
        <script>measure 14 18; measure 11 17</script>
        <text>TS C-C Equilibrium Distance</text>
        <target>Endo</target>
     </jmolbutton>
     <jmolbutton>
        <script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
        <text>Spin</text>
        <target>Endo</target>
     </jmolbutton>
<jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>Endo</target>
     </jmolbutton>
     <jmolmenu>                                                                                                                                                //The dropdown menu. Each item has to be declared individually and can execute script
       <item>
       <script>vibrating=0; vibration off</script>
            <text>=Select Vibration=</text>
        <target>Endo</target>
        </item>
        <item>
            <script>frame 15; if(vibrating==0) vibration off; else; vibration 2; endif</script>                         //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
            <text>i334/cm</text>
        <target>Endo</target>
        </item>
        <item>
            <script>frame 16; if(vibrating==0) vibration off; else; vibration 2; endif</script>
            <text>63/cm</text>
        <target>Endo</target>
        </item>
     </jmolmenu>
</jmol>


<jmol>                                                                                                                                                              //Group all the HTML within "jmol"
    <jmolApplet>
<title>Figure 5.3.28: Interactive Vibration Animation of the Exo TS (PM6 Method).</title>                                                                                                                                               //Initialise the applet
        <uploadedFileContents>KH1015 EXO DIELS ALDER-ULTRAFINEGRID FRAGMENT TS MO.LOG</uploadedFileContents>                                     
        <script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script>                                     //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
        <name>Exo</name>                                                                                                                       //The name of the applet must be set. This is the name that the controls refer to (the target)
    </jmolApplet>
    <jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>Exo</target>
     </jmolbutton>
     <jmolbutton>
        <script>measure 14 18; measure 11 17</script>
        <text>TS C-C Equilibrium Distance</text>
        <target>Exo</target>
     </jmolbutton>
     <jmolbutton>
        <script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
        <text>Spin</text>
        <target>Exo</target>
     </jmolbutton>
<jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>Exo</target>
     </jmolbutton>
     <jmolmenu>                                                                                                                                                //The dropdown menu. Each item has to be declared individually and can execute script
       <item>
       <script>vibrating=0; vibration off</script>
            <text>=Select Vibration=</text>
        <target>Exo</target>
        </item>
        <item>
            <script>frame 75; if(vibrating==0) vibration off; else; vibration 2; endif</script>                         //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
            <text>i352/cm</text>
        <target>Exo</target>
        </item>
        <item>
            <script>frame 76; if(vibrating==0) vibration off; else; vibration 2; endif</script>
            <text>66/cm</text>
        <target>Exo</target>
        </item>
<jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>Exo</target>
     </jmolbutton>
     </jmolmenu>
</jmol>

<jmol>                                                                                                                                                              //Group all the HTML within "jmol"
    <jmolApplet>
<title>Figure 5.3.29: Interactive Vibration Animation of the Endo Minor-Regioisomer TS (PM6 Method).</title>                                                                                                                                               //Initialise the applet
        <uploadedFileContents>KH1015 VAR ENDO DIELS ALDER PM6 FRAGMENT TS MO.LOG</uploadedFileContents>                                     
        <script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script>                                     //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
        <name>EndoVar</name>                                                                                                                       //The name of the applet must be set. This is the name that the controls refer to (the target)
    </jmolApplet>
    <jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>EndoVar</target>
     </jmolbutton>
     <jmolbutton>
        <script>measure 5 17; measure 2 18</script>
        <text>TS C-C Equilibrium Distance</text>
        <target>EndoVar</target>
     </jmolbutton>
     <jmolbutton>
        <script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
        <text>Spin</text>
        <target>EndoVar</target>
     </jmolbutton>
<jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>EndoVar</target>
     </jmolbutton>
     <jmolmenu>                                                                                                                                                //The dropdown menu. Each item has to be declared individually and can execute script
       <item>
       <script>vibrating=0; vibration off</script>
            <text>=Select Vibration=</text>
        <target>EndoVar</target>
        </item>
        <item>
            <script>frame 25; if(vibrating==0) vibration off; else; vibration 2; endif</script>                         //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
            <text>i453/cm</text>
        <target>EndoVar</target>
        </item>
        <item>
            <script>frame 26; if(vibrating==0) vibration off; else; vibration 2; endif</script>
            <text>57/cm</text>
        <target>EndoVar</target>
        </item>
     </jmolmenu>
</jmol>

<jmol>                                                                                                                                                              //Group all the HTML within "jmol"
    <jmolApplet>
<title>Figure 5.3.30: Interactive Vibration Animation of the Exo Minor-Regioisomer TS (PM6 Method).</title>                                                                                                                                               //Initialise the applet
        <uploadedFileContents>KH1015 VAR DIELS ALDER PM6 FRAGMENT TS MO.LOG</uploadedFileContents>                                     
        <script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script>                                     //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
        <name>ExoVar</name>                                                                                                                       //The name of the applet must be set. This is the name that the controls refer to (the target)
    </jmolApplet>
    <jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>ExoVar</target>
     </jmolbutton>
     <jmolbutton>
        <script>measure 2 18; measure 5 17</script>
        <text>TS C-C Equilibrium Distance</text>
        <target>ExoVar</target>
     </jmolbutton>
     <jmolbutton>
        <script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
        <text>Spin</text>
        <target>ExoVar</target>
     </jmolbutton>
<jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>ExoVar</target>
     </jmolbutton>
     <jmolmenu>                                                                                                                                                //The dropdown menu. Each item has to be declared individually and can execute script
       <item>
       <script>vibrating=0; vibration off</script>
            <text>=Select Vibration=</text>
        <target>ExoVar</target>
        </item>
        <item>
            <script>frame 17; if(vibrating==0) vibration off; else; vibration 2; endif</script>                         //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
            <text>i483/cm</text>
        <target>ExoVar</target>
        </item>
        <item>
            <script>frame 18; if(vibrating==0) vibration off; else; vibration 2; endif</script>
            <text>53/cm</text>
        <target>ExoVar</target>
        </item>
     </jmolmenu>
</jmol>

<jmol>                                                                                                                                                              //Group all the HTML within "jmol"
    <jmolApplet>
<title>Figure 5.3.31: Interactive Vibration Animation of the Cheletropic TS (PM6 Method).</title>                                                                                                                                               //Initialise the applet
        <uploadedFileContents>KH1015 ISOINDENE ULTRAFINEGRID FRAGMENT TS MO.LOG</uploadedFileContents>                                     
        <script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script>                                     //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
        <name>Cyclohexene</name>                                                                                                                       //The name of the applet must be set. This is the name that the controls refer to (the target)
    </jmolApplet>
    <jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>Cyclohexene</target>
     </jmolbutton>
     <jmolbutton>
        <script>measure 11 17; measure 14 17</script>
        <text>TS C-C Equilibrium Distance</text>
        <target>Cyclohexene</target>
     </jmolbutton>
     <jmolbutton>
        <script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
        <text>Spin</text>
        <target>Cyclohexene</target>
     </jmolbutton>
<jmolbutton>                                                                                                                                               //Adding a jmol button, which executes code on the target
        <script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>    //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
        <text>Vibrate</text>
        <target>Cyclohexene</target>
     </jmolbutton>
     <jmolmenu>                                                                                                                                                //The dropdown menu. Each item has to be declared individually and can execute script
       <item>
       <script>vibrating=0; vibration off</script>
            <text>=Select Vibration=</text>
        <target>Cyclohexene</target>
        </item>
        <item>
            <script>frame 37; if(vibrating==0) vibration off; else; vibration 2; endif</script>                         //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
            <text>i487/cm</text>
        <target>Cyclohexene</target>
        </item>
        <item>
            <script>frame 38; if(vibrating==0) vibration off; else; vibration 2; endif</script>
            <text>74/cm</text>
        <target>Cyclohexene</target>
        </item>
     </jmolmenu>
</jmol>