2017-11-20T22:15:01Z

Yts15: /* Exercise 3 */

== Introduction ==

<font color="#0000FF">'In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)''</font>

== Exercise 1: Reaction of Butadiene with Ethylene ==

<br />

[[File:Reaction scheme.png|thumb|center|500px|alt=''Figure 1. Reaction Scheme''|Fig. 1: ''Reaction Scheme of Butadiene with Ethylene in Exercise 1'']]

<br />

=== Optimization Result ===

{| class="wikitable"
|+Table 1. Optimization Result of Reactant, TS and Products at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT1_2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 80; vibration 2;rotate x -20; </script>
<uploadedFileContents>P_FINALOPT_2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

The ''Table 1'' shows the result of optimisation of reactants, TS and product at '''PM6 level''' respectively. Correct TS was further confirmed by '''frequency calculation''' and '''IRC'''.
<font color="#0000FF">ELABORATION''</font>

====Frequency====
[[File:Yts15 freq 1.PNG|thumb|none|1000px|alt=''Figure 2. Frequency Calculation of TS''|Fig. 2: ''Frequency Calculation of TS'']]

From Fig. 2, a '''negative frequency''' is shown in the final optimised TS. This indicates imaginary vibrational frequency associated with a TS which corresponds to the translational motion of carbon. At Gaussian, second derivative of the energy with respect to the nuclear position is calculated by the frequency. Hence, the first negative frequency indicates one negative second derivation, a saddle point, which is the highest point on the minimum energy path linking the reactants and products<ref>Houston, P. L. Chemical kinetics and reaction dynamics; Dover: Mineola, NY, 2006.</ref>. High frequency, greater than |100<sup>-1</sup>|, is consistent with this kind of molecule. As a result, this represents a correct TS is obtained from final optimisation . Additionally, this plays an important part in defining chemical reactions. One negative frequency also indicates the presence of single TS which illustrates a well-defined reaction profile and complete reaction.

====IRC====
[[File:YtsIRC final.PNG|thumb|none|500px|alt=''Figure 3. IRC of TS''|Fig. 3: ''IRC'']]

Transition state geometries can be connected to ground state geometries with an '''Intrinsic Reaction Coordination calculation (IRC)''' performed by Gaussian. In Fig 3., the downhill path from the transition is followed in '''forward direction'''. A well defined and asymmetric Free Energy Surface as shown in Fig. 3 confirms that TS is correctly optimised.

=== MO Analysis===
<font color="#0000FF">
Construct an MO diagram for the formation of the butadiene/ethene TS, including basic symmetry labels (symmetric/antisymmetric or s/a).For each of the reactants and the TS, open the .chk (checkpoint) file. Under the '''Edit''' menu, choose '''MOs''' and visualise the MOs. Include images (or '''[[Mod:Cheatsheet#MOs_with_Jmol|Jmol objects]]''') for each of the HOMO and LUMO of butadiene and ethene, and the four MOs these produce for the TS. Correlate these MOs with the ones in your MO diagram to show which orbitals interact.
</font>

MO diagram for the formation of butadiene/ethene TS is illustrated in Fig. 4 MO Diagram for the formation of Butadiene/ Ethene. Actual MOs are performed by Gaussian at Basis Set PM6. It is shown that TS LUMO +1 has energy lower than expected (''stabilisation'') and TS HOMO has energy higher than expected (''destabilisation''). Hence, this suggested that significant mixing between orbitals.

[[File:Yts MO 1 mix.png|thumb|none|600px|alt=''Figure 4. MO diagram for the formation of the Butadiene/Ethene TS''|Fig. 4: ''MO diagram for the formation of the butadiene/ethene TS'']]

{| class="wikitable"
|+Table 2a. HOMO and LUMO of Reactants, Butadiene and ethene
! style="background: #0D4F8B; color: white;" | Orbital type
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO11, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO6, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO12, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO7, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable"
|+Table 2b. Four MOs produced from reactants for TS
! style="background: #0D4F8B; color: white;" | HOMO-1
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | LUMO+1
|-
| <jmol>
<jmolApplet>
<title> MO 16, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO17, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO18, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO19, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<font color="#0000FF"> What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')?

'' Woodward and Hoffmann[6] ascribe endo addition to interaction of occupied orbitals with unoccupied orbitals, the endo transition state conformation being favored by orbital symmetry relative to the exo conformation. With the model of frontier orbitals, we have interaction of HOMOs (Highest Occupied Molecular Orbitals) with LUMOs (Lowest Unoccupied Molecular Orbitals). Those interactions are represented in figure 4. The main interactions that will form the bonds are shown by plain bold lines, the secondary interactions, responsible for the endo-exo selectivity, are shown by small squiggly lines. We do not know if the molecules approch so closely that the secondary interactions can be as important as shown in figure 1. ''

Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction and an antisymmetric-antisymmetric interaction.'''</font>

=== Bond Length Analysis ===

{| class="wikitable"
|+Table 3. Carbon Carbon bond length of Reactants, TS and Products; and Literature value
! style="background: #0D4F8B; color: white;" | Reactant
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" | Literature value
|-
| [[File:Yts Cbond length reactant.PNG|500px]]
| [[File:Yts Cbond length TS.PNG|300px]]
| [[File:Yts Cbond length P.PNG|300px]]
|<div style="text-align: center;">Van der Waals radius of the C atom: 1.7 Å <ref>Bondi, A. The Journal of Physical Chemistry 1964, 68 (3), 441–451.</ref><br />Typical sp<sup>3</sup> C-C bond length and sp<sup>2</sup> C=C bond lengths : 1.54 Å, 1.34 Å<ref>Fox, M. A.; Whitesell, J. K. Organische Chemie: Grundlagen, Mechanismen, bioorganische Anwendungen; Spektrum Akadem. Verl.: Heidelberg, 1995.</ref><br /> [[File:Yts cyclohexenelitlength.PNG|450px]]<br />Bond length of cyclohexene<ref>Chiang, J. F.; Bauer, S. H. Journal of the American Chemical Society 1969, 91 (8), 1898–1901.</ref><br /> </div>
|-
|}

Experimental carbon carbon bond length of cyclohexene is consistent with the literature value as shown in Table 3 which confirm correct structure of TS and Cyclohexene Product is obtained. Comparing the Van der Waals radius of C atom and the length of the partly formed C-C bonds in the TS, a much lower C-C bond length at TS indicates formation of bond. Typically, sp<sup>2</sup> C=C bond lengths is much shorter than sp<sup>3</sup> C-C bond length as shown in table 3 due to a higher bond order and hence, closer the Carbon atoms are.

As reaction proceed, bond length corresponds to different carbon atoms change which the result is shown in Table 4.

{| class="wikitable"
|+Table 4. Change of Bond Length as the reaction proceed
[[File:YtsIRC finallabel.PNG|thumb|center|400px|alt=''Figure 5. Labelled Carbon atoms in reactants''|Fig. 5: ''Labelled Carbon atoms in reactants'']]
|-
|[[File:Yts BL 1,4.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6a: ''Plot of change of Bond Length between C1 and C4'']]
|[[File:Yts BL 4,14.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6b: ''Plot of change of Bond Length between C4 and C14'']]
|[[File:Yts BL 14,12.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6c: ''Plot of change of Bond Length between C14 and C12'']]
|-
|[[File:Yts BL 12,10.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6d: ''Plot of change of Bond Length between C12 and C10'']]
|[[File:Yts BL 10,7.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6e: ''Plot of change of Bond Length between C10 and C7'']]
|[[File:Yts BL 7,1.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6f: ''Plot of change of Bond Length between C7 and C1'']]
|}

===Vibrational Analysis===

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

The vibration that corresponds to the reaction path at transition state is -949.15 cm<sup>-1</sup>. In the transition state of this reaction, the two forming bonds have the same lengths. Hence, this confirms the '''synchronous''' mechanism where two new bonds are formed simultaneously.

<jmol>
<jmolApplet>
<title> Vibrational Analysis of TS </title>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==

<br />

[[File:Yts ex2 reaction scheme.png|thumb|center|500px|alt=''Figure 7. Reaction Scheme''|Fig. 7: ''Reaction Scheme of Diels Alder reaction'']]

<br />

=== Optimisation Result ===

Table 5 shows the result of the Optimisation of reactants; endo and exo TSs. It was first optimised at PM6 method then a more accurate method, at B3LYP/6-31G(d) Basis Set

{| class="wikitable"
|+Table 5. Optimization Result of Reactant and Exo, Endo TS at PM6 and B3LYP/6-31G(d) Basis Set
! style="background: #0D4F8B; color: white;" | Basic Set
! style="background: #0D4F8B; color: white;" | Cyclohexadiene
! style="background: #0D4F8B; color: white;" | 1,3-Dioxole
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
| '''PM6'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 62; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN PM6 3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 30; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 22; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| '''B3LYP/6-31G(d)'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 18; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 24; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN B3LYP 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 34; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

===Frequency Analysis===

A correct TS is further confirmed by the frequency analysis. Only one negative frequency at Exo and Endo TS indicates a saddle point reached which confirms the correct TS obtained.
{| class="wikitable"
|+Table 6. Frequency Analysis of Exo and Endo TS and Products respectively at PM6 and B3LYP/6-31G(d) Basis Set
!
! style="background: #0D4F8B; color: white;" colspan="2"| Exo
! style="background: #0D4F8B; color: white;" colspan="2" | Endo
|-
|
! '''PM6'''
! '''B3LYP/6-31G(d)'''
! '''PM6'''
! '''B3LYP/6-31G(d)'''
|-
| '''TS'''
| [[File:Yts ex2exo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8a: ''Frequency Calculation of Exo TS at PM6'']]
| [[File:Yts ex2exo TS freqB3LYP.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8b: ''Frequency Calculation of Exo TS at B3LYP'']]
| [[File:Yts ex2endo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9a: ''Frequency Calculation of Endo TS at PM6'']]
| [[File:Yts ex2endo TS freqB3LYP 2.PNG|thumb|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9b:''Frequency Calculation of Endo TS at B3LYP'']]
|-
| '''Product'''
| [[File:Yts ex2 exo P PM6freq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10a: ''Frequency Calculation of Exo Product at PM6'']]
| [[File:Yts ex2 exo P B3LYPfreq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10b: ''Frequency Calculation of Exo Product at B3LYP'']]
| [[File:Yts ex2 endo P PM6freq.PNG|thumb|none|400px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11a: ''Frequency Calculation of Endo Product at PM6'']]
| [[File:Yts ex2 endo P B3LYPfreq.PNG|thumb|1000px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11b:''Frequency Calculation of Endo Product at B3LYP'']]
|}

=== MO Analysis ===

Figure 12 and 13 shows the MO digram for the Diels-Alder reaction (Exo and Endo) , which correlate with the actual MOs performed by Gaussian at B3LYP/6-31G(d) basis set.

{| class="wikitable"
|[[File:Yts ex2endo MO 2.png|thumb|none|600px|alt=''Figure 11. MO diagram for the Endo Diels-Alder reaction''|Fig. 12: ''MO diagram for the Exo Diels-Alder reaction'']]
|[[File:Yts ex2exo MO.png|thumb|none|600px|alt=''Figure 12. MO diagram for the Exo Diels-Alder reaction''|Fig. 13: ''MO diagram for the Endo Diels-Alder reaction'']]
|}

{| class="wikitable"
|+Table 6. HOMO and LUMO of Exo and Endo TS at '''B3LYP/6-31G(d)'''
! style="background: #0D4F8B; color: white;" =2'' | Orbital type
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
|HOMO-1
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO+1
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - ''Energy''' under '''Job Type''' - will yield an ordered list of MOs that you can use to start you off).

This reaction is an '''inverse demand DA reaction ''' since diene is less electron rich than dienophile in this reaction. Hence, the '''Frontier Molecular Orbitals ''' the '''LUMO of Cyclohexadiene '''(Antisymmetric) interact with the '''HOMO of 1,3-Dioxole, dienophile''', are closer in energy than that of HOMO of diene and LUMO of dienophile. As a result, they interact most strongly and form most energetically favourable bond formation. <ref> Fleming, I. Frontier orbitals and organic chemical reactions; Wiley: London, 2007.</ref>

=== Reaction Thermodynamics ===
{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Cyclohexadiene
! style="background: #0D4F8B; color: white;" " colspan="2"| 1,3-Dioxole
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.116878
| 306.863212
| −0.0522760
| −137.25064846
|0.138903
|364.689854
|0.137941
|362.164123
|0.037972
|99.6954936
|0.037807
|99.2622861
|-
| '''B3LYP/6-31G(d)'''
|−233.324375
|−612593.19323
|–267.068645
|–701188.78086
|–500.329165
|–1313614.3228
|–500.332147
|–1313622.152
|–500.417322
|–1313845.779
|−500.418691
|–1313849.3733
|}

{| class="wikitable"
|+Table 8. Activation Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>168
|<nowiki>-</nowiki>63.80491
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>163
|<nowiki>-</nowiki>67.39921
|}

<br/>
Table 8. shows the result of the Activation Barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

<br/>

'''Kinetic favourable''' of the products can be determined by the Activation Barrier. As shown in Table 8, Endo reaction pathway has a lower Activation energy and hence Endo product is more kinetically favourable. This can be further explained by '''secondary (non-bonding) orbital interaction''' in the endo TS HOMO as shown in Table 9. Secondary orbital interaction between diene and the dienophile substituent's π system lowers the energy of the endo TS and hence, lower activation barrier and the reaction proceed much faster towards endo-product. <ref>Alston, P. V.; Ottenbrite, R. M.; Cohen, T. The Journal of Organic Chemistry 1978, 43 (10), 1864–1867.</ref>As a result, '''endo product''' is more kinetically stable. On the other hand, there is no such interaction between Diene and the substituent in exo TS as shown in the HOMO of exo TS in table 9. Hence, there is no stabilisation of the exo Transistion state. Only primary (bonding) interaction present in the Exo-TS.

<br/>
Moreover, '''endo product''' is more '''thermodynamically favourable'''. Comparing the Gibbs free energy between Endo- product and Exo- product, more negative number is obtained at the Endo-product. Hence, this confirms that the endo-product is more thermodynamically stable. In fact, less sterically-hindered Exo-TS is expected to be more thermodynamically favourable. This unexpected result of Endo-Product being more more thermodynamic favourable of can be explained by Hammonds Postulate. Since this is an endothermic reaction (bond forming), according to Hammonds Postulate, it is expected that TS is more product like. As a consequence, stabilisation by secondary (non-bonding) orbital interaction will also apply to the endo-product.

{| class="wikitable"'
|+ '''Table 9. shows secondary orbital interactions or sterics on TS
! style="background: #0D4F8B; color: white;"| HOMO of Exo TS
! style="background: #0D4F8B; color: white;"|HOMO of Endo TS
|-
| <jmol>
<jmolApplet>
<title> Sterics only </title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> Secondary Orbital Interaction</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<br/>

As a result, it can be concluded that inverse electron demand Diels Alder reaction favours '''endo-Product''' in terms of '''thermodynamics''' and '''kinetic ''' argument.

<br/>

== Exercise 3: Diels-Alder vs Cheletropic ==

<br />
[[File:Yts ex3 reaction scheme.png|thumb|center|1000px|alt=''Figure X. Reaction Profile for different pathway''|Fig. 1: ''Reaction Profile of the Exo, Endo and Cheletropic pathway '']]
<br />

===Optimisation Result===

Table X. shows the optimisation result of the exo TS, endo TS and Cheletropic TS at PM6 Basis Set.

{| class="wikitable"
|+Table 11. Optimization Result of Exo, Endo and Cheletropic TS at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
! style="background: #0D4F8B; color: white;" | Cheletropic TS
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts_3_DA_TSOPT_exo.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>YtsCHEL_TS_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

===IRC Analysis===

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

The reaction coordinate for each path is visualise in the following animation with an IRC calculation.

<center>[[File:Yts ex3Endo IRC.gif]] </center>
<center>''Animation 1. IRC for Endothermic reaction pathway </center>

<center>[[File:Yts ex3Exo IRC.gif]] </center>
<center>''Animation 2. IRC for Exothermic reaction pathway </center>

<center>[[File:Yts ex3chel IRC.gif]] </center>
<center>''Animation 3. IRC for Cheletropic reaction pathway </center>

===Reaction Thermodynamics===

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" |Cheletropic TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Cheletropic Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
|0.092078
|241.750807
|0.090560
|237.765298
| 0.099062
|260.087301
| 0.021455
|56.3301068
|0.021706
|56.9891073
|−0.000002
|−0.0052510004
|}

Table 8. shows the result of the reaction barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>85.6
|<nowiki>-</nowiki>99.7
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>81.7
|<nowiki>-</nowiki>99.1
|-
| '''Cheletropic Pathway '''''
|<nowiki>+</nowiki>104.0
|<nowiki>-</nowiki>156.1
|}

<br />

[[File:Yts ex3 reactionprofile3.PNG|thumb|center|600px|alt=''Figure X. Reaction Profile for different pathway''|Fig. 1: ''Reaction Profile of the Exo, Endo and Cheletropic pathway '']]

<br />

== Extra ==

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. Table X, X+1 shows the result of the potential energy of reactants, TS and products; Activation energy and Reaction energy of of this Diels-Alder reaction.

<br />
[[File:Yts extra reaction scheme.png|thumb|center|600px|alt=''Figure X. Reaction Profile for different pathway''|Fig. 1: ''Reaction Profile of the Exo, Endo and Cheletropic pathway '']]
<br />

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
| 0.105053
|275.816673
| 0.102071
|267.9874309
| 0.067304
|176.7066655
| 0.065610
|172.2590681
|}

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>119.7
|<nowiki>+</nowiki>20.6
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>111.9
|<nowiki>+</nowiki>16.2
|}

If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

==Conclusion==

== Log Files ==

=== Exercise 1 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Product
|-
| PM6
| [[File:REACTANT1_2_OPTMIN.LOG]]
| [[File:REACTANT2_OPTMIN.LOG‎]]
| [[File:TS_2_OPTTS.LOG]]
| [[File:TS_2_IRC_out.log]]
| [[File:P_FINALOPT_2.LOG]]
|}

=== Exercise 2 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Exo-Products
! style="background: #0D4F8B; color: white;" | Endo-Products
|-
| PM6
!rowspan ="2" |[[File:Endo IRC output final.log]]<br/>[[File:EXO IRC 5.LOG]]<br/>
| [[File:Yts EXO P FINALOPTMIN 1.LOG]]
|[[File:Yts ENDO P OPTMIN PM6.LOG]]

|-
| B3LYP/6-31G(d)
| [[File:EXO P FINALOPTMIN B3LYP.LOG]]
| [[File:Yts ENDO P OPTMIN B3LYP.LOG]]
|}

=== Exercise 3 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | reaction
! style="background: #0D4F8B; color: white;" | Xylylene
! style="background: #0D4F8B; color: white;" | SO<sub>2</sub>
! style="background: #0D4F8B; color: white;"| IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
!rowspan ="3"|[[File:REACTANT 1 OPTMIN 3.LOG]]]
!rowspan ="3"|[[File:SO2 OPTMIN PM6.LOG]]
| [[File:3 DA IRC opt.log]]
| [[File:EX3 EXO P OPTMIN FINAL.LOG]]
|-
| Endo
| [[File:ENDO IRC 6.LOG]]
| [[File:ENDO_P_FINAL_OPTMIN.LOG]]
|-
| Cheletropic
| [[File:CHEL IRC.LOG]]
| [[File:CHEL FINALP2.LOG]]

|}

===Extra===

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Reaction type
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| [[File:YTSTSOPTTS_EXO.LOG]]
| Column 3, Row 2
| [[File:YTS_EXO_PRODUCT_OPTMIN.LOG]]
|-
| Endo
| [[File:YTSTSOPTTS ENDO.LOG]]
| Column 3, Row 2
| [[File:YTS ENDO PRODUCT OPTMIN.LOG]]
|-

|}

==References==

File:REACTANT 1 OPTMIN 3.LOG

2017-11-20T22:14:14Z

Yts15:

File:SO2 OPTMIN PM6.LOG

2017-11-20T22:13:17Z

Yts15:

Rep:Mod:TSYts15

2017-11-20T22:12:15Z

File:Yts extra reaction scheme.png

2017-11-20T21:56:59Z

Yts15:

Rep:Mod:TSYts15

2017-11-20T21:49:37Z

Yts15: /* Exercise 3: Diels-Alder vs Cheletropic */

== Introduction ==

<font color="#0000FF">'In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)''</font>

== Exercise 1: Reaction of Butadiene with Ethylene ==

<br />

[[File:Reaction scheme.png|thumb|center|500px|alt=''Figure 1. Reaction Scheme''|Fig. 1: ''Reaction Scheme of Butadiene with Ethylene in Exercise 1'']]

<br />

=== Optimization Result ===

{| class="wikitable"
|+Table 1. Optimization Result of Reactant, TS and Products at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT1_2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 80; vibration 2;rotate x -20; </script>
<uploadedFileContents>P_FINALOPT_2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

The ''Table 1'' shows the result of optimisation of reactants, TS and product at '''PM6 level''' respectively. Correct TS was further confirmed by '''frequency calculation''' and '''IRC'''.
<font color="#0000FF">ELABORATION''</font>

====Frequency====
[[File:Yts15 freq 1.PNG|thumb|none|1000px|alt=''Figure 2. Frequency Calculation of TS''|Fig. 2: ''Frequency Calculation of TS'']]

From Fig. 2, a '''negative frequency''' is shown in the final optimised TS. This indicates imaginary vibrational frequency associated with a TS which corresponds to the translational motion of carbon. At Gaussian, second derivative of the energy with respect to the nuclear position is calculated by the frequency. Hence, the first negative frequency indicates one negative second derivation, a saddle point, which is the highest point on the minimum energy path linking the reactants and products<ref>Houston, P. L. Chemical kinetics and reaction dynamics; Dover: Mineola, NY, 2006.</ref>. High frequency, greater than |100<sup>-1</sup>|, is consistent with this kind of molecule. As a result, this represents a correct TS is obtained from final optimisation . Additionally, this plays an important part in defining chemical reactions. One negative frequency also indicates the presence of single TS which illustrates a well-defined reaction profile and complete reaction.

====IRC====
[[File:YtsIRC final.PNG|thumb|none|500px|alt=''Figure 3. IRC of TS''|Fig. 3: ''IRC'']]

Transition state geometries can be connected to ground state geometries with an '''Intrinsic Reaction Coordination calculation (IRC)''' performed by Gaussian. In Fig 3., the downhill path from the transition is followed in '''forward direction'''. A well defined and asymmetric Free Energy Surface as shown in Fig. 3 confirms that TS is correctly optimised.

=== MO Analysis===
<font color="#0000FF">
Construct an MO diagram for the formation of the butadiene/ethene TS, including basic symmetry labels (symmetric/antisymmetric or s/a).For each of the reactants and the TS, open the .chk (checkpoint) file. Under the '''Edit''' menu, choose '''MOs''' and visualise the MOs. Include images (or '''[[Mod:Cheatsheet#MOs_with_Jmol|Jmol objects]]''') for each of the HOMO and LUMO of butadiene and ethene, and the four MOs these produce for the TS. Correlate these MOs with the ones in your MO diagram to show which orbitals interact.
</font>

MO diagram for the formation of butadiene/ethene TS is illustrated in Fig. 4 MO Diagram for the formation of Butadiene/ Ethene. Actual MOs are performed by Gaussian at Basis Set PM6. It is shown that TS LUMO +1 has energy lower than expected (''stabilisation'') and TS HOMO has energy higher than expected (''destabilisation''). Hence, this suggested that significant mixing between orbitals.

[[File:Yts MO 1 mix.png|thumb|none|600px|alt=''Figure 4. MO diagram for the formation of the Butadiene/Ethene TS''|Fig. 4: ''MO diagram for the formation of the butadiene/ethene TS'']]

{| class="wikitable"
|+Table 2a. HOMO and LUMO of Reactants, Butadiene and ethene
! style="background: #0D4F8B; color: white;" | Orbital type
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO11, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO6, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO12, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO7, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable"
|+Table 2b. Four MOs produced from reactants for TS
! style="background: #0D4F8B; color: white;" | HOMO-1
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | LUMO+1
|-
| <jmol>
<jmolApplet>
<title> MO 16, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO17, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO18, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO19, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<font color="#0000FF"> What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')?

'' Woodward and Hoffmann[6] ascribe endo addition to interaction of occupied orbitals with unoccupied orbitals, the endo transition state conformation being favored by orbital symmetry relative to the exo conformation. With the model of frontier orbitals, we have interaction of HOMOs (Highest Occupied Molecular Orbitals) with LUMOs (Lowest Unoccupied Molecular Orbitals). Those interactions are represented in figure 4. The main interactions that will form the bonds are shown by plain bold lines, the secondary interactions, responsible for the endo-exo selectivity, are shown by small squiggly lines. We do not know if the molecules approch so closely that the secondary interactions can be as important as shown in figure 1. ''

Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction and an antisymmetric-antisymmetric interaction.'''</font>

=== Bond Length Analysis ===

{| class="wikitable"
|+Table 3. Carbon Carbon bond length of Reactants, TS and Products; and Literature value
! style="background: #0D4F8B; color: white;" | Reactant
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" | Literature value
|-
| [[File:Yts Cbond length reactant.PNG|500px]]
| [[File:Yts Cbond length TS.PNG|300px]]
| [[File:Yts Cbond length P.PNG|300px]]
|<div style="text-align: center;">Van der Waals radius of the C atom: 1.7 Å <ref>Bondi, A. The Journal of Physical Chemistry 1964, 68 (3), 441–451.</ref><br />Typical sp<sup>3</sup> C-C bond length and sp<sup>2</sup> C=C bond lengths : 1.54 Å, 1.34 Å<ref>Fox, M. A.; Whitesell, J. K. Organische Chemie: Grundlagen, Mechanismen, bioorganische Anwendungen; Spektrum Akadem. Verl.: Heidelberg, 1995.</ref><br /> [[File:Yts cyclohexenelitlength.PNG|450px]]<br />Bond length of cyclohexene<ref>Chiang, J. F.; Bauer, S. H. Journal of the American Chemical Society 1969, 91 (8), 1898–1901.</ref><br /> </div>
|-
|}

Experimental carbon carbon bond length of cyclohexene is consistent with the literature value as shown in Table 3 which confirm correct structure of TS and Cyclohexene Product is obtained. Comparing the Van der Waals radius of C atom and the length of the partly formed C-C bonds in the TS, a much lower C-C bond length at TS indicates formation of bond. Typically, sp<sup>2</sup> C=C bond lengths is much shorter than sp<sup>3</sup> C-C bond length as shown in table 3 due to a higher bond order and hence, closer the Carbon atoms are.

As reaction proceed, bond length corresponds to different carbon atoms change which the result is shown in Table 4.

{| class="wikitable"
|+Table 4. Change of Bond Length as the reaction proceed
[[File:YtsIRC finallabel.PNG|thumb|center|400px|alt=''Figure 5. Labelled Carbon atoms in reactants''|Fig. 5: ''Labelled Carbon atoms in reactants'']]
|-
|[[File:Yts BL 1,4.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6a: ''Plot of change of Bond Length between C1 and C4'']]
|[[File:Yts BL 4,14.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6b: ''Plot of change of Bond Length between C4 and C14'']]
|[[File:Yts BL 14,12.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6c: ''Plot of change of Bond Length between C14 and C12'']]
|-
|[[File:Yts BL 12,10.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6d: ''Plot of change of Bond Length between C12 and C10'']]
|[[File:Yts BL 10,7.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6e: ''Plot of change of Bond Length between C10 and C7'']]
|[[File:Yts BL 7,1.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6f: ''Plot of change of Bond Length between C7 and C1'']]
|}

===Vibrational Analysis===

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

The vibration that corresponds to the reaction path at transition state is -949.15 cm<sup>-1</sup>. In the transition state of this reaction, the two forming bonds have the same lengths. Hence, this confirms the '''synchronous''' mechanism where two new bonds are formed simultaneously.

<jmol>
<jmolApplet>
<title> Vibrational Analysis of TS </title>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==

<br />

[[File:Yts ex2 reaction scheme.png|thumb|center|500px|alt=''Figure 7. Reaction Scheme''|Fig. 7: ''Reaction Scheme of Diels Alder reaction'']]

<br />

=== Optimisation Result ===

Table 5 shows the result of the Optimisation of reactants; endo and exo TSs. It was first optimised at PM6 method then a more accurate method, at B3LYP/6-31G(d) Basis Set

{| class="wikitable"
|+Table 5. Optimization Result of Reactant and Exo, Endo TS at PM6 and B3LYP/6-31G(d) Basis Set
! style="background: #0D4F8B; color: white;" | Basic Set
! style="background: #0D4F8B; color: white;" | Cyclohexadiene
! style="background: #0D4F8B; color: white;" | 1,3-Dioxole
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
| '''PM6'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 62; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN PM6 3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 30; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 22; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| '''B3LYP/6-31G(d)'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 18; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 24; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN B3LYP 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 34; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

===Frequency Analysis===

A correct TS is further confirmed by the frequency analysis. Only one negative frequency at Exo and Endo TS indicates a saddle point reached which confirms the correct TS obtained.
{| class="wikitable"
|+Table 6. Frequency Analysis of Exo and Endo TS and Products respectively at PM6 and B3LYP/6-31G(d) Basis Set
!
! style="background: #0D4F8B; color: white;" colspan="2"| Exo
! style="background: #0D4F8B; color: white;" colspan="2" | Endo
|-
|
! '''PM6'''
! '''B3LYP/6-31G(d)'''
! '''PM6'''
! '''B3LYP/6-31G(d)'''
|-
| '''TS'''
| [[File:Yts ex2exo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8a: ''Frequency Calculation of Exo TS at PM6'']]
| [[File:Yts ex2exo TS freqB3LYP.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8b: ''Frequency Calculation of Exo TS at B3LYP'']]
| [[File:Yts ex2endo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9a: ''Frequency Calculation of Endo TS at PM6'']]
| [[File:Yts ex2endo TS freqB3LYP 2.PNG|thumb|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9b:''Frequency Calculation of Endo TS at B3LYP'']]
|-
| '''Product'''
| [[File:Yts ex2 exo P PM6freq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10a: ''Frequency Calculation of Exo Product at PM6'']]
| [[File:Yts ex2 exo P B3LYPfreq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10b: ''Frequency Calculation of Exo Product at B3LYP'']]
| [[File:Yts ex2 endo P PM6freq.PNG|thumb|none|400px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11a: ''Frequency Calculation of Endo Product at PM6'']]
| [[File:Yts ex2 endo P B3LYPfreq.PNG|thumb|1000px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11b:''Frequency Calculation of Endo Product at B3LYP'']]
|}

=== MO Analysis ===

Figure 12 and 13 shows the MO digram for the Diels-Alder reaction (Exo and Endo) , which correlate with the actual MOs performed by Gaussian at B3LYP/6-31G(d) basis set.

{| class="wikitable"
|[[File:Yts ex2endo MO 2.png|thumb|none|600px|alt=''Figure 11. MO diagram for the Endo Diels-Alder reaction''|Fig. 12: ''MO diagram for the Exo Diels-Alder reaction'']]
|[[File:Yts ex2exo MO.png|thumb|none|600px|alt=''Figure 12. MO diagram for the Exo Diels-Alder reaction''|Fig. 13: ''MO diagram for the Endo Diels-Alder reaction'']]
|}

{| class="wikitable"
|+Table 6. HOMO and LUMO of Exo and Endo TS at '''B3LYP/6-31G(d)'''
! style="background: #0D4F8B; color: white;" =2'' | Orbital type
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
|HOMO-1
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO+1
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - ''Energy''' under '''Job Type''' - will yield an ordered list of MOs that you can use to start you off).

This reaction is an '''inverse demand DA reaction ''' since diene is less electron rich than dienophile in this reaction. Hence, the '''Frontier Molecular Orbitals ''' the '''LUMO of Cyclohexadiene '''(Antisymmetric) interact with the '''HOMO of 1,3-Dioxole, dienophile''', are closer in energy than that of HOMO of diene and LUMO of dienophile. As a result, they interact most strongly and form most energetically favourable bond formation. <ref> Fleming, I. Frontier orbitals and organic chemical reactions; Wiley: London, 2007.</ref>

=== Reaction Thermodynamics ===
{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Cyclohexadiene
! style="background: #0D4F8B; color: white;" " colspan="2"| 1,3-Dioxole
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.116878
| 306.863212
| −0.0522760
| −137.25064846
|0.138903
|364.689854
|0.137941
|362.164123
|0.037972
|99.6954936
|0.037807
|99.2622861
|-
| '''B3LYP/6-31G(d)'''
|−233.324375
|−612593.19323
|–267.068645
|–701188.78086
|–500.329165
|–1313614.3228
|–500.332147
|–1313622.152
|–500.417322
|–1313845.779
|−500.418691
|–1313849.3733
|}

{| class="wikitable"
|+Table 8. Activation Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>168
|<nowiki>-</nowiki>63.80491
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>163
|<nowiki>-</nowiki>67.39921
|}

<br/>
Table 8. shows the result of the Activation Barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

<br/>

'''Kinetic favourable''' of the products can be determined by the Activation Barrier. As shown in Table 8, Endo reaction pathway has a lower Activation energy and hence Endo product is more kinetically favourable. This can be further explained by '''secondary (non-bonding) orbital interaction''' in the endo TS HOMO as shown in Table 9. Secondary orbital interaction between diene and the dienophile substituent's π system lowers the energy of the endo TS and hence, lower activation barrier and the reaction proceed much faster towards endo-product. <ref>Alston, P. V.; Ottenbrite, R. M.; Cohen, T. The Journal of Organic Chemistry 1978, 43 (10), 1864–1867.</ref>As a result, '''endo product''' is more kinetically stable. On the other hand, there is no such interaction between Diene and the substituent in exo TS as shown in the HOMO of exo TS in table 9. Hence, there is no stabilisation of the exo Transistion state. Only primary (bonding) interaction present in the Exo-TS.

<br/>
Moreover, '''endo product''' is more '''thermodynamically favourable'''. Comparing the Gibbs free energy between Endo- product and Exo- product, more negative number is obtained at the Endo-product. Hence, this confirms that the endo-product is more thermodynamically stable. In fact, less sterically-hindered Exo-TS is expected to be more thermodynamically favourable. This unexpected result of Endo-Product being more more thermodynamic favourable of can be explained by Hammonds Postulate. Since this is an endothermic reaction (bond forming), according to Hammonds Postulate, it is expected that TS is more product like. As a consequence, stabilisation by secondary (non-bonding) orbital interaction will also apply to the endo-product.

{| class="wikitable"'
|+ '''Table 9. shows secondary orbital interactions or sterics on TS
! style="background: #0D4F8B; color: white;"| HOMO of Exo TS
! style="background: #0D4F8B; color: white;"|HOMO of Endo TS
|-
| <jmol>
<jmolApplet>
<title> Sterics only </title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> Secondary Orbital Interaction</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<br/>

As a result, it can be concluded that inverse electron demand Diels Alder reaction favours '''endo-Product''' in terms of '''thermodynamics''' and '''kinetic ''' argument.

<br/>

== Exercise 3: Diels-Alder vs Cheletropic ==

<br />
[[File:Yts ex3 reaction scheme.png|thumb|center|1000px|alt=''Figure X. Reaction Profile for different pathway''|Fig. 1: ''Reaction Profile of the Exo, Endo and Cheletropic pathway '']]
<br />

===Optimisation Result===

Table X. shows the optimisation result of the exo TS, endo TS and Cheletropic TS at PM6 Basis Set.

{| class="wikitable"
|+Table 11. Optimization Result of Exo, Endo and Cheletropic TS at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
! style="background: #0D4F8B; color: white;" | Cheletropic TS
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts_3_DA_TSOPT_exo.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>YtsCHEL_TS_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

===IRC Analysis===

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

The reaction coordinate for each path is visualise in the following animation with an IRC calculation.

<center>[[File:Yts ex3Endo IRC.gif]] </center>
<center>''Animation 1. IRC for Endothermic reaction pathway </center>

<center>[[File:Yts ex3Exo IRC.gif]] </center>
<center>''Animation 2. IRC for Exothermic reaction pathway </center>

<center>[[File:Yts ex3chel IRC.gif]] </center>
<center>''Animation 3. IRC for Cheletropic reaction pathway </center>

===Reaction Thermodynamics===

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" |Cheletropic TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Cheletropic Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
|0.092078
|241.750807
|0.090560
|237.765298
| 0.099062
|260.087301
| 0.021455
|56.3301068
|0.021706
|56.9891073
|−0.000002
|−0.0052510004
|}

Table 8. shows the result of the reaction barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>85.6
|<nowiki>-</nowiki>99.7
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>81.7
|<nowiki>-</nowiki>99.1
|-
| '''Cheletropic Pathway '''''
|<nowiki>+</nowiki>104.0
|<nowiki>-</nowiki>156.1
|}

<br />

[[File:Yts ex3 reactionprofile3.PNG|thumb|center|600px|alt=''Figure X. Reaction Profile for different pathway''|Fig. 1: ''Reaction Profile of the Exo, Endo and Cheletropic pathway '']]

<br />

== Extra ==

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. Table X, X+1 shows the result of the potential energy of reactants, TS and products; Activation energy and Reaction energy of of this Diels-Alder reaction.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
| 0.105053
|275.816673
| 0.102071
|267.9874309
| 0.067304
|176.7066655
| 0.065610
|172.2590681
|}

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>119.7
|<nowiki>+</nowiki>20.6
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>111.9
|<nowiki>+</nowiki>16.2
|}

If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

==Conclusion==

== Log Files ==

=== Exercise 1 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Product
|-
| PM6
| [[File:REACTANT1_2_OPTMIN.LOG]]
| [[File:REACTANT2_OPTMIN.LOG‎]]
| [[File:TS_2_OPTTS.LOG]]
| [[File:TS_2_IRC_out.log]]
| [[File:P_FINALOPT_2.LOG]]
|}

=== Exercise 2 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Exo-Products
! style="background: #0D4F8B; color: white;" | Endo-Products
|-
| PM6
!rowspan ="2" |[[File:Endo IRC output final.log]]<br/>[[File:EXO IRC 5.LOG]]<br/>
| [[File:Yts EXO P FINALOPTMIN 1.LOG]]
|[[File:Yts ENDO P OPTMIN PM6.LOG]]

|-
| B3LYP/6-31G(d)
| [[File:EXO P FINALOPTMIN B3LYP.LOG]]
| [[File:Yts ENDO P OPTMIN B3LYP.LOG]]
|}

=== Exercise 3 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | reaction
! style="background: #0D4F8B; color: white;"| Xylylene
! style="background: #0D4F8B; color: white;" | SO<sub>2</sub>
! style="background: #0D4F8B; color: white;"| IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
| Endo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
|
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|}

===Extra===

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Reaction type
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| [[File:YTSTSOPTTS_EXO.LOG]]
| Column 3, Row 2
| [[File:YTS_EXO_PRODUCT_OPTMIN.LOG]]
|-
| Endo
| [[File:YTSTSOPTTS ENDO.LOG]]
| Column 3, Row 2
| [[File:YTS ENDO PRODUCT OPTMIN.LOG]]
|-

|}

==References==

File:Yts ex3 reaction scheme.png

2017-11-20T21:48:28Z

Yts15:

Rep:Mod:TSYts15

2017-11-20T21:25:15Z

Yts15: /* Extra */

== Introduction ==

<font color="#0000FF">'In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)''</font>

== Exercise 1: Reaction of Butadiene with Ethylene ==

<br />

[[File:Reaction scheme.png|thumb|center|500px|alt=''Figure 1. Reaction Scheme''|Fig. 1: ''Reaction Scheme of Butadiene with Ethylene in Exercise 1'']]

<br />

=== Optimization Result ===

{| class="wikitable"
|+Table 1. Optimization Result of Reactant, TS and Products at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT1_2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 80; vibration 2;rotate x -20; </script>
<uploadedFileContents>P_FINALOPT_2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

The ''Table 1'' shows the result of optimisation of reactants, TS and product at '''PM6 level''' respectively. Correct TS was further confirmed by '''frequency calculation''' and '''IRC'''.
<font color="#0000FF">ELABORATION''</font>

====Frequency====
[[File:Yts15 freq 1.PNG|thumb|none|1000px|alt=''Figure 2. Frequency Calculation of TS''|Fig. 2: ''Frequency Calculation of TS'']]

From Fig. 2, a '''negative frequency''' is shown in the final optimised TS. This indicates imaginary vibrational frequency associated with a TS which corresponds to the translational motion of carbon. At Gaussian, second derivative of the energy with respect to the nuclear position is calculated by the frequency. Hence, the first negative frequency indicates one negative second derivation, a saddle point, which is the highest point on the minimum energy path linking the reactants and products<ref>Houston, P. L. Chemical kinetics and reaction dynamics; Dover: Mineola, NY, 2006.</ref>. High frequency, greater than |100<sup>-1</sup>|, is consistent with this kind of molecule. As a result, this represents a correct TS is obtained from final optimisation . Additionally, this plays an important part in defining chemical reactions. One negative frequency also indicates the presence of single TS which illustrates a well-defined reaction profile and complete reaction.

====IRC====
[[File:YtsIRC final.PNG|thumb|none|500px|alt=''Figure 3. IRC of TS''|Fig. 3: ''IRC'']]

Transition state geometries can be connected to ground state geometries with an '''Intrinsic Reaction Coordination calculation (IRC)''' performed by Gaussian. In Fig 3., the downhill path from the transition is followed in '''forward direction'''. A well defined and asymmetric Free Energy Surface as shown in Fig. 3 confirms that TS is correctly optimised.

=== MO Analysis===
<font color="#0000FF">
Construct an MO diagram for the formation of the butadiene/ethene TS, including basic symmetry labels (symmetric/antisymmetric or s/a).For each of the reactants and the TS, open the .chk (checkpoint) file. Under the '''Edit''' menu, choose '''MOs''' and visualise the MOs. Include images (or '''[[Mod:Cheatsheet#MOs_with_Jmol|Jmol objects]]''') for each of the HOMO and LUMO of butadiene and ethene, and the four MOs these produce for the TS. Correlate these MOs with the ones in your MO diagram to show which orbitals interact.
</font>

MO diagram for the formation of butadiene/ethene TS is illustrated in Fig. 4 MO Diagram for the formation of Butadiene/ Ethene. Actual MOs are performed by Gaussian at Basis Set PM6. It is shown that TS LUMO +1 has energy lower than expected (''stabilisation'') and TS HOMO has energy higher than expected (''destabilisation''). Hence, this suggested that significant mixing between orbitals.

[[File:Yts MO 1 mix.png|thumb|none|600px|alt=''Figure 4. MO diagram for the formation of the Butadiene/Ethene TS''|Fig. 4: ''MO diagram for the formation of the butadiene/ethene TS'']]

{| class="wikitable"
|+Table 2a. HOMO and LUMO of Reactants, Butadiene and ethene
! style="background: #0D4F8B; color: white;" | Orbital type
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO11, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO6, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO12, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO7, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable"
|+Table 2b. Four MOs produced from reactants for TS
! style="background: #0D4F8B; color: white;" | HOMO-1
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | LUMO+1
|-
| <jmol>
<jmolApplet>
<title> MO 16, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO17, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO18, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO19, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<font color="#0000FF"> What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')?

'' Woodward and Hoffmann[6] ascribe endo addition to interaction of occupied orbitals with unoccupied orbitals, the endo transition state conformation being favored by orbital symmetry relative to the exo conformation. With the model of frontier orbitals, we have interaction of HOMOs (Highest Occupied Molecular Orbitals) with LUMOs (Lowest Unoccupied Molecular Orbitals). Those interactions are represented in figure 4. The main interactions that will form the bonds are shown by plain bold lines, the secondary interactions, responsible for the endo-exo selectivity, are shown by small squiggly lines. We do not know if the molecules approch so closely that the secondary interactions can be as important as shown in figure 1. ''

Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction and an antisymmetric-antisymmetric interaction.'''</font>

=== Bond Length Analysis ===

{| class="wikitable"
|+Table 3. Carbon Carbon bond length of Reactants, TS and Products; and Literature value
! style="background: #0D4F8B; color: white;" | Reactant
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" | Literature value
|-
| [[File:Yts Cbond length reactant.PNG|500px]]
| [[File:Yts Cbond length TS.PNG|300px]]
| [[File:Yts Cbond length P.PNG|300px]]
|<div style="text-align: center;">Van der Waals radius of the C atom: 1.7 Å <ref>Bondi, A. The Journal of Physical Chemistry 1964, 68 (3), 441–451.</ref><br />Typical sp<sup>3</sup> C-C bond length and sp<sup>2</sup> C=C bond lengths : 1.54 Å, 1.34 Å<ref>Fox, M. A.; Whitesell, J. K. Organische Chemie: Grundlagen, Mechanismen, bioorganische Anwendungen; Spektrum Akadem. Verl.: Heidelberg, 1995.</ref><br /> [[File:Yts cyclohexenelitlength.PNG|450px]]<br />Bond length of cyclohexene<ref>Chiang, J. F.; Bauer, S. H. Journal of the American Chemical Society 1969, 91 (8), 1898–1901.</ref><br /> </div>
|-
|}

Experimental carbon carbon bond length of cyclohexene is consistent with the literature value as shown in Table 3 which confirm correct structure of TS and Cyclohexene Product is obtained. Comparing the Van der Waals radius of C atom and the length of the partly formed C-C bonds in the TS, a much lower C-C bond length at TS indicates formation of bond. Typically, sp<sup>2</sup> C=C bond lengths is much shorter than sp<sup>3</sup> C-C bond length as shown in table 3 due to a higher bond order and hence, closer the Carbon atoms are.

As reaction proceed, bond length corresponds to different carbon atoms change which the result is shown in Table 4.

{| class="wikitable"
|+Table 4. Change of Bond Length as the reaction proceed
[[File:YtsIRC finallabel.PNG|thumb|center|400px|alt=''Figure 5. Labelled Carbon atoms in reactants''|Fig. 5: ''Labelled Carbon atoms in reactants'']]
|-
|[[File:Yts BL 1,4.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6a: ''Plot of change of Bond Length between C1 and C4'']]
|[[File:Yts BL 4,14.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6b: ''Plot of change of Bond Length between C4 and C14'']]
|[[File:Yts BL 14,12.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6c: ''Plot of change of Bond Length between C14 and C12'']]
|-
|[[File:Yts BL 12,10.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6d: ''Plot of change of Bond Length between C12 and C10'']]
|[[File:Yts BL 10,7.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6e: ''Plot of change of Bond Length between C10 and C7'']]
|[[File:Yts BL 7,1.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6f: ''Plot of change of Bond Length between C7 and C1'']]
|}

===Vibrational Analysis===

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

The vibration that corresponds to the reaction path at transition state is -949.15 cm<sup>-1</sup>. In the transition state of this reaction, the two forming bonds have the same lengths. Hence, this confirms the '''synchronous''' mechanism where two new bonds are formed simultaneously.

<jmol>
<jmolApplet>
<title> Vibrational Analysis of TS </title>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==

<br />

[[File:Yts ex2 reaction scheme.png|thumb|center|500px|alt=''Figure 7. Reaction Scheme''|Fig. 7: ''Reaction Scheme of Diels Alder reaction'']]

<br />

=== Optimisation Result ===

Table 5 shows the result of the Optimisation of reactants; endo and exo TSs. It was first optimised at PM6 method then a more accurate method, at B3LYP/6-31G(d) Basis Set

{| class="wikitable"
|+Table 5. Optimization Result of Reactant and Exo, Endo TS at PM6 and B3LYP/6-31G(d) Basis Set
! style="background: #0D4F8B; color: white;" | Basic Set
! style="background: #0D4F8B; color: white;" | Cyclohexadiene
! style="background: #0D4F8B; color: white;" | 1,3-Dioxole
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
| '''PM6'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 62; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN PM6 3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 30; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 22; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| '''B3LYP/6-31G(d)'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 18; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 24; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN B3LYP 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 34; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

===Frequency Analysis===

A correct TS is further confirmed by the frequency analysis. Only one negative frequency at Exo and Endo TS indicates a saddle point reached which confirms the correct TS obtained.
{| class="wikitable"
|+Table 6. Frequency Analysis of Exo and Endo TS and Products respectively at PM6 and B3LYP/6-31G(d) Basis Set
!
! style="background: #0D4F8B; color: white;" colspan="2"| Exo
! style="background: #0D4F8B; color: white;" colspan="2" | Endo
|-
|
! '''PM6'''
! '''B3LYP/6-31G(d)'''
! '''PM6'''
! '''B3LYP/6-31G(d)'''
|-
| '''TS'''
| [[File:Yts ex2exo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8a: ''Frequency Calculation of Exo TS at PM6'']]
| [[File:Yts ex2exo TS freqB3LYP.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8b: ''Frequency Calculation of Exo TS at B3LYP'']]
| [[File:Yts ex2endo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9a: ''Frequency Calculation of Endo TS at PM6'']]
| [[File:Yts ex2endo TS freqB3LYP 2.PNG|thumb|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9b:''Frequency Calculation of Endo TS at B3LYP'']]
|-
| '''Product'''
| [[File:Yts ex2 exo P PM6freq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10a: ''Frequency Calculation of Exo Product at PM6'']]
| [[File:Yts ex2 exo P B3LYPfreq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10b: ''Frequency Calculation of Exo Product at B3LYP'']]
| [[File:Yts ex2 endo P PM6freq.PNG|thumb|none|400px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11a: ''Frequency Calculation of Endo Product at PM6'']]
| [[File:Yts ex2 endo P B3LYPfreq.PNG|thumb|1000px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11b:''Frequency Calculation of Endo Product at B3LYP'']]
|}

=== MO Analysis ===

Figure 12 and 13 shows the MO digram for the Diels-Alder reaction (Exo and Endo) , which correlate with the actual MOs performed by Gaussian at B3LYP/6-31G(d) basis set.

{| class="wikitable"
|[[File:Yts ex2endo MO 2.png|thumb|none|600px|alt=''Figure 11. MO diagram for the Endo Diels-Alder reaction''|Fig. 12: ''MO diagram for the Exo Diels-Alder reaction'']]
|[[File:Yts ex2exo MO.png|thumb|none|600px|alt=''Figure 12. MO diagram for the Exo Diels-Alder reaction''|Fig. 13: ''MO diagram for the Endo Diels-Alder reaction'']]
|}

{| class="wikitable"
|+Table 6. HOMO and LUMO of Exo and Endo TS at '''B3LYP/6-31G(d)'''
! style="background: #0D4F8B; color: white;" =2'' | Orbital type
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
|HOMO-1
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO+1
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - ''Energy''' under '''Job Type''' - will yield an ordered list of MOs that you can use to start you off).

This reaction is an '''inverse demand DA reaction ''' since diene is less electron rich than dienophile in this reaction. Hence, the '''Frontier Molecular Orbitals ''' the '''LUMO of Cyclohexadiene '''(Antisymmetric) interact with the '''HOMO of 1,3-Dioxole, dienophile''', are closer in energy than that of HOMO of diene and LUMO of dienophile. As a result, they interact most strongly and form most energetically favourable bond formation. <ref> Fleming, I. Frontier orbitals and organic chemical reactions; Wiley: London, 2007.</ref>

=== Reaction Thermodynamics ===
{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Cyclohexadiene
! style="background: #0D4F8B; color: white;" " colspan="2"| 1,3-Dioxole
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.116878
| 306.863212
| −0.0522760
| −137.25064846
|0.138903
|364.689854
|0.137941
|362.164123
|0.037972
|99.6954936
|0.037807
|99.2622861
|-
| '''B3LYP/6-31G(d)'''
|−233.324375
|−612593.19323
|–267.068645
|–701188.78086
|–500.329165
|–1313614.3228
|–500.332147
|–1313622.152
|–500.417322
|–1313845.779
|−500.418691
|–1313849.3733
|}

{| class="wikitable"
|+Table 8. Activation Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>168
|<nowiki>-</nowiki>63.80491
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>163
|<nowiki>-</nowiki>67.39921
|}

<br/>
Table 8. shows the result of the Activation Barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

<br/>

'''Kinetic favourable''' of the products can be determined by the Activation Barrier. As shown in Table 8, Endo reaction pathway has a lower Activation energy and hence Endo product is more kinetically favourable. This can be further explained by '''secondary (non-bonding) orbital interaction''' in the endo TS HOMO as shown in Table 9. Secondary orbital interaction between diene and the dienophile substituent's π system lowers the energy of the endo TS and hence, lower activation barrier and the reaction proceed much faster towards endo-product. <ref>Alston, P. V.; Ottenbrite, R. M.; Cohen, T. The Journal of Organic Chemistry 1978, 43 (10), 1864–1867.</ref>As a result, '''endo product''' is more kinetically stable. On the other hand, there is no such interaction between Diene and the substituent in exo TS as shown in the HOMO of exo TS in table 9. Hence, there is no stabilisation of the exo Transistion state. Only primary (bonding) interaction present in the Exo-TS.

<br/>
Moreover, '''endo product''' is more '''thermodynamically favourable'''. Comparing the Gibbs free energy between Endo- product and Exo- product, more negative number is obtained at the Endo-product. Hence, this confirms that the endo-product is more thermodynamically stable. In fact, less sterically-hindered Exo-TS is expected to be more thermodynamically favourable. This unexpected result of Endo-Product being more more thermodynamic favourable of can be explained by Hammonds Postulate. Since this is an endothermic reaction (bond forming), according to Hammonds Postulate, it is expected that TS is more product like. As a consequence, stabilisation by secondary (non-bonding) orbital interaction will also apply to the endo-product.

{| class="wikitable"'
|+ '''Table 9. shows secondary orbital interactions or sterics on TS
! style="background: #0D4F8B; color: white;"| HOMO of Exo TS
! style="background: #0D4F8B; color: white;"|HOMO of Endo TS
|-
| <jmol>
<jmolApplet>
<title> Sterics only </title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> Secondary Orbital Interaction</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<br/>

As a result, it can be concluded that inverse electron demand Diels Alder reaction favours '''endo-Product''' in terms of '''thermodynamics''' and '''kinetic ''' argument.

<br/>

== Exercise 3: Diels-Alder vs Cheletropic ==

See the '''[[Mod:ts_tutorial#Xylylene-SO2_Diels_Alder_Cycloaddition|o-Xylylene-SO2 Cycloaddition]]''' section in the tutorial as a guide.

<br />

[[File:Ts_tutorial_xylylene_so2_scheme.png|600px]]

<br />

===Optimisation Result===

Table X. shows the optimisation result of the exo TS, endo TS and Cheletropic TS at PM6 Basis Set.

{| class="wikitable"
|+Table 11. Optimization Result of Exo, Endo and Cheletropic TS at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
! style="background: #0D4F8B; color: white;" | Cheletropic TS
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts_3_DA_TSOPT_exo.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>YtsCHEL_TS_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

===IRC Analysis===

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

The reaction coordinate for each path is visualise in the following animation with an IRC calculation.

<center>[[File:Yts ex3Endo IRC.gif]] </center>
<center>''Animation 1. IRC for Endothermic reaction pathway </center>

<center>[[File:Yts ex3Exo IRC.gif]] </center>
<center>''Animation 2. IRC for Exothermic reaction pathway </center>

<center>[[File:Yts ex3chel IRC.gif]] </center>
<center>''Animation 3. IRC for Cheletropic reaction pathway </center>

===Reaction Thermodynamics===

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" |Cheletropic TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Cheletropic Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
|0.092078
|241.750807
|0.090560
|237.765298
| 0.099062
|260.087301
| 0.021455
|56.3301068
|0.021706
|56.9891073
|−0.000002
|−0.0052510004
|}

Table 8. shows the result of the reaction barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>85.6
|<nowiki>-</nowiki>99.7
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>81.7
|<nowiki>-</nowiki>99.1
|-
| '''Cheletropic Pathway '''''
|<nowiki>+</nowiki>104.0
|<nowiki>-</nowiki>156.1
|}

<br />

[[File:Yts ex3 reactionprofile3.PNG|thumb|center|600px|alt=''Figure X. Reaction Profile for different pathway''|Fig. 1: ''Reaction Profile of the Exo, Endo and Cheletropic pathway '']]

<br />

== Extra ==

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. Table X, X+1 shows the result of the potential energy of reactants, TS and products; Activation energy and Reaction energy of of this Diels-Alder reaction.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
| 0.105053
|275.816673
| 0.102071
|267.9874309
| 0.067304
|176.7066655
| 0.065610
|172.2590681
|}

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>119.7
|<nowiki>+</nowiki>20.6
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>111.9
|<nowiki>+</nowiki>16.2
|}

If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

==Conclusion==

== Log Files ==

=== Exercise 1 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Product
|-
| PM6
| [[File:REACTANT1_2_OPTMIN.LOG]]
| [[File:REACTANT2_OPTMIN.LOG‎]]
| [[File:TS_2_OPTTS.LOG]]
| [[File:TS_2_IRC_out.log]]
| [[File:P_FINALOPT_2.LOG]]
|}

=== Exercise 2 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Exo-Products
! style="background: #0D4F8B; color: white;" | Endo-Products
|-
| PM6
!rowspan ="2" |[[File:Endo IRC output final.log]]<br/>[[File:EXO IRC 5.LOG]]<br/>
| [[File:Yts EXO P FINALOPTMIN 1.LOG]]
|[[File:Yts ENDO P OPTMIN PM6.LOG]]

|-
| B3LYP/6-31G(d)
| [[File:EXO P FINALOPTMIN B3LYP.LOG]]
| [[File:Yts ENDO P OPTMIN B3LYP.LOG]]
|}

=== Exercise 3 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | reaction
! style="background: #0D4F8B; color: white;"| Xylylene
! style="background: #0D4F8B; color: white;" | SO<sub>2</sub>
! style="background: #0D4F8B; color: white;"| IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
| Endo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
|
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|}

===Extra===

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Reaction type
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| [[File:YTSTSOPTTS_EXO.LOG]]
| Column 3, Row 2
| [[File:YTS_EXO_PRODUCT_OPTMIN.LOG]]
|-
| Endo
| [[File:YTSTSOPTTS ENDO.LOG]]
| Column 3, Row 2
| [[File:YTS ENDO PRODUCT OPTMIN.LOG]]
|-

|}

==References==

Rep:Mod:TSYts15

2017-11-20T21:11:39Z

Yts15: /* Reaction Thermodynamics */

== Introduction ==

<font color="#0000FF">'In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)''</font>

== Exercise 1: Reaction of Butadiene with Ethylene ==

<br />

[[File:Reaction scheme.png|thumb|center|500px|alt=''Figure 1. Reaction Scheme''|Fig. 1: ''Reaction Scheme of Butadiene with Ethylene in Exercise 1'']]

<br />

=== Optimization Result ===

{| class="wikitable"
|+Table 1. Optimization Result of Reactant, TS and Products at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT1_2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 80; vibration 2;rotate x -20; </script>
<uploadedFileContents>P_FINALOPT_2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

The ''Table 1'' shows the result of optimisation of reactants, TS and product at '''PM6 level''' respectively. Correct TS was further confirmed by '''frequency calculation''' and '''IRC'''.
<font color="#0000FF">ELABORATION''</font>

====Frequency====
[[File:Yts15 freq 1.PNG|thumb|none|1000px|alt=''Figure 2. Frequency Calculation of TS''|Fig. 2: ''Frequency Calculation of TS'']]

From Fig. 2, a '''negative frequency''' is shown in the final optimised TS. This indicates imaginary vibrational frequency associated with a TS which corresponds to the translational motion of carbon. At Gaussian, second derivative of the energy with respect to the nuclear position is calculated by the frequency. Hence, the first negative frequency indicates one negative second derivation, a saddle point, which is the highest point on the minimum energy path linking the reactants and products<ref>Houston, P. L. Chemical kinetics and reaction dynamics; Dover: Mineola, NY, 2006.</ref>. High frequency, greater than |100<sup>-1</sup>|, is consistent with this kind of molecule. As a result, this represents a correct TS is obtained from final optimisation . Additionally, this plays an important part in defining chemical reactions. One negative frequency also indicates the presence of single TS which illustrates a well-defined reaction profile and complete reaction.

====IRC====
[[File:YtsIRC final.PNG|thumb|none|500px|alt=''Figure 3. IRC of TS''|Fig. 3: ''IRC'']]

Transition state geometries can be connected to ground state geometries with an '''Intrinsic Reaction Coordination calculation (IRC)''' performed by Gaussian. In Fig 3., the downhill path from the transition is followed in '''forward direction'''. A well defined and asymmetric Free Energy Surface as shown in Fig. 3 confirms that TS is correctly optimised.

=== MO Analysis===
<font color="#0000FF">
Construct an MO diagram for the formation of the butadiene/ethene TS, including basic symmetry labels (symmetric/antisymmetric or s/a).For each of the reactants and the TS, open the .chk (checkpoint) file. Under the '''Edit''' menu, choose '''MOs''' and visualise the MOs. Include images (or '''[[Mod:Cheatsheet#MOs_with_Jmol|Jmol objects]]''') for each of the HOMO and LUMO of butadiene and ethene, and the four MOs these produce for the TS. Correlate these MOs with the ones in your MO diagram to show which orbitals interact.
</font>

MO diagram for the formation of butadiene/ethene TS is illustrated in Fig. 4 MO Diagram for the formation of Butadiene/ Ethene. Actual MOs are performed by Gaussian at Basis Set PM6. It is shown that TS LUMO +1 has energy lower than expected (''stabilisation'') and TS HOMO has energy higher than expected (''destabilisation''). Hence, this suggested that significant mixing between orbitals.

[[File:Yts MO 1 mix.png|thumb|none|600px|alt=''Figure 4. MO diagram for the formation of the Butadiene/Ethene TS''|Fig. 4: ''MO diagram for the formation of the butadiene/ethene TS'']]

{| class="wikitable"
|+Table 2a. HOMO and LUMO of Reactants, Butadiene and ethene
! style="background: #0D4F8B; color: white;" | Orbital type
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO11, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO6, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO12, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO7, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable"
|+Table 2b. Four MOs produced from reactants for TS
! style="background: #0D4F8B; color: white;" | HOMO-1
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | LUMO+1
|-
| <jmol>
<jmolApplet>
<title> MO 16, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO17, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO18, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO19, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<font color="#0000FF"> What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')?

'' Woodward and Hoffmann[6] ascribe endo addition to interaction of occupied orbitals with unoccupied orbitals, the endo transition state conformation being favored by orbital symmetry relative to the exo conformation. With the model of frontier orbitals, we have interaction of HOMOs (Highest Occupied Molecular Orbitals) with LUMOs (Lowest Unoccupied Molecular Orbitals). Those interactions are represented in figure 4. The main interactions that will form the bonds are shown by plain bold lines, the secondary interactions, responsible for the endo-exo selectivity, are shown by small squiggly lines. We do not know if the molecules approch so closely that the secondary interactions can be as important as shown in figure 1. ''

Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction and an antisymmetric-antisymmetric interaction.'''</font>

=== Bond Length Analysis ===

{| class="wikitable"
|+Table 3. Carbon Carbon bond length of Reactants, TS and Products; and Literature value
! style="background: #0D4F8B; color: white;" | Reactant
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" | Literature value
|-
| [[File:Yts Cbond length reactant.PNG|500px]]
| [[File:Yts Cbond length TS.PNG|300px]]
| [[File:Yts Cbond length P.PNG|300px]]
|<div style="text-align: center;">Van der Waals radius of the C atom: 1.7 Å <ref>Bondi, A. The Journal of Physical Chemistry 1964, 68 (3), 441–451.</ref><br />Typical sp<sup>3</sup> C-C bond length and sp<sup>2</sup> C=C bond lengths : 1.54 Å, 1.34 Å<ref>Fox, M. A.; Whitesell, J. K. Organische Chemie: Grundlagen, Mechanismen, bioorganische Anwendungen; Spektrum Akadem. Verl.: Heidelberg, 1995.</ref><br /> [[File:Yts cyclohexenelitlength.PNG|450px]]<br />Bond length of cyclohexene<ref>Chiang, J. F.; Bauer, S. H. Journal of the American Chemical Society 1969, 91 (8), 1898–1901.</ref><br /> </div>
|-
|}

Experimental carbon carbon bond length of cyclohexene is consistent with the literature value as shown in Table 3 which confirm correct structure of TS and Cyclohexene Product is obtained. Comparing the Van der Waals radius of C atom and the length of the partly formed C-C bonds in the TS, a much lower C-C bond length at TS indicates formation of bond. Typically, sp<sup>2</sup> C=C bond lengths is much shorter than sp<sup>3</sup> C-C bond length as shown in table 3 due to a higher bond order and hence, closer the Carbon atoms are.

As reaction proceed, bond length corresponds to different carbon atoms change which the result is shown in Table 4.

{| class="wikitable"
|+Table 4. Change of Bond Length as the reaction proceed
[[File:YtsIRC finallabel.PNG|thumb|center|400px|alt=''Figure 5. Labelled Carbon atoms in reactants''|Fig. 5: ''Labelled Carbon atoms in reactants'']]
|-
|[[File:Yts BL 1,4.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6a: ''Plot of change of Bond Length between C1 and C4'']]
|[[File:Yts BL 4,14.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6b: ''Plot of change of Bond Length between C4 and C14'']]
|[[File:Yts BL 14,12.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6c: ''Plot of change of Bond Length between C14 and C12'']]
|-
|[[File:Yts BL 12,10.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6d: ''Plot of change of Bond Length between C12 and C10'']]
|[[File:Yts BL 10,7.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6e: ''Plot of change of Bond Length between C10 and C7'']]
|[[File:Yts BL 7,1.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6f: ''Plot of change of Bond Length between C7 and C1'']]
|}

===Vibrational Analysis===

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

The vibration that corresponds to the reaction path at transition state is -949.15 cm<sup>-1</sup>. In the transition state of this reaction, the two forming bonds have the same lengths. Hence, this confirms the '''synchronous''' mechanism where two new bonds are formed simultaneously.

<jmol>
<jmolApplet>
<title> Vibrational Analysis of TS </title>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==

<br />

[[File:Yts ex2 reaction scheme.png|thumb|center|500px|alt=''Figure 7. Reaction Scheme''|Fig. 7: ''Reaction Scheme of Diels Alder reaction'']]

<br />

=== Optimisation Result ===

Table 5 shows the result of the Optimisation of reactants; endo and exo TSs. It was first optimised at PM6 method then a more accurate method, at B3LYP/6-31G(d) Basis Set

{| class="wikitable"
|+Table 5. Optimization Result of Reactant and Exo, Endo TS at PM6 and B3LYP/6-31G(d) Basis Set
! style="background: #0D4F8B; color: white;" | Basic Set
! style="background: #0D4F8B; color: white;" | Cyclohexadiene
! style="background: #0D4F8B; color: white;" | 1,3-Dioxole
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
| '''PM6'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 62; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN PM6 3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 30; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 22; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| '''B3LYP/6-31G(d)'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 18; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 24; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN B3LYP 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 34; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

===Frequency Analysis===

A correct TS is further confirmed by the frequency analysis. Only one negative frequency at Exo and Endo TS indicates a saddle point reached which confirms the correct TS obtained.
{| class="wikitable"
|+Table 6. Frequency Analysis of Exo and Endo TS and Products respectively at PM6 and B3LYP/6-31G(d) Basis Set
!
! style="background: #0D4F8B; color: white;" colspan="2"| Exo
! style="background: #0D4F8B; color: white;" colspan="2" | Endo
|-
|
! '''PM6'''
! '''B3LYP/6-31G(d)'''
! '''PM6'''
! '''B3LYP/6-31G(d)'''
|-
| '''TS'''
| [[File:Yts ex2exo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8a: ''Frequency Calculation of Exo TS at PM6'']]
| [[File:Yts ex2exo TS freqB3LYP.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8b: ''Frequency Calculation of Exo TS at B3LYP'']]
| [[File:Yts ex2endo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9a: ''Frequency Calculation of Endo TS at PM6'']]
| [[File:Yts ex2endo TS freqB3LYP 2.PNG|thumb|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9b:''Frequency Calculation of Endo TS at B3LYP'']]
|-
| '''Product'''
| [[File:Yts ex2 exo P PM6freq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10a: ''Frequency Calculation of Exo Product at PM6'']]
| [[File:Yts ex2 exo P B3LYPfreq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10b: ''Frequency Calculation of Exo Product at B3LYP'']]
| [[File:Yts ex2 endo P PM6freq.PNG|thumb|none|400px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11a: ''Frequency Calculation of Endo Product at PM6'']]
| [[File:Yts ex2 endo P B3LYPfreq.PNG|thumb|1000px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11b:''Frequency Calculation of Endo Product at B3LYP'']]
|}

=== MO Analysis ===

Figure 12 and 13 shows the MO digram for the Diels-Alder reaction (Exo and Endo) , which correlate with the actual MOs performed by Gaussian at B3LYP/6-31G(d) basis set.

{| class="wikitable"
|[[File:Yts ex2endo MO 2.png|thumb|none|600px|alt=''Figure 11. MO diagram for the Endo Diels-Alder reaction''|Fig. 12: ''MO diagram for the Exo Diels-Alder reaction'']]
|[[File:Yts ex2exo MO.png|thumb|none|600px|alt=''Figure 12. MO diagram for the Exo Diels-Alder reaction''|Fig. 13: ''MO diagram for the Endo Diels-Alder reaction'']]
|}

{| class="wikitable"
|+Table 6. HOMO and LUMO of Exo and Endo TS at '''B3LYP/6-31G(d)'''
! style="background: #0D4F8B; color: white;" =2'' | Orbital type
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
|HOMO-1
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO+1
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - ''Energy''' under '''Job Type''' - will yield an ordered list of MOs that you can use to start you off).

This reaction is an '''inverse demand DA reaction ''' since diene is less electron rich than dienophile in this reaction. Hence, the '''Frontier Molecular Orbitals ''' the '''LUMO of Cyclohexadiene '''(Antisymmetric) interact with the '''HOMO of 1,3-Dioxole, dienophile''', are closer in energy than that of HOMO of diene and LUMO of dienophile. As a result, they interact most strongly and form most energetically favourable bond formation. <ref> Fleming, I. Frontier orbitals and organic chemical reactions; Wiley: London, 2007.</ref>

=== Reaction Thermodynamics ===
{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Cyclohexadiene
! style="background: #0D4F8B; color: white;" " colspan="2"| 1,3-Dioxole
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.116878
| 306.863212
| −0.0522760
| −137.25064846
|0.138903
|364.689854
|0.137941
|362.164123
|0.037972
|99.6954936
|0.037807
|99.2622861
|-
| '''B3LYP/6-31G(d)'''
|−233.324375
|−612593.19323
|–267.068645
|–701188.78086
|–500.329165
|–1313614.3228
|–500.332147
|–1313622.152
|–500.417322
|–1313845.779
|−500.418691
|–1313849.3733
|}

{| class="wikitable"
|+Table 8. Activation Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>168
|<nowiki>-</nowiki>63.80491
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>163
|<nowiki>-</nowiki>67.39921
|}

<br/>
Table 8. shows the result of the Activation Barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

<br/>

'''Kinetic favourable''' of the products can be determined by the Activation Barrier. As shown in Table 8, Endo reaction pathway has a lower Activation energy and hence Endo product is more kinetically favourable. This can be further explained by '''secondary (non-bonding) orbital interaction''' in the endo TS HOMO as shown in Table 9. Secondary orbital interaction between diene and the dienophile substituent's π system lowers the energy of the endo TS and hence, lower activation barrier and the reaction proceed much faster towards endo-product. <ref>Alston, P. V.; Ottenbrite, R. M.; Cohen, T. The Journal of Organic Chemistry 1978, 43 (10), 1864–1867.</ref>As a result, '''endo product''' is more kinetically stable. On the other hand, there is no such interaction between Diene and the substituent in exo TS as shown in the HOMO of exo TS in table 9. Hence, there is no stabilisation of the exo Transistion state. Only primary (bonding) interaction present in the Exo-TS.

<br/>
Moreover, '''endo product''' is more '''thermodynamically favourable'''. Comparing the Gibbs free energy between Endo- product and Exo- product, more negative number is obtained at the Endo-product. Hence, this confirms that the endo-product is more thermodynamically stable. In fact, less sterically-hindered Exo-TS is expected to be more thermodynamically favourable. This unexpected result of Endo-Product being more more thermodynamic favourable of can be explained by Hammonds Postulate. Since this is an endothermic reaction (bond forming), according to Hammonds Postulate, it is expected that TS is more product like. As a consequence, stabilisation by secondary (non-bonding) orbital interaction will also apply to the endo-product.

{| class="wikitable"'
|+ '''Table 9. shows secondary orbital interactions or sterics on TS
! style="background: #0D4F8B; color: white;"| HOMO of Exo TS
! style="background: #0D4F8B; color: white;"|HOMO of Endo TS
|-
| <jmol>
<jmolApplet>
<title> Sterics only </title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> Secondary Orbital Interaction</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<br/>

As a result, it can be concluded that inverse electron demand Diels Alder reaction favours '''endo-Product''' in terms of '''thermodynamics''' and '''kinetic ''' argument.

<br/>

== Exercise 3: Diels-Alder vs Cheletropic ==

See the '''[[Mod:ts_tutorial#Xylylene-SO2_Diels_Alder_Cycloaddition|o-Xylylene-SO2 Cycloaddition]]''' section in the tutorial as a guide.

<br />

[[File:Ts_tutorial_xylylene_so2_scheme.png|600px]]

<br />

===Optimisation Result===

Table X. shows the optimisation result of the exo TS, endo TS and Cheletropic TS at PM6 Basis Set.

{| class="wikitable"
|+Table 11. Optimization Result of Exo, Endo and Cheletropic TS at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
! style="background: #0D4F8B; color: white;" | Cheletropic TS
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts_3_DA_TSOPT_exo.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>YtsCHEL_TS_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

===IRC Analysis===

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

The reaction coordinate for each path is visualise in the following animation with an IRC calculation.

<center>[[File:Yts ex3Endo IRC.gif]] </center>
<center>''Animation 1. IRC for Endothermic reaction pathway </center>

<center>[[File:Yts ex3Exo IRC.gif]] </center>
<center>''Animation 2. IRC for Exothermic reaction pathway </center>

<center>[[File:Yts ex3chel IRC.gif]] </center>
<center>''Animation 3. IRC for Cheletropic reaction pathway </center>

===Reaction Thermodynamics===

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" |Cheletropic TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Cheletropic Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
|0.092078
|241.750807
|0.090560
|237.765298
| 0.099062
|260.087301
| 0.021455
|56.3301068
|0.021706
|56.9891073
|−0.000002
|−0.0052510004
|}

Table 8. shows the result of the reaction barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>85.6
|<nowiki>-</nowiki>99.7
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>81.7
|<nowiki>-</nowiki>99.1
|-
| '''Cheletropic Pathway '''''
|<nowiki>+</nowiki>104.0
|<nowiki>-</nowiki>156.1
|}

<br />

[[File:Yts ex3 reactionprofile3.PNG|thumb|center|600px|alt=''Figure X. Reaction Profile for different pathway''|Fig. 1: ''Reaction Profile of the Exo, Endo and Cheletropic pathway '']]

<br />

== Extra ==

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. Table X, X+1 shows the result of the potential energy of reactants, TS and products; Activation energy and Reaction energy of of this Diels-Alder reaction.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
|5
|6
|7
|8
| 9
|10
|11
|12
|}

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>85.6
|<nowiki>-</nowiki>99.7
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>81.7
|<nowiki>-</nowiki>99.1
|-
| '''Cheletropic Pathway '''''
|<nowiki>+</nowiki>104.0
|<nowiki>-</nowiki>156.1
|}

If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

==Conclusion==

== Log Files ==

=== Exercise 1 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Product
|-
| PM6
| [[File:REACTANT1_2_OPTMIN.LOG]]
| [[File:REACTANT2_OPTMIN.LOG‎]]
| [[File:TS_2_OPTTS.LOG]]
| [[File:TS_2_IRC_out.log]]
| [[File:P_FINALOPT_2.LOG]]
|}

=== Exercise 2 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Exo-Products
! style="background: #0D4F8B; color: white;" | Endo-Products
|-
| PM6
!rowspan ="2" |[[File:Endo IRC output final.log]]<br/>[[File:EXO IRC 5.LOG]]<br/>
| [[File:Yts EXO P FINALOPTMIN 1.LOG]]
|[[File:Yts ENDO P OPTMIN PM6.LOG]]

|-
| B3LYP/6-31G(d)
| [[File:EXO P FINALOPTMIN B3LYP.LOG]]
| [[File:Yts ENDO P OPTMIN B3LYP.LOG]]
|}

=== Exercise 3 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | reaction
! style="background: #0D4F8B; color: white;"| Xylylene
! style="background: #0D4F8B; color: white;" | SO<sub>2</sub>
! style="background: #0D4F8B; color: white;"| IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
| Endo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
|
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|}

===Extra===

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Reaction type
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| [[File:YTSTSOPTTS_EXO.LOG]]
| Column 3, Row 2
| [[File:YTS_EXO_PRODUCT_OPTMIN.LOG]]
|-
| Endo
| [[File:YTSTSOPTTS ENDO.LOG]]
| Column 3, Row 2
| [[File:YTS ENDO PRODUCT OPTMIN.LOG]]
|-

|}

==References==

Rep:Mod:TSYts15

2017-11-20T21:10:17Z

Yts15: /* Extra */

== Introduction ==

<font color="#0000FF">'In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)''</font>

== Exercise 1: Reaction of Butadiene with Ethylene ==

<br />

[[File:Reaction scheme.png|thumb|center|500px|alt=''Figure 1. Reaction Scheme''|Fig. 1: ''Reaction Scheme of Butadiene with Ethylene in Exercise 1'']]

<br />

=== Optimization Result ===

{| class="wikitable"
|+Table 1. Optimization Result of Reactant, TS and Products at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT1_2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 80; vibration 2;rotate x -20; </script>
<uploadedFileContents>P_FINALOPT_2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

The ''Table 1'' shows the result of optimisation of reactants, TS and product at '''PM6 level''' respectively. Correct TS was further confirmed by '''frequency calculation''' and '''IRC'''.
<font color="#0000FF">ELABORATION''</font>

====Frequency====
[[File:Yts15 freq 1.PNG|thumb|none|1000px|alt=''Figure 2. Frequency Calculation of TS''|Fig. 2: ''Frequency Calculation of TS'']]

From Fig. 2, a '''negative frequency''' is shown in the final optimised TS. This indicates imaginary vibrational frequency associated with a TS which corresponds to the translational motion of carbon. At Gaussian, second derivative of the energy with respect to the nuclear position is calculated by the frequency. Hence, the first negative frequency indicates one negative second derivation, a saddle point, which is the highest point on the minimum energy path linking the reactants and products<ref>Houston, P. L. Chemical kinetics and reaction dynamics; Dover: Mineola, NY, 2006.</ref>. High frequency, greater than |100<sup>-1</sup>|, is consistent with this kind of molecule. As a result, this represents a correct TS is obtained from final optimisation . Additionally, this plays an important part in defining chemical reactions. One negative frequency also indicates the presence of single TS which illustrates a well-defined reaction profile and complete reaction.

====IRC====
[[File:YtsIRC final.PNG|thumb|none|500px|alt=''Figure 3. IRC of TS''|Fig. 3: ''IRC'']]

Transition state geometries can be connected to ground state geometries with an '''Intrinsic Reaction Coordination calculation (IRC)''' performed by Gaussian. In Fig 3., the downhill path from the transition is followed in '''forward direction'''. A well defined and asymmetric Free Energy Surface as shown in Fig. 3 confirms that TS is correctly optimised.

=== MO Analysis===
<font color="#0000FF">
Construct an MO diagram for the formation of the butadiene/ethene TS, including basic symmetry labels (symmetric/antisymmetric or s/a).For each of the reactants and the TS, open the .chk (checkpoint) file. Under the '''Edit''' menu, choose '''MOs''' and visualise the MOs. Include images (or '''[[Mod:Cheatsheet#MOs_with_Jmol|Jmol objects]]''') for each of the HOMO and LUMO of butadiene and ethene, and the four MOs these produce for the TS. Correlate these MOs with the ones in your MO diagram to show which orbitals interact.
</font>

MO diagram for the formation of butadiene/ethene TS is illustrated in Fig. 4 MO Diagram for the formation of Butadiene/ Ethene. Actual MOs are performed by Gaussian at Basis Set PM6. It is shown that TS LUMO +1 has energy lower than expected (''stabilisation'') and TS HOMO has energy higher than expected (''destabilisation''). Hence, this suggested that significant mixing between orbitals.

[[File:Yts MO 1 mix.png|thumb|none|600px|alt=''Figure 4. MO diagram for the formation of the Butadiene/Ethene TS''|Fig. 4: ''MO diagram for the formation of the butadiene/ethene TS'']]

{| class="wikitable"
|+Table 2a. HOMO and LUMO of Reactants, Butadiene and ethene
! style="background: #0D4F8B; color: white;" | Orbital type
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO11, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO6, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO12, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO7, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable"
|+Table 2b. Four MOs produced from reactants for TS
! style="background: #0D4F8B; color: white;" | HOMO-1
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | LUMO+1
|-
| <jmol>
<jmolApplet>
<title> MO 16, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO17, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO18, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO19, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<font color="#0000FF"> What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')?

'' Woodward and Hoffmann[6] ascribe endo addition to interaction of occupied orbitals with unoccupied orbitals, the endo transition state conformation being favored by orbital symmetry relative to the exo conformation. With the model of frontier orbitals, we have interaction of HOMOs (Highest Occupied Molecular Orbitals) with LUMOs (Lowest Unoccupied Molecular Orbitals). Those interactions are represented in figure 4. The main interactions that will form the bonds are shown by plain bold lines, the secondary interactions, responsible for the endo-exo selectivity, are shown by small squiggly lines. We do not know if the molecules approch so closely that the secondary interactions can be as important as shown in figure 1. ''

Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction and an antisymmetric-antisymmetric interaction.'''</font>

=== Bond Length Analysis ===

{| class="wikitable"
|+Table 3. Carbon Carbon bond length of Reactants, TS and Products; and Literature value
! style="background: #0D4F8B; color: white;" | Reactant
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" | Literature value
|-
| [[File:Yts Cbond length reactant.PNG|500px]]
| [[File:Yts Cbond length TS.PNG|300px]]
| [[File:Yts Cbond length P.PNG|300px]]
|<div style="text-align: center;">Van der Waals radius of the C atom: 1.7 Å <ref>Bondi, A. The Journal of Physical Chemistry 1964, 68 (3), 441–451.</ref><br />Typical sp<sup>3</sup> C-C bond length and sp<sup>2</sup> C=C bond lengths : 1.54 Å, 1.34 Å<ref>Fox, M. A.; Whitesell, J. K. Organische Chemie: Grundlagen, Mechanismen, bioorganische Anwendungen; Spektrum Akadem. Verl.: Heidelberg, 1995.</ref><br /> [[File:Yts cyclohexenelitlength.PNG|450px]]<br />Bond length of cyclohexene<ref>Chiang, J. F.; Bauer, S. H. Journal of the American Chemical Society 1969, 91 (8), 1898–1901.</ref><br /> </div>
|-
|}

Experimental carbon carbon bond length of cyclohexene is consistent with the literature value as shown in Table 3 which confirm correct structure of TS and Cyclohexene Product is obtained. Comparing the Van der Waals radius of C atom and the length of the partly formed C-C bonds in the TS, a much lower C-C bond length at TS indicates formation of bond. Typically, sp<sup>2</sup> C=C bond lengths is much shorter than sp<sup>3</sup> C-C bond length as shown in table 3 due to a higher bond order and hence, closer the Carbon atoms are.

As reaction proceed, bond length corresponds to different carbon atoms change which the result is shown in Table 4.

{| class="wikitable"
|+Table 4. Change of Bond Length as the reaction proceed
[[File:YtsIRC finallabel.PNG|thumb|center|400px|alt=''Figure 5. Labelled Carbon atoms in reactants''|Fig. 5: ''Labelled Carbon atoms in reactants'']]
|-
|[[File:Yts BL 1,4.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6a: ''Plot of change of Bond Length between C1 and C4'']]
|[[File:Yts BL 4,14.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6b: ''Plot of change of Bond Length between C4 and C14'']]
|[[File:Yts BL 14,12.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6c: ''Plot of change of Bond Length between C14 and C12'']]
|-
|[[File:Yts BL 12,10.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6d: ''Plot of change of Bond Length between C12 and C10'']]
|[[File:Yts BL 10,7.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6e: ''Plot of change of Bond Length between C10 and C7'']]
|[[File:Yts BL 7,1.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6f: ''Plot of change of Bond Length between C7 and C1'']]
|}

===Vibrational Analysis===

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

The vibration that corresponds to the reaction path at transition state is -949.15 cm<sup>-1</sup>. In the transition state of this reaction, the two forming bonds have the same lengths. Hence, this confirms the '''synchronous''' mechanism where two new bonds are formed simultaneously.

<jmol>
<jmolApplet>
<title> Vibrational Analysis of TS </title>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==

<br />

[[File:Yts ex2 reaction scheme.png|thumb|center|500px|alt=''Figure 7. Reaction Scheme''|Fig. 7: ''Reaction Scheme of Diels Alder reaction'']]

<br />

=== Optimisation Result ===

Table 5 shows the result of the Optimisation of reactants; endo and exo TSs. It was first optimised at PM6 method then a more accurate method, at B3LYP/6-31G(d) Basis Set

{| class="wikitable"
|+Table 5. Optimization Result of Reactant and Exo, Endo TS at PM6 and B3LYP/6-31G(d) Basis Set
! style="background: #0D4F8B; color: white;" | Basic Set
! style="background: #0D4F8B; color: white;" | Cyclohexadiene
! style="background: #0D4F8B; color: white;" | 1,3-Dioxole
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
| '''PM6'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 62; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN PM6 3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 30; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 22; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| '''B3LYP/6-31G(d)'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 18; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 24; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN B3LYP 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 34; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

===Frequency Analysis===

A correct TS is further confirmed by the frequency analysis. Only one negative frequency at Exo and Endo TS indicates a saddle point reached which confirms the correct TS obtained.
{| class="wikitable"
|+Table 6. Frequency Analysis of Exo and Endo TS and Products respectively at PM6 and B3LYP/6-31G(d) Basis Set
!
! style="background: #0D4F8B; color: white;" colspan="2"| Exo
! style="background: #0D4F8B; color: white;" colspan="2" | Endo
|-
|
! '''PM6'''
! '''B3LYP/6-31G(d)'''
! '''PM6'''
! '''B3LYP/6-31G(d)'''
|-
| '''TS'''
| [[File:Yts ex2exo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8a: ''Frequency Calculation of Exo TS at PM6'']]
| [[File:Yts ex2exo TS freqB3LYP.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8b: ''Frequency Calculation of Exo TS at B3LYP'']]
| [[File:Yts ex2endo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9a: ''Frequency Calculation of Endo TS at PM6'']]
| [[File:Yts ex2endo TS freqB3LYP 2.PNG|thumb|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9b:''Frequency Calculation of Endo TS at B3LYP'']]
|-
| '''Product'''
| [[File:Yts ex2 exo P PM6freq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10a: ''Frequency Calculation of Exo Product at PM6'']]
| [[File:Yts ex2 exo P B3LYPfreq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10b: ''Frequency Calculation of Exo Product at B3LYP'']]
| [[File:Yts ex2 endo P PM6freq.PNG|thumb|none|400px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11a: ''Frequency Calculation of Endo Product at PM6'']]
| [[File:Yts ex2 endo P B3LYPfreq.PNG|thumb|1000px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11b:''Frequency Calculation of Endo Product at B3LYP'']]
|}

=== MO Analysis ===

Figure 12 and 13 shows the MO digram for the Diels-Alder reaction (Exo and Endo) , which correlate with the actual MOs performed by Gaussian at B3LYP/6-31G(d) basis set.

{| class="wikitable"
|[[File:Yts ex2endo MO 2.png|thumb|none|600px|alt=''Figure 11. MO diagram for the Endo Diels-Alder reaction''|Fig. 12: ''MO diagram for the Exo Diels-Alder reaction'']]
|[[File:Yts ex2exo MO.png|thumb|none|600px|alt=''Figure 12. MO diagram for the Exo Diels-Alder reaction''|Fig. 13: ''MO diagram for the Endo Diels-Alder reaction'']]
|}

{| class="wikitable"
|+Table 6. HOMO and LUMO of Exo and Endo TS at '''B3LYP/6-31G(d)'''
! style="background: #0D4F8B; color: white;" =2'' | Orbital type
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
|HOMO-1
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO+1
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - ''Energy''' under '''Job Type''' - will yield an ordered list of MOs that you can use to start you off).

This reaction is an '''inverse demand DA reaction ''' since diene is less electron rich than dienophile in this reaction. Hence, the '''Frontier Molecular Orbitals ''' the '''LUMO of Cyclohexadiene '''(Antisymmetric) interact with the '''HOMO of 1,3-Dioxole, dienophile''', are closer in energy than that of HOMO of diene and LUMO of dienophile. As a result, they interact most strongly and form most energetically favourable bond formation. <ref> Fleming, I. Frontier orbitals and organic chemical reactions; Wiley: London, 2007.</ref>

=== Reaction Thermodynamics ===
{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Cyclohexadiene
! style="background: #0D4F8B; color: white;" " colspan="2"| 1,3-Dioxole
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.116878
| 306.863212
| −0.0522760
| −137.25064846
|0.138903
|364.689854
|0.137941
|362.164123
|0.037972
|99.6954936
|0.037807
|99.2622861
|-
| '''B3LYP/6-31G(d)'''
|−233.324375
|−612593.19323
|–267.068645
|–701188.78086
|–500.329165
|–1313614.3228
|–500.332147
|–1313622.152
|–500.417322
|–1313845.779
|−500.418691
|–1313849.3733
|}

{| class="wikitable"
|+Table 8. Activation Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>168
|<nowiki>-</nowiki>63.80491
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>163
|<nowiki>-</nowiki>67.39921
|}

<br/>
Table 8. shows the result of the Activation Barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

<br/>

'''Kinetic favourable''' of the products can be determined by the Activation Barrier. As shown in Table 8, Endo reaction pathway has a lower Activation energy and hence Endo product is more kinetically favourable. This can be further explained by '''secondary (non-bonding) orbital interaction''' in the endo TS HOMO as shown in Table 9. Secondary orbital interaction between diene and the dienophile substituent's π system lowers the energy of the endo TS and hence, lower activation barrier and the reaction proceed much faster towards endo-product. <ref>Alston, P. V.; Ottenbrite, R. M.; Cohen, T. The Journal of Organic Chemistry 1978, 43 (10), 1864–1867.</ref>As a result, '''endo product''' is more kinetically stable. On the other hand, there is no such interaction between Diene and the substituent in exo TS as shown in the HOMO of exo TS in table 9. Hence, there is no stabilisation of the exo Transistion state. Only primary (bonding) interaction present in the Exo-TS.

<br/>
Moreover, '''endo product''' is more '''thermodynamically favourable'''. Comparing the Gibbs free energy between Endo- product and Exo- product, more negative number is obtained at the Endo-product. Hence, this confirms that the endo-product is more thermodynamically stable. In fact, less sterically-hindered Exo-TS is expected to be more thermodynamically favourable. This unexpected result of Endo-Product being more more thermodynamic favourable of can be explained by Hammonds Postulate. Since this is an endothermic reaction (bond forming), according to Hammonds Postulate, it is expected that TS is more product like. As a consequence, stabilisation by secondary (non-bonding) orbital interaction will also apply to the endo-product.

{| class="wikitable"'
|+ '''Table 9. shows secondary orbital interactions or sterics on TS
! style="background: #0D4F8B; color: white;"| HOMO of Exo TS
! style="background: #0D4F8B; color: white;"|HOMO of Endo TS
|-
| <jmol>
<jmolApplet>
<title> Sterics only </title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> Secondary Orbital Interaction</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<br/>

As a result, it can be concluded that inverse electron demand Diels Alder reaction favours '''endo-Product''' in terms of '''thermodynamics''' and '''kinetic argument'''.

<br/>

== Exercise 3: Diels-Alder vs Cheletropic ==

See the '''[[Mod:ts_tutorial#Xylylene-SO2_Diels_Alder_Cycloaddition|o-Xylylene-SO2 Cycloaddition]]''' section in the tutorial as a guide.

<br />

[[File:Ts_tutorial_xylylene_so2_scheme.png|600px]]

<br />

===Optimisation Result===

Table X. shows the optimisation result of the exo TS, endo TS and Cheletropic TS at PM6 Basis Set.

{| class="wikitable"
|+Table 11. Optimization Result of Exo, Endo and Cheletropic TS at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
! style="background: #0D4F8B; color: white;" | Cheletropic TS
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts_3_DA_TSOPT_exo.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>YtsCHEL_TS_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

===IRC Analysis===

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

The reaction coordinate for each path is visualise in the following animation with an IRC calculation.

<center>[[File:Yts ex3Endo IRC.gif]] </center>
<center>''Animation 1. IRC for Endothermic reaction pathway </center>

<center>[[File:Yts ex3Exo IRC.gif]] </center>
<center>''Animation 2. IRC for Exothermic reaction pathway </center>

<center>[[File:Yts ex3chel IRC.gif]] </center>
<center>''Animation 3. IRC for Cheletropic reaction pathway </center>

===Reaction Thermodynamics===

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" |Cheletropic TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Cheletropic Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
|0.092078
|241.750807
|0.090560
|237.765298
| 0.099062
|260.087301
| 0.021455
|56.3301068
|0.021706
|56.9891073
|−0.000002
|−0.0052510004
|}

Table 8. shows the result of the reaction barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>85.6
|<nowiki>-</nowiki>99.7
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>81.7
|<nowiki>-</nowiki>99.1
|-
| '''Cheletropic Pathway '''''
|<nowiki>+</nowiki>104.0
|<nowiki>-</nowiki>156.1
|}

<br />

[[File:Yts ex3 reactionprofile3.PNG|thumb|center|600px|alt=''Figure X. Reaction Profile for different pathway''|Fig. 1: ''Reaction Profile of the Exo, Endo and Cheletropic pathway '']]

<br />

== Extra ==

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. Table X, X+1 shows the result of the potential energy of reactants, TS and products; Activation energy and Reaction energy of of this Diels-Alder reaction.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
|5
|6
|7
|8
| 9
|10
|11
|12
|}

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>85.6
|<nowiki>-</nowiki>99.7
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>81.7
|<nowiki>-</nowiki>99.1
|-
| '''Cheletropic Pathway '''''
|<nowiki>+</nowiki>104.0
|<nowiki>-</nowiki>156.1
|}

If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

==Conclusion==

== Log Files ==

=== Exercise 1 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Product
|-
| PM6
| [[File:REACTANT1_2_OPTMIN.LOG]]
| [[File:REACTANT2_OPTMIN.LOG‎]]
| [[File:TS_2_OPTTS.LOG]]
| [[File:TS_2_IRC_out.log]]
| [[File:P_FINALOPT_2.LOG]]
|}

=== Exercise 2 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Exo-Products
! style="background: #0D4F8B; color: white;" | Endo-Products
|-
| PM6
!rowspan ="2" |[[File:Endo IRC output final.log]]<br/>[[File:EXO IRC 5.LOG]]<br/>
| [[File:Yts EXO P FINALOPTMIN 1.LOG]]
|[[File:Yts ENDO P OPTMIN PM6.LOG]]

|-
| B3LYP/6-31G(d)
| [[File:EXO P FINALOPTMIN B3LYP.LOG]]
| [[File:Yts ENDO P OPTMIN B3LYP.LOG]]
|}

=== Exercise 3 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | reaction
! style="background: #0D4F8B; color: white;"| Xylylene
! style="background: #0D4F8B; color: white;" | SO<sub>2</sub>
! style="background: #0D4F8B; color: white;"| IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
| Endo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
|
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|}

===Extra===

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Reaction type
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| [[File:YTSTSOPTTS_EXO.LOG]]
| Column 3, Row 2
| [[File:YTS_EXO_PRODUCT_OPTMIN.LOG]]
|-
| Endo
| [[File:YTSTSOPTTS ENDO.LOG]]
| Column 3, Row 2
| [[File:YTS ENDO PRODUCT OPTMIN.LOG]]
|-

|}

==References==

Rep:Mod:TSYts15

2017-11-20T21:06:28Z

Yts15: /* Extra */

== Introduction ==

<font color="#0000FF">'In your introduction, briefly describe what is meant by a minimum and transition state in the context of a potential energy surface. What is the gradient and the curvature at each of these points? (for thought later on, how would a frequency calculation confirm a structure is at either of these points?)''</font>

== Exercise 1: Reaction of Butadiene with Ethylene ==

<br />

[[File:Reaction scheme.png|thumb|center|500px|alt=''Figure 1. Reaction Scheme''|Fig. 1: ''Reaction Scheme of Butadiene with Ethylene in Exercise 1'']]

<br />

=== Optimization Result ===

{| class="wikitable"
|+Table 1. Optimization Result of Reactant, TS and Products at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT1_2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>REACTANT2_OPTMIN.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 80; vibration 2;rotate x -20; </script>
<uploadedFileContents>P_FINALOPT_2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

The ''Table 1'' shows the result of optimisation of reactants, TS and product at '''PM6 level''' respectively. Correct TS was further confirmed by '''frequency calculation''' and '''IRC'''.
<font color="#0000FF">ELABORATION''</font>

====Frequency====
[[File:Yts15 freq 1.PNG|thumb|none|1000px|alt=''Figure 2. Frequency Calculation of TS''|Fig. 2: ''Frequency Calculation of TS'']]

From Fig. 2, a '''negative frequency''' is shown in the final optimised TS. This indicates imaginary vibrational frequency associated with a TS which corresponds to the translational motion of carbon. At Gaussian, second derivative of the energy with respect to the nuclear position is calculated by the frequency. Hence, the first negative frequency indicates one negative second derivation, a saddle point, which is the highest point on the minimum energy path linking the reactants and products<ref>Houston, P. L. Chemical kinetics and reaction dynamics; Dover: Mineola, NY, 2006.</ref>. High frequency, greater than |100<sup>-1</sup>|, is consistent with this kind of molecule. As a result, this represents a correct TS is obtained from final optimisation . Additionally, this plays an important part in defining chemical reactions. One negative frequency also indicates the presence of single TS which illustrates a well-defined reaction profile and complete reaction.

====IRC====
[[File:YtsIRC final.PNG|thumb|none|500px|alt=''Figure 3. IRC of TS''|Fig. 3: ''IRC'']]

Transition state geometries can be connected to ground state geometries with an '''Intrinsic Reaction Coordination calculation (IRC)''' performed by Gaussian. In Fig 3., the downhill path from the transition is followed in '''forward direction'''. A well defined and asymmetric Free Energy Surface as shown in Fig. 3 confirms that TS is correctly optimised.

=== MO Analysis===
<font color="#0000FF">
Construct an MO diagram for the formation of the butadiene/ethene TS, including basic symmetry labels (symmetric/antisymmetric or s/a).For each of the reactants and the TS, open the .chk (checkpoint) file. Under the '''Edit''' menu, choose '''MOs''' and visualise the MOs. Include images (or '''[[Mod:Cheatsheet#MOs_with_Jmol|Jmol objects]]''') for each of the HOMO and LUMO of butadiene and ethene, and the four MOs these produce for the TS. Correlate these MOs with the ones in your MO diagram to show which orbitals interact.
</font>

MO diagram for the formation of butadiene/ethene TS is illustrated in Fig. 4 MO Diagram for the formation of Butadiene/ Ethene. Actual MOs are performed by Gaussian at Basis Set PM6. It is shown that TS LUMO +1 has energy lower than expected (''stabilisation'') and TS HOMO has energy higher than expected (''destabilisation''). Hence, this suggested that significant mixing between orbitals.

[[File:Yts MO 1 mix.png|thumb|none|600px|alt=''Figure 4. MO diagram for the formation of the Butadiene/Ethene TS''|Fig. 4: ''MO diagram for the formation of the butadiene/ethene TS'']]

{| class="wikitable"
|+Table 2a. HOMO and LUMO of Reactants, Butadiene and ethene
! style="background: #0D4F8B; color: white;" | Orbital type
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO11, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO6, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO12, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT1_OPTMIN_MO.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO7, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>YTS_REACTANT2_OPTMIN_MO3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

{| class="wikitable"
|+Table 2b. Four MOs produced from reactants for TS
! style="background: #0D4F8B; color: white;" | HOMO-1
! style="background: #0D4F8B; color: white;" | HOMO
! style="background: #0D4F8B; color: white;" | LUMO
! style="background: #0D4F8B; color: white;" | LUMO+1
|-
| <jmol>
<jmolApplet>
<title> MO 16, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO17, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO18, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO19, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>TS_2_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<font color="#0000FF"> What can you conclude about the requirements for symmetry for a reaction (when is a reaction 'allowed' and when is it 'forbidden')?

'' Woodward and Hoffmann[6] ascribe endo addition to interaction of occupied orbitals with unoccupied orbitals, the endo transition state conformation being favored by orbital symmetry relative to the exo conformation. With the model of frontier orbitals, we have interaction of HOMOs (Highest Occupied Molecular Orbitals) with LUMOs (Lowest Unoccupied Molecular Orbitals). Those interactions are represented in figure 4. The main interactions that will form the bonds are shown by plain bold lines, the secondary interactions, responsible for the endo-exo selectivity, are shown by small squiggly lines. We do not know if the molecules approch so closely that the secondary interactions can be as important as shown in figure 1. ''

Write whether the orbital overlap integral is zero or non-zero for the case of a symmetric-antisymmetric interaction, a symmetric-symmetric interaction and an antisymmetric-antisymmetric interaction.'''</font>

=== Bond Length Analysis ===

{| class="wikitable"
|+Table 3. Carbon Carbon bond length of Reactants, TS and Products; and Literature value
! style="background: #0D4F8B; color: white;" | Reactant
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | Product
! style="background: #0D4F8B; color: white;" | Literature value
|-
| [[File:Yts Cbond length reactant.PNG|500px]]
| [[File:Yts Cbond length TS.PNG|300px]]
| [[File:Yts Cbond length P.PNG|300px]]
|<div style="text-align: center;">Van der Waals radius of the C atom: 1.7 Å <ref>Bondi, A. The Journal of Physical Chemistry 1964, 68 (3), 441–451.</ref><br />Typical sp<sup>3</sup> C-C bond length and sp<sup>2</sup> C=C bond lengths : 1.54 Å, 1.34 Å<ref>Fox, M. A.; Whitesell, J. K. Organische Chemie: Grundlagen, Mechanismen, bioorganische Anwendungen; Spektrum Akadem. Verl.: Heidelberg, 1995.</ref><br /> [[File:Yts cyclohexenelitlength.PNG|450px]]<br />Bond length of cyclohexene<ref>Chiang, J. F.; Bauer, S. H. Journal of the American Chemical Society 1969, 91 (8), 1898–1901.</ref><br /> </div>
|-
|}

Experimental carbon carbon bond length of cyclohexene is consistent with the literature value as shown in Table 3 which confirm correct structure of TS and Cyclohexene Product is obtained. Comparing the Van der Waals radius of C atom and the length of the partly formed C-C bonds in the TS, a much lower C-C bond length at TS indicates formation of bond. Typically, sp<sup>2</sup> C=C bond lengths is much shorter than sp<sup>3</sup> C-C bond length as shown in table 3 due to a higher bond order and hence, closer the Carbon atoms are.

As reaction proceed, bond length corresponds to different carbon atoms change which the result is shown in Table 4.

{| class="wikitable"
|+Table 4. Change of Bond Length as the reaction proceed
[[File:YtsIRC finallabel.PNG|thumb|center|400px|alt=''Figure 5. Labelled Carbon atoms in reactants''|Fig. 5: ''Labelled Carbon atoms in reactants'']]
|-
|[[File:Yts BL 1,4.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6a: ''Plot of change of Bond Length between C1 and C4'']]
|[[File:Yts BL 4,14.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6b: ''Plot of change of Bond Length between C4 and C14'']]
|[[File:Yts BL 14,12.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6c: ''Plot of change of Bond Length between C14 and C12'']]
|-
|[[File:Yts BL 12,10.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6d: ''Plot of change of Bond Length between C12 and C10'']]
|[[File:Yts BL 10,7.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6e: ''Plot of change of Bond Length between C10 and C7'']]
|[[File:Yts BL 7,1.PNG|thumb|center|800px|alt=''Figure 3. Label of Carbon atom in Product''|Fig. 6f: ''Plot of change of Bond Length between C7 and C1'']]
|}

===Vibrational Analysis===

Illustrate the vibration that corresponds to the reaction path at the transition state. Is the formation of the two bonds synchronous or asynchronous?

The vibration that corresponds to the reaction path at transition state is -949.15 cm<sup>-1</sup>. In the transition state of this reaction, the two forming bonds have the same lengths. Hence, this confirms the '''synchronous''' mechanism where two new bonds are formed simultaneously.

<jmol>
<jmolApplet>
<title> Vibrational Analysis of TS </title>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>TS 2 OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

== Exercise 2: Reaction of Cyclohexadiene and 1,3-Dioxole ==

<br />

[[File:Yts ex2 reaction scheme.png|thumb|center|500px|alt=''Figure 7. Reaction Scheme''|Fig. 7: ''Reaction Scheme of Diels Alder reaction'']]

<br />

=== Optimisation Result ===

Table 5 shows the result of the Optimisation of reactants; endo and exo TSs. It was first optimised at PM6 method then a more accurate method, at B3LYP/6-31G(d) Basis Set

{| class="wikitable"
|+Table 5. Optimization Result of Reactant and Exo, Endo TS at PM6 and B3LYP/6-31G(d) Basis Set
! style="background: #0D4F8B; color: white;" | Basic Set
! style="background: #0D4F8B; color: white;" | Cyclohexadiene
! style="background: #0D4F8B; color: white;" | 1,3-Dioxole
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
| '''PM6'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 62; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN PM6 3.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 30; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 22; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
| '''B3LYP/6-31G(d)'''
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 18; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts REACTANT OPTMIN B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 24; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts OXOLE OPTMIN B3LYP 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 34; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

===Frequency Analysis===

A correct TS is further confirmed by the frequency analysis. Only one negative frequency at Exo and Endo TS indicates a saddle point reached which confirms the correct TS obtained.
{| class="wikitable"
|+Table 6. Frequency Analysis of Exo and Endo TS and Products respectively at PM6 and B3LYP/6-31G(d) Basis Set
!
! style="background: #0D4F8B; color: white;" colspan="2"| Exo
! style="background: #0D4F8B; color: white;" colspan="2" | Endo
|-
|
! '''PM6'''
! '''B3LYP/6-31G(d)'''
! '''PM6'''
! '''B3LYP/6-31G(d)'''
|-
| '''TS'''
| [[File:Yts ex2exo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8a: ''Frequency Calculation of Exo TS at PM6'']]
| [[File:Yts ex2exo TS freqB3LYP.PNG|thumb|none|400px|alt=''Figure 8. Frequency Calculation of exo TS''|Fig. 8b: ''Frequency Calculation of Exo TS at B3LYP'']]
| [[File:Yts ex2endo TS freqPM6.PNG|thumb|none|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9a: ''Frequency Calculation of Endo TS at PM6'']]
| [[File:Yts ex2endo TS freqB3LYP 2.PNG|thumb|400px|alt=''Figure 9. Frequency Calculation of endo TS''|Fig. 9b:''Frequency Calculation of Endo TS at B3LYP'']]
|-
| '''Product'''
| [[File:Yts ex2 exo P PM6freq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10a: ''Frequency Calculation of Exo Product at PM6'']]
| [[File:Yts ex2 exo P B3LYPfreq.PNG|thumb|none|400px|alt=''Figure 10. Frequency Calculation of exo P''|Fig. 10b: ''Frequency Calculation of Exo Product at B3LYP'']]
| [[File:Yts ex2 endo P PM6freq.PNG|thumb|none|400px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11a: ''Frequency Calculation of Endo Product at PM6'']]
| [[File:Yts ex2 endo P B3LYPfreq.PNG|thumb|1000px|alt=''Figure 11. Frequency Calculation of endo P''|Fig. 11b:''Frequency Calculation of Endo Product at B3LYP'']]
|}

=== MO Analysis ===

Figure 12 and 13 shows the MO digram for the Diels-Alder reaction (Exo and Endo) , which correlate with the actual MOs performed by Gaussian at B3LYP/6-31G(d) basis set.

{| class="wikitable"
|[[File:Yts ex2endo MO 2.png|thumb|none|600px|alt=''Figure 11. MO diagram for the Endo Diels-Alder reaction''|Fig. 12: ''MO diagram for the Exo Diels-Alder reaction'']]
|[[File:Yts ex2exo MO.png|thumb|none|600px|alt=''Figure 12. MO diagram for the Exo Diels-Alder reaction''|Fig. 13: ''MO diagram for the Endo Diels-Alder reaction'']]
|}

{| class="wikitable"
|+Table 6. HOMO and LUMO of Exo and Endo TS at '''B3LYP/6-31G(d)'''
! style="background: #0D4F8B; color: white;" =2'' | Orbital type
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
|-
|HOMO-1
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO40, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 40; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|HOMO
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO41, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO42, Symmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 42; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|-
|LUMO+1
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> MO43, Antisymmetric</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 43; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

Is this a normal or inverse demand DA reaction? (Hint: Run an IRC calculation on the TSs. Running a single point energy calculation - ''Energy''' under '''Job Type''' - will yield an ordered list of MOs that you can use to start you off).

This reaction is an '''inverse demand DA reaction ''' since diene is less electron rich than dienophile in this reaction. Hence, the '''Frontier Molecular Orbitals ''' the '''LUMO of Cyclohexadiene '''(Antisymmetric) interact with the '''HOMO of 1,3-Dioxole, dienophile''', are closer in energy than that of HOMO of diene and LUMO of dienophile. As a result, they interact most strongly and form most energetically favourable bond formation. <ref> Fleming, I. Frontier orbitals and organic chemical reactions; Wiley: London, 2007.</ref>

=== Reaction Thermodynamics ===
{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Cyclohexadiene
! style="background: #0D4F8B; color: white;" " colspan="2"| 1,3-Dioxole
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.116878
| 306.863212
| −0.0522760
| −137.25064846
|0.138903
|364.689854
|0.137941
|362.164123
|0.037972
|99.6954936
|0.037807
|99.2622861
|-
| '''B3LYP/6-31G(d)'''
|−233.324375
|−612593.19323
|–267.068645
|–701188.78086
|–500.329165
|–1313614.3228
|–500.332147
|–1313622.152
|–500.417322
|–1313845.779
|−500.418691
|–1313849.3733
|}

{| class="wikitable"
|+Table 8. Activation Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>168
|<nowiki>-</nowiki>63.80491
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>163
|<nowiki>-</nowiki>67.39921
|}

<br/>
Table 8. shows the result of the Activation Barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

<br/>

'''Kinetic favourable''' of the products can be determined by the Activation Barrier. As shown in Table 8, Endo reaction pathway has a lower Activation energy and hence Endo product is more kinetically favourable. This can be further explained by '''secondary (non-bonding) orbital interaction''' in the endo TS HOMO as shown in Table 9. Secondary orbital interaction between diene and the dienophile substituent's π system lowers the energy of the endo TS and hence, lower activation barrier and the reaction proceed much faster towards endo-product. <ref>Alston, P. V.; Ottenbrite, R. M.; Cohen, T. The Journal of Organic Chemistry 1978, 43 (10), 1864–1867.</ref>As a result, '''endo product''' is more kinetically stable. On the other hand, there is no such interaction between Diene and the substituent in exo TS as shown in the HOMO of exo TS in table 9. Hence, there is no stabilisation of the exo Transistion state. Only primary (bonding) interaction present in the Exo-TS.

<br/>
Moreover, '''endo product''' is more '''thermodynamically favourable'''. Comparing the Gibbs free energy between Endo- product and Exo- product, more negative number is obtained at the Endo-product. Hence, this confirms that the endo-product is more thermodynamically stable. In fact, less sterically-hindered Exo-TS is expected to be more thermodynamically favourable. This unexpected result of Endo-Product being more more thermodynamic favourable of can be explained by Hammonds Postulate. Since this is an endothermic reaction (bond forming), according to Hammonds Postulate, it is expected that TS is more product like. As a consequence, stabilisation by secondary (non-bonding) orbital interaction will also apply to the endo-product.

{| class="wikitable"'
|+ '''Table 9. shows secondary orbital interactions or sterics on TS
! style="background: #0D4F8B; color: white;"| HOMO of Exo TS
! style="background: #0D4F8B; color: white;"|HOMO of Endo TS
|-
| <jmol>
<jmolApplet>
<title> Sterics only </title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts EXO TS OPTTS B3LYP.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<title> Secondary Orbital Interaction</title>
<color>white</color>
<size>200</size>
<script>frame 2; mo 41; mo cutoff 0.01 mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>Yts Endo TS B3LYP final.log</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<br/>

As a result, it can be concluded that inverse electron demand Diels Alder reaction favours '''endo-Product''' in terms of '''thermodynamics''' and '''kinetic argument'''.

<br/>

== Exercise 3: Diels-Alder vs Cheletropic ==

See the '''[[Mod:ts_tutorial#Xylylene-SO2_Diels_Alder_Cycloaddition|o-Xylylene-SO2 Cycloaddition]]''' section in the tutorial as a guide.

<br />

[[File:Ts_tutorial_xylylene_so2_scheme.png|600px]]

<br />

===Optimisation Result===

Table X. shows the optimisation result of the exo TS, endo TS and Cheletropic TS at PM6 Basis Set.

{| class="wikitable"
|+Table 11. Optimization Result of Exo, Endo and Cheletropic TS at PM6 Basics Set
! style="background: #0D4F8B; color: white;" | Exo TS
! style="background: #0D4F8B; color: white;" | Endo TS
! style="background: #0D4F8B; color: white;" | Cheletropic TS
|-
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 14; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts_3_DA_TSOPT_exo.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 16; vibration 2;rotate x -20; </script>
<uploadedFileContents>Yts ENDO TS OPTTS PM6 2.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
| <jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 20; vibration 2;rotate x -20; </script>
<uploadedFileContents>YtsCHEL_TS_OPTTS.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

|}

===IRC Analysis===

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

The reaction coordinate for each path is visualise in the following animation with an IRC calculation.

<center>[[File:Yts ex3Endo IRC.gif]] </center>
<center>''Animation 1. IRC for Endothermic reaction pathway </center>

<center>[[File:Yts ex3Exo IRC.gif]] </center>
<center>''Animation 2. IRC for Exothermic reaction pathway </center>

<center>[[File:Yts ex3chel IRC.gif]] </center>
<center>''Animation 3. IRC for Cheletropic reaction pathway </center>

===Reaction Thermodynamics===

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" |Cheletropic TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Cheletropic Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
|0.092078
|241.750807
|0.090560
|237.765298
| 0.099062
|260.087301
| 0.021455
|56.3301068
|0.021706
|56.9891073
|−0.000002
|−0.0052510004
|}

Table 8. shows the result of the reaction barrier and reaction energy on the reaction of Cyclohexadiene and 1,3-Dioxole. '''Activation Barrier''' is calculated by the difference between the energy of product and TS. While '''Reaction Energy''' is the differences between product and reactants energies. It is important to note that Basis set of B3LYP/6-31G(d) is used to provide more accurate calculation.

{| class="wikitable"
|+Table 8. Reaction Barrier and energy, at room temperature
! style="background: #0D4F8B; color: white;" rowspan="1" |
! style="background: #0D4F8B; color: white;" "|Activation Barrier/''kJ/mol
! style="background: #0D4F8B; color: white;" " |Reaction Energy/''kJ/mol
|-
| '''Exo Reaction pathway '''''
|<nowiki>+</nowiki>85.6
|<nowiki>-</nowiki>99.7
|-
|'''Endo Reaction pathway '''''
|<nowiki>+</nowiki>81.7
|<nowiki>-</nowiki>99.1
|-
| '''Cheletropic Pathway '''''
|<nowiki>+</nowiki>104.0
|<nowiki>-</nowiki>156.1
|}

<br />

[[File:Yts ex3 reactionprofile3.PNG|thumb|center|600px|alt=''Figure X. Reaction Profile for different pathway''|Fig. 1: ''Reaction Profile of the Exo, Endo and Cheletropic pathway '']]

<br />

== Extra ==

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. Table X, X+1 shows the result of the potential energy of reactants, TS and products; Activation energy and Reaction energy of of this Diels-Alder reaction.

{| class="wikitable"
|+Table 7. Reaction Energy of Reactants, TS and Product
! style="background: #0D4F8B; color: white;" rowspan="2" | Basic Set
! style="background: #0D4F8B; color: white;" " colspan="2"|Xylylene
! style="background: #0D4F8B; color: white;" " colspan="2"|SO2
! style="background: #0D4F8B; color: white;" colspan="2"| Exo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Endo TS
! style="background: #0D4F8B; color: white;" colspan="2" | Exo Product
! style="background: #0D4F8B; color: white;" colspan="2" | Endo Product
|-
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
! style="background: #0D4F8B; color: white;"|Energy/ ''Hatress''
! style="background: #0D4F8B; color: white;"|Energy/ ''kJ/mol''
|-
| '''PM6'''
| 0.178070
| 467.522821
| −0.118614
| −311.421081
|5
|6
|7
|8
| 9
|10
|11
|12
|}

If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

==Conclusion==

== Log Files ==

=== Exercise 1 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | Butadiene
! style="background: #0D4F8B; color: white;" | Ethylene
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Product
|-
| PM6
| [[File:REACTANT1_2_OPTMIN.LOG]]
| [[File:REACTANT2_OPTMIN.LOG‎]]
| [[File:TS_2_OPTTS.LOG]]
| [[File:TS_2_IRC_out.log]]
| [[File:P_FINALOPT_2.LOG]]
|}

=== Exercise 2 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Basics Set
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Exo-Products
! style="background: #0D4F8B; color: white;" | Endo-Products
|-
| PM6
!rowspan ="2" |[[File:Endo IRC output final.log]]<br/>[[File:EXO IRC 5.LOG]]<br/>
| [[File:Yts EXO P FINALOPTMIN 1.LOG]]
|[[File:Yts ENDO P OPTMIN PM6.LOG]]

|-
| B3LYP/6-31G(d)
| [[File:EXO P FINALOPTMIN B3LYP.LOG]]
| [[File:Yts ENDO P OPTMIN B3LYP.LOG]]
|}

=== Exercise 3 ===
{| class="wikitable"
! style="background: #0D4F8B; color: white;" | reaction
! style="background: #0D4F8B; color: white;"| Xylylene
! style="background: #0D4F8B; color: white;" | SO<sub>2</sub>
! style="background: #0D4F8B; color: white;"| IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
| Endo
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|-
|
| Xylylene
| Column 3, Row 2
| Column 3, Row 2
| Column 3, Row 2
|}

===Extra===

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Reaction type
! style="background: #0D4F8B; color: white;" | Transition States
! style="background: #0D4F8B; color: white;" | IRC
! style="background: #0D4F8B; color: white;" | Products
|-
| Exo
| [[File:YTSTSOPTTS_EXO.LOG]]
| Column 3, Row 2
| [[File:YTS_EXO_PRODUCT_OPTMIN.LOG]]
|-
| Endo
| [[File:YTSTSOPTTS ENDO.LOG]]
| Column 3, Row 2
| [[File:YTS ENDO PRODUCT OPTMIN.LOG]]
|-

|}

==References==

File:YTSTSOPTTS ENDO.LOG

2017-11-20T21:05:52Z

Yts15: