== Transition States and Reactivity ==

=== Introduction ===
The transition state (TS) is defined as the highest energy point (maximum) on the minimum energy path linking reactants and products whereas the reactant and product are the minimum along a reaction coordinate. They are thus a stationary point with a first derivative or a gradient of zero (2). The second derivative or the curvature (4) is negative for a TS (maximum point) whereas it is positive for the reactant and product (minimum point).
[[File:Xlt15formula1.PNG|frame|center|Figure 1: Equation of potential energy and its first and second derivative, vibrational frequency and reduced mass <ref name=":0">J. J. W. McDouall, ''Computational Quantum Chemistry: Molecular Structure and Properties in Silico'', Royal Society of Chemistry, London, United Kingdom, 2013.</ref>.]]
where V(x) is the potential energy, k is the force constant, x is the displacement, ν is vibrational frequency, μ is the reduced mass of 2 atoms of mass m<sub>1</sub> and m<sub>2</sub>. The negative sign in (3) implying that the force acting in that direction lowers the PE <ref name=":0">J. J. W. McDouall, ''Computational Quantum Chemistry: Molecular Structure and Properties in Silico'', Royal Society of Chemistry, London, United Kingdom, 2013.</ref>.
[[File:Xlt15inroreactionprofilr.PNG|frame|center|Figure 2: Reaction profile of an exothermic reaction <ref name=":1"> J. Clayden, N. Greeves, S. Warren, P. Wothers, ''Organic Chemistry'', Oxford University Press Inc., New York, 2001.</ref>.]]
<br>
The reaction coordinate diagram provides kinetics and thermodynamics information of a reaction. The higher the activation energy, the lower the rate of reaction. A pathway with more exothermic reaction energy is more thermodynamically favoured.
<br>
<br>
However, a non-linear molecule undergoing a reaction will have 3N<sub>atoms</sub>-6 reaction coordinates. <ref name=":0">J. J. W. McDouall, ''Computational Quantum Chemistry: Molecular Structure and Properties in Silico'', Royal Society of Chemistry, London, United Kingdom, 2013.</ref>. The 3N<sub>atoms</sub>-6 specifies the number of internal degree of freedom or the number of normal vibrational mode that a molecule can possess <ref name=":0">J. J. W. McDouall, ''Computational Quantum Chemistry: Molecular Structure and Properties in Silico'', Royal Society of Chemistry, London, United Kingdom, 2013.</ref>. For a linear molecule, the number of internal degree of freedom is 3N<sub>atoms</sub>-5 as rotation along bond axis give the identical molecule <ref name=":0">J. J. W. McDouall, ''Computational Quantum Chemistry: Molecular Structure and Properties in Silico'', Royal Society of Chemistry, London, United Kingdom, 2013.</ref>. Hence, a reaction coordinate diagram beyond 1D is called a potential energy surface. The transition state in a PES is define as the first order saddle point on PES with the first derivative with respect to all coordinates is 0 <ref name=":2">A. R. Rossil, ''Reaction Paths and Transition States'', lecture notes, Department of Chemistry, The University of Connecticut, http://rossi.chemistry.uconn.edu/chem5326/files/reaction_pathways.pdf, (accessed Feb 2018)</ref>. The first order saddle point has a maximum energy for displacement between 2 minima in a direction whereas in all the remaining direction the energy is a minimum <ref name=":2">A. R. Rossil, ''Reaction Paths and Transition States'', lecture notes, Department of Chemistry, The University of Connecticut, http://rossi.chemistry.uconn.edu/chem5326/files/reaction_pathways.pdf, (accessed Feb 2018)</ref>. Hence, the transition state has only a unique normal coordinate that corresponds to reaction coordinate with second derivative < 0 (negative force constant). This negative force constant can then be related to the vibrational frequency (5) which is an imaginary frequency. The chemical reactant and products are characterized as minima and must have second derivative > 0 (positive force constant and hence positive vibrational frequency).
<br>
<br>
Two different electronic structure methods, the semi-empirical method PM6 and Density Functional Theory (DFT) method B3LYP were used in optimizing the reactants, transition state and product. The semi-empirical PM6 is a faster method to generate a reasonable result as it uses the experimental data whereas B3LYP is more time-consuming and accurate method <ref name=":3"> Year 3 Computational Chemistry Lab, Transition State and Reactivity,https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:ts_exercise, (accessed Feb 2018)</ref>. Hence, PM6 method was firstly used to generate an approximate structure and then reoptimize with DFT method B3LYP.

=== Exercise 1: Reaction of Butadiene with Ethylene ===
[[File:Xlt15reactionscheme4ex1.PNG|frame|center|Figure 3: Reaction scheme of Diels-Alder reaction of 1,3-butadiene and ethylene.]]
Diels-Alder (D-A) reaction or [4+2]-cycloaddition occur between a conjugated diene and an alkene (dienophile). The diene component must adopt a ''s''-cis conformation. D-A reaction involved a one step, concerted formation of 2 new σ bonds. The D-A reaction proceeds with no reaction intermediates and the transition state has aromatic character with six delocalized π electron.
<br>
<br>
''' Method Used In Optimization and Analysis '''
<br>
Method 3 was employed in locating the transition state by which the product, cyclohexene was drawn and optimized to minimum at PM6 level. With the optimized cyclohexene, the C-C single bonds formed during the reaction of 1,3-butadiene and ethylene were deleted, froze at 2.20 Å and optimized to minimum at PM6 level to identify the frozen guess transition state. The distance 2.20 Å is the approximate separation between the reacting termini in guess transition state. It is a value between a C-C single bond length and their combined Van der Waals radii. The guess TS structure was then optimized at PM6 level and the PM6 optimized TS was used to run a IRC calculation. For reactants, 1,3-butadiene and ethylene, they were each obtained from the first frame of IRC calculation and optimized to minimum at PM6 level.
==== Optimized Reactants, Transition State and Product and at PM6 level ====
{| class="wikitable"
! colspan="4" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 1: Optimized Reactants, Transition State and Product at PM6 level
|-
! style="text-align: center;" | 1,3-Butadiene
! style="text-align: center;" | Ethylene
! style="text-align: center;" | Transition State
! style="text-align: center;" | Cyclohexene
|-
|<jmol>
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==== Determination of The Correct TS with a Frequency and IRC Calculation ====
===== Frequency calculation =====
[[File:Xlt15tsnegative frequencyex1.PNG|center|frame|Figure 4: Screenshot of the "Display Vibrations" of transition structure.]]
<br>
[[File:Xlt15tsconvergedex1.PNG|center|frame|Figure 5: Screenshot of a section of transition structure's log file.]]
<br>
According to Figure 4 and 5, the transition structure has shown to properly converged with the presence of only one imaginary frequency at -949 cm<sup>-1</sup> and a stationary point corresponds to the transition structure is found. The imaginary frequency is then visualized to ensure a correct transition state structure is obtained (See Section 1.2.5 for the visualization of the imaginary frequency). For reactants (1,3-butadiene and ethylene) and product, their structures are checked to properly converge with no negative frequency obtained and their respective stationary points are found in log files.

===== IRC Calculation =====
{| class="wikitable"
! colspan="3" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 2. IRC Calculation of PM6 Optimized Transition Structures
|-
! style="text-align: center;" | Reaction Progress
! style="text-align: center;" | IRC Output
! style="text-align: center;" | Explanation
|-
|[[File:Xlt15irc3.gif|center]]
|[[File:Xlt15ircpathex1redo.PNG|350px|center]]
|An IRC (Intrinsic reaction coordinate) calculation is obtained for the PM6 optimized transition structure. The plot of total energy against IRC is asymmetric and all the gradients for reactants, product and transition state (minima) are zero, indicating that the transition structure is properly converged and optimized.
|}

==== MO Analysis ====
===== MO Diagram of The Formation of 1,3-Butadiene/Ethylene TS =====
[[File:Modiagram2xlt156.PNG|center|frame|Figure 6: MO diagram for the formation of the 1,3-butadiene/ethylene TS with basic symmetry labels shown; A= Antisymmetric and S= Symmetric.]]
HOMO: Highest Occupied Molecular Orbital
<br>
LUMO: Lowest Unoccupied Molecular Orbital
<br>
<br>
As seen in the MO diagram drawn in Figure 6, it is a normal electron demand Diels-Alder reaction because the HOMO of 1,3-butadiene (diene) is higher in energy than the HOMO of ethylene (dienophile). The combination of the high energy HOMO (diene) and low energy LUMO of dienophile gives a better overlap in the transition state. As their energy gap is smaller, it is more favoured than the interaction between LUMO of 1,3-butadiene and HOMO of ethylene (larger energy gap and hence worse overlap).

===== Frontier MO of Reactants and Transition State =====
{| class="wikitable"
! colspan="5" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 3: Frontier MO of 1,3-Butadiene, Ethylene and Transition State.
|-
! style="text-align: center;" | 1,3-Butadiene
! style="text-align: center;" | Ethylene
! style="text-align: center;" | Transition State
! style="text-align: center;" | Orbital Interaction and Discussion
|-
|<jmol>
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|'''“+” stands for an in-phase combination and “-” stands for an out-of-phase interaction'''
<br>
1,3-Butadiene (LUMO, MO12, S) + Ethylene (HOMO, MO6, S) = TS (HOMO, MO17, S)
<br>
1,3-Butadiene (LUMO, MO12, S) - Ethylene (HOMO, MO6, S) = TS (LUMO, MO18, S)
<br>
<br>
MO17: Although the orbital lobes on the reacting C termini of 1,3-butadiene is not observed but there is an increased in the size of the blue lobe of ethylene MO6, implying a bonding interaction between the two.
<br>
MO18: The ethylene MO6 has diminished; Antibonding interaction.
|-
|<jmol>
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|<jmol>
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|'''“+” stands for an in-phase combination and “-” stands for an out-of-phase interaction'''
<br>
1,3-Butadiene (HOMO, MO11, A) + Ethylene (LUMO, MO6, S) = TS (HOMO-1, MO16, A)
1,3-Butadiene (HOMO, MO11, A) + Ethylene (LUMO, MO6, S) = TS (LUMO+1, MO19, A)
<br>
<br>
MO16: A very clear bonding interaction can be observed.
<br>
MO19: Again, the orbital lobes are not observed for the reacting termini in 1,3-butadiene; Antibonding interaction.
|}

{| class="wikitable"
! colspan="2" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 4: Summary of orbital overlap integral.
|-
! style="text-align: center;" | Interaction Type
! style="text-align: center;" | Orbital Overlap Integral
|-
| style="text-align: center;" | Symmetric-symmetric
| style="text-align: center;" | Non-zero
|-
| style="text-align: center;" | Antisymmetric-antisymmetric
| style="text-align: center;" | Non-zero
|-
| style="text-align: center;" | Symmetric-antisymmetric
| style="text-align: center;" | Zero
|}
The Table 4 above summarizes the overlap integral for three different interactions. Each transition state MO is designated as symmetric (S) or antisymmetric (A) with respect to the persistent symmetry element, a mirror plane perpendicular to the central C-C bond in 1,3-butadiene. According to conservation of orbital symmetry, the orbital symmetry of reactants is smoothly transformed to an orbital of product with the same symmetry <ref name=":4"> E. V. Anslyn, D. A. Dougherty, ''Modern Physical Organic Chemistry'', University Science Books, Sausalito, United States, 2006.</ref>. Thus, this symmetry will certainly persist in transition state. In addition, the frontier molecular orbital (FMO) theory states that a reaction is only allowed if there is favourable mixing between HOMO and LUMO of the reactants <ref name=":4"> E. V. Anslyn, D. A. Dougherty, ''Modern Physical Organic Chemistry'', University Science Books, Sausalito, United States, 2006.</ref>. By referring to the MO diagram in Figure 6, the HOMO of 1,3-butadiene is of the same symmetry as the LUMO of ethylene and the vice versa. Both interactions are thus allowed because of the matching in phases. In conclusion, only orbitals of the same symmetry in reactants can combine to form the TS molecular orbitals with the same symmetry to have a significant overlap of the combining orbitals. Fragment orbitals of different symmetry combine to give zero overlap integral and thus no bond formation.

According to Woodward Hoffmann rules, the total number of (4q+2)<sub>s</sub> and (4r)<sub>a</sub> components must be odd in an allowed thermal pericyclic reaction. The suffix “s” stands for suprafacial and “a” stands for antarafacial. A suprafacial component forms new bonds at the same face at both ends. An antarafacial component forms new bonds on opposite faces at both ends <ref name=":1"> J. Clayden, N. Greeves, S. Warren, P. Wothers, ''Organic Chemistry'', Oxford University Press Inc., New York, 2001.</ref>. The thermal pericyclic reaction is forbidden if the number is even. However, a thermally forbidden pericyclic reaction is photochemically allowed. Using the Woodward Hoffmann rules, [<sub>π</sub>4<sub>s</sub> + <sub>π</sub>2<sub>s</sub>]-cycloaddition is thermally allowed as there is one (4q+2)<sub> s</sub> component (the ethylene) and no (4r)<sub>a</sub> component.

==== C-C Bond Length Measurements and Analysis ====
'''Typical C-C Bond Length''' <ref name=":5"> S. M. Mukherji, S. P. Singh, R. P.Feynman,R. Dass, ''Organic Chemistry Vol I'', New Age International, New Delhi, India, 2010.</ref> <ref name=":6"> I. L. Shabalin, ''Ultra-High Temperature Materials I Carbon (Graphene/Graphite) and Refractory Metals'', Springer, Netherlands, 2014.</ref>

{| class="wikitable"
! colspan="2" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 5: Typical C-C bond lengths.
|-
! style="text-align: center;" | Bond Type
! style="text-align: center;" | Bond Length/ Å
|-
| style="text-align: center;" | '''C–C'''
sp<sup>3</sup> C–sp<sup>3</sup> C
<br>
sp<sup>3</sup> C–sp<sup>2</sup> C
<br>
sp<sup>2</sup> C–sp<sup>2</sup> C
| style="text-align: center;" |
<br>
1.54
<br>
1.50
<br>
1.48
|-
| style="text-align: center;" | '''C=C'''
sp<sup>2</sup> C–sp<sup>2</sup> C
| style="text-align: center;" |
<br>
1.34
|}

''' C-C Bond Length Measurements'''
[[File:Xlt15reactionscheme4ex1numbering.PNG|frame|left|Figure 7: Reaction scheme with the all carbons numbered.]]
<br style="clear:right">
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{| class="wikitable"
! colspan="7" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 6: C-C bond length measurements in reactants, transition state and product.
|-
! rowspan="2" style="text-align: center;" | Molecule
! colspan="6" style="text-align: center;" | Bond Length/ Å
|-
!style="text-align: center;" |C1-C2
!style="text-align: center;" |C2-C3
!style="text-align: center;" |C3-C4
!style="text-align: center;" |C4-C5
!style="text-align: center;" |C5-C6
!style="text-align: center;" |C1-C6
|-
!style="text-align: center;" |1,3-Butadiene
|style="text-align: center;" |–
|style="text-align: center;" |–
|style="text-align: center;" |1.33344
|style="text-align: center;" |1.47077
|style="text-align: center;" |1.33342
|style="text-align: center;" |–
|-
!style="text-align: center;" |Ethylene
|style="text-align: center;" |1.32731
|style="text-align: center;" |–
|style="text-align: center;" |–
|style="text-align: center;" |–
|style="text-align: center;" |–
|style="text-align: center;" |–
|-
!style="text-align: center;" |Transition State
|style="text-align: center;" |1.38173
|style="text-align: center;" |2.11470
|style="text-align: center;" |1.37976
|style="text-align: center;" |1.41112
|style="text-align: center;" |1.37973
|style="text-align: center;" |2.11478
|-
!style="text-align: center;" |Cyclohexene
|style="text-align: center;" |1.53767
|style="text-align: center;" |1.53577
|style="text-align: center;" |1.49262
|style="text-align: center;" |1.33305
|style="text-align: center;" |1.49263
|style="text-align: center;" |1.53577
|}

The C-C bond length measurement with the PM6 level optimized structures is in good accordance to the typical C-C and C=C bond length. There are 2 factors affecting the bond lengths:
<br>
(a) ''Bond order'': The higher the bond order of a given bond, the shorter the bond length and hence the stronger the bond.
<br>
(b) ''Type of Hybridization'': The size of hybrid orbitals increases in the order of sp C > sp<sup>2</sup> C > sp<sup>3</sup> C. The larger valence orbitals of sp<sup>3</sup> C has poorer overlap, forming a longer and weaker bond. The percentage of ''s''-character in hybrid orbitals decreases in the order of sp C (50%) > sp<sup>2</sup> C (33%) > sp<sup>3</sup> C (25%). The higher the ''s''-character of a given hybrid orbital, the shorter the bond. Because the electron in high ''s''-character hybrid orbital can penetrate better into the nucleus and experience a higher effective nuclear attraction, resulting in a shorter bond.
<br>
<br>
'''Atomic Van der Waals radius of C atom: 1.70 Å'''
<br>
'''Van der Waals distance between 2 C atom: 3.40 Å'''
<br>
<br>
Van der Waals distance between any 2 atoms is the minimum distance beyond which the electrostatic attractive force turn into repulsive force. The length of partially formed C–C bonds in transition state is 2.11 Å, which is smaller than the Van der Waals radii between 2 C atoms but is greater than the typical C-C bond lengths listed in Table x. This indicates the 2p atomic orbitals of C atom are partially overlap in transition state, resulting in the partly formed C-C single bond. The bond length of a partially formed or broken C=C double bond in transition state has a value between a full C-C single and C=C double bond.

{| class="wikitable"
! colspan="2" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 7: Change in C-C bond length during Diels-Alder reaction.
|-
! style="text-align: center;" | Bond Length against Reaction Coordinate
! style="text-align: center;" | Explanation
|-
|[[File:Xlt15ex1ircexcel.PNG|center]]
|
*'''C1-C2, C3-C4, and C5-C6'''
All the plots show the bond length change when a C=C double bond breaks (in 1,3-butadiene and ethylene) into a C-C single bond (in cyclohexene). C=C bond length remains constant at 1.33 Å for a certain period of time. Then, the transition of transition state to product shows a gradual increase in bond length to 1.54 Å for C1-C2 and 1.49 Å for C3-C4 and C5-C6. The slight difference in C-C single bond length in cyclohexene is due to the difference in the hybridization type of C atom.
<br>
*'''C2-C3 and C6-C1'''
All the plots show change in bond length during the C-C single bond formation. The initial separation of terminal Cs between the 1,3-butadiene and ethylene is at 3.4 Å which is the VDW distance between 2 C atoms. As the reaction proceeds, their separation decreases almost linearly along the IRC and then it remains constant at 1.54 Å (single C-C bond formed).
<br>
*'''C4-C5'''
The plot shows the change in bond length when a C-C single bond (in 1,3-butadiene) forms a C=C double bond (in cyclohexene). C-C bond length remains constant at 1.47 Å for a certain period of time. Then, the transition of transition state to product shows a gradual decrease in bond length to 1.33 Å (C=C double bond formed).
|}

==== Vibration That Corresponds to The Reaction Path at The Transition State ====
<jmol>
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<script>vibrating=0; spinning=0; frame 21; rotate x -20; frank off</script>
<name>xlt15TS_1</name>
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<jmolbutton>
<script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>
<text>Vibration</text>
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<script>measure 2 3; measure 1 6</script>
<text>C-C Distances</text>
<target>xlt15TS_1</target>
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<jmolmenu>
<item>
<script>frame 7; if(vibrating==0) vibration off; else; vibration 2; endif</script>
<text>i949/cm<sup>-1</sup></text>
<target>xlt15TS_1</target>
</item>
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<br>
As shown in vibration mode of the imaginary vibrational frequency at -949 cm<sup>-1</sup>, the formation of the two C-C single bonds are clearly '''synchronous''' as they are formed simultaneously. Thus, the [4+2]-cycloaddition of 1,3-butadiene and ethylene is concerted and stereospecific. In addition, this is supported by the fact the C-C bond distance of the reacting termini are the same in the transition state at 2.11 Å. Also, both 1,3-butadiene and ethylene are symmetrical and so it is expected that one C-C bond will not formed faster than the other.

====Log File For IRC Calculation====
''IRC calculation of PM6 optimised TS:'' [[File:XLT15 IRCTS1.LOG]]

=== Exercise 2 ===
http://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex2

=== Exercise 3 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex3
=== Further Work ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_FURTHER

=== References for Exercise 1 ===

Rep:Xlt15 TS

2018-02-12T21:37:31Z

Xlt15: /* Exercise 2 */

=== Further Work: Electrocyclic Reaction ===
[[File:Xlt15reactionscextraa.PNG|frame|center|Figure 1: Reaction scheme of 4π electrocyclic reaction of 1,3-butadiene derivative.]]
A 4π electrocyclic reaction in Figure 1 is investigated as a further work to the computational lab. An electrocyclic reaction is the formation or the breaking of σ bonds across the end of a conjugated π system <ref name=":0"> J. Clayden, N. Greeves, S. Warren, P. Wothers, ''Organic Chemistry'', Oxford University Press Inc., New York, 2001.</ref>. The equilibrium favoured towards left hand side because of the ring strain in the 4-membered ring.
<br>
<br>
''' Method Used In Optimization and Analysis '''
<br>
Method 3 was employed in locating the transition state by which the product, cyclobut-1-ene derivative was drawn and optimized to minimum at PM6 level. With the optimized product, the C-C single bond formed during the pericyclic reaction was deleted, froze at 2.20 Å and optimized to minimum at PM6 level to identify the frozen guess transition state. The guess TS structure was then optimized at PM6 level and the PM6 optimized TS was used to run a IRC calculation. For reactant, 1,3-butadiene derivative, it was obtained from the first frame of IRC calculation and optimized to minimum at PM6 level.
==== Optimized Reactant, Transition State, and Product at PM6 Level ====
{| class="wikitable"
! colspan="3" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 1: Optimized Reactants, Transition State and Product at PM6 Level.
|-
! style="text-align: center;" | 1,3-Butadiene Derivative
! style="text-align: center;" | Transition State
! style="text-align: center;" | 3,4-Dimethylcyclobut-1-ene
|-
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 24</script>
<uploadedFileContents>XLT15REACTANTSUE.LOG</uploadedFileContents>
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|<jmol>
<jmolApplet>
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<uploadedFileContents>XLT15TS SUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 30</script>
<uploadedFileContents>XLT15PRODUCT PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}
The geometry of reactants, transition structure and product are checked to properly converge with their respective stationary points are found in log files. In addition, transition structure has only one imaginary frequency and that imaginary frequency is then visualized to ensure a correct transition state structure is obtained. There is no imaginary frequency obtained in reactants and products.

==== IRC Calculation ====
{| class="wikitable"
! colspan="3" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 3. IRC Calculation of PM6 Optimized Transition Structures
|-
! style="text-align: center;" | Reaction Progress
! style="text-align: center;" | IRC Output
! style="text-align: center;" | Discussion
|-
|[[File:Xlt15sueextra.gif|center]]
|[[File:Xlt15ircpathex1redo.PNG|350px|center]]
| The ring closing process of 1,3-butadiene derivative clearly proceed via conratation where both hydrogens of terminal alkene carbon rotate in the same direction, clockwise as shown in the IRC. This results in the trans-arrangement of the methyl groups in the product.
|}

==== Conrotation or Disrotation Analysis Using MO ====
{| class="wikitable"
! colspan="4" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 4. MO of Reactant, Transition Structure and Product.
|-
! style="text-align: center;" | Molecular Orbital
! style="text-align: center;" | 1,3 Butadiene Derivative
! style="text-align: center;" | Transition Structure
! style="text-align: center;" | 3,4-Dimethylcyclobut-1-ene
|-
!MO18
LUMO
|<jmol>
<jmolApplet>
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|-
!MO17
HOMO
|<jmol>
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|<jmol>
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<uploadedFileContents>XLT15PRODUCT PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}
{| class="wikitable"
! colspan="2" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 5. Orbital Correlation Diagram of Reactant, TS and Product.
|-
! style="text-align: center;" | Orbital Correlation Diagram
! style="text-align: center;" | Explanation
|-
|[[File:Xlt15correlationdiagra2.PNG|frame|center|Figure 2: Simplied MO of TS and orbital correlation diagram between reactant and product.]]
<br>
[[File:Xlt15cccconndissss.PNG|frame|center|Figure 3: Conrotation and disrotation under thermal and photochemical condition.]]
|The orbital correlation diagram in Figure 2 shows the simplified version of the MOs observed in reactant, transition structure and product, with their actual HOMO and LUMO displayed in Table 4. The MOs are labelled symmetric (S) or antisymmetric (A) using the persistent symmetry element, C<sub>2</sub>-rotational axis. The type of bonding or antibonding interaction in product is also shown and coloured in orange. The conservation of orbital symmetry introduced by Woodward and Hoffmann states that an orbital of a given symmetry in the reactant is converted smoothly to a product's orbital with the identical symmetry <ref name=":1"> E. V. Anslyn, D. A. Dougherty, ''Modern Physical Organic Chemistry'', University Science Books, Sausalito, United States, 2006.</ref> <ref name=":2"> R. Hoffmann, R. B. Woodward, ''Acc. Chem. Res'', 1968, '''1'''(1), 17-22, DOI: 10.1021/ar50001a003</ref> . Hence, the orbitals in reactant and product can correlate to one another as shown in the diagram on the left. Also, they suggested that the symmetry properties of HOMO in the open-chain conjugated π system control the stereochemical outcome of the electrocyclic reaction <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>.
<br>
The pericyclic reaction calculated using Gussian at PM6 level assumed a thermal reaction condition. By examining the HOMO (MO17) of 1,3-butadiene derivative, under thermal condition, the conrotatory motion (anticlockwise direction) of the methyl groups allows an in-phase and constructive orbital interaction to form a σ bond between the terminal Cs. In contrast, disrotation brings the lobes of of the opposite phases for antibonding formation with a high energy transition structure and hence it is symmetry forbidden reaction path. Hence, under thermal condition, the '''4π electron''' conjugated system reacts with itself '''antarafacially''' via a '''Mobius aromatic transition state''' and is an orbital symmetry allowed process <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>. A C<sub>2</sub> axis of symmetry is preserved during this reaction.
<br>
<br>
On the other hand, under photochemical condition, the electron in MO17 gets excited into MO18, leading to the HOMO to be considered now is MO18. The disrotatory motion of the methyl group on the terminal Cs of 1,3-butadiene derivative brings the lobes of the same phase for bonding interaction and hence it has low activation energy and is an orbital symmetry allowed process <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>. This results in the cis-arrangement of methyl groups in the cyclobut-1ene product. In contrast, the conrotatory motion leads to an antibonding interaction and is an orbital symmetry forbidden pathway <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>.
<br>
<br>
A summary diagram for conrotation of MO17 under thermal condition and disrotation of MO18 under photochemical condition is shown in Figure 3.
|}

==== Log File For IRC Calculation ====
''IRC Calculation of PM6 Optimized TS'': [[File:XLT15SUETS IRC.LOG]]
=== Exercise 1 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_TS
=== Exercise 2 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex2

=== Exercise 3 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex2

=== References in Further Work ===

Rep:Xlt15 FURTHER

2018-02-12T21:36:50Z

Xlt15: /* Conrotation or Disrotation Analysis Using MO */

=== Further Work: Electrocyclic Reaction ===
[[File:Xlt15reactionscextraa.PNG|frame|center|Figure 1: Reaction scheme of 4π electrocyclic reaction of 1,3-butadiene derivative.]]
A 4π electrocyclic reaction in Figure 1 is investigated as a further work to the computational lab. An electrocyclic reaction is the formation or the breaking of σ bonds across the end of a conjugated π system <ref name=":0"> J. Clayden, N. Greeves, S. Warren, P. Wothers, ''Organic Chemistry'', Oxford University Press Inc., New York, 2001.</ref>. The equilibrium favoured towards left hand side because of the ring strain in the 4-membered ring.
<br>
<br>
''' Method Used In Optimization and Analysis '''
<br>
Method 3 was employed in locating the transition state by which the product, cyclobut-1-ene derivative was drawn and optimized to minimum at PM6 level. With the optimized product, the C-C single bond formed during the pericyclic reaction was deleted, froze at 2.20 Å and optimized to minimum at PM6 level to identify the frozen guess transition state. The guess TS structure was then optimized at PM6 level and the PM6 optimized TS was used to run a IRC calculation. For reactant, 1,3-butadiene derivative, it was obtained from the first frame of IRC calculation and optimized to minimum at PM6 level.
==== Optimized Reactant, Transition State, and Product at PM6 Level ====
{| class="wikitable"
! colspan="3" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 1: Optimized Reactants, Transition State and Product at PM6 Level.
|-
! style="text-align: center;" | 1,3-Butadiene Derivative
! style="text-align: center;" | Transition State
! style="text-align: center;" | 3,4-Dimethylcyclobut-1-ene
|-
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 24</script>
<uploadedFileContents>XLT15REACTANTSUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 100</script>
<uploadedFileContents>XLT15TS SUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 30</script>
<uploadedFileContents>XLT15PRODUCT PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}
The geometry of reactants, transition structure and product are checked to properly converge with their respective stationary points are found in log files. In addition, transition structure has only one imaginary frequency and that imaginary frequency is then visualized to ensure a correct transition state structure is obtained. There is no imaginary frequency obtained in reactants and products.

==== IRC Calculation ====
{| class="wikitable"
! colspan="3" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 3. IRC Calculation of PM6 Optimized Transition Structures
|-
! style="text-align: center;" | Reaction Progress
! style="text-align: center;" | IRC Output
! style="text-align: center;" | Discussion
|-
|[[File:Xlt15sueextra.gif|center]]
|[[File:Xlt15ircpathex1redo.PNG|350px|center]]
| The ring closing process of 1,3-butadiene derivative clearly proceed via conratation where both hydrogens of terminal alkene carbon rotate in the same direction, clockwise as shown in the IRC. This results in the trans-arrangement of the methyl groups in the product.
|}

==== Conrotation or Disrotation Analysis Using MO ====
{| class="wikitable"
! colspan="4" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 4. MO of Reactant, Transition Structure and Product.
|-
! style="text-align: center;" | Molecular Orbital
! style="text-align: center;" | 1,3 Butadiene Derivative
! style="text-align: center;" | Transition Structure
! style="text-align: center;" | 3,4-Dimethylcyclobut-1-ene
|-
!MO18
LUMO
|<jmol>
<jmolApplet>
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|-
!MO17
HOMO
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|<jmol>
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</jmolApplet>
</jmol>
|}
{| class="wikitable"
! colspan="2" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 5. Orbital Correlation Diagram of Reactant, TS and Product.
|-
! style="text-align: center;" | Orbital Correlation Diagram
! style="text-align: center;" | Explanation
|-
|[[File:Xlt15correlationdiagra2.PNG|frame|center|Figure 2: Simplied MO of TS and orbital correlation diagram between reactant and product.]]
<br>
[[File:Xlt15cccconndissss.PNG|frame|center|Figure 3: Conrotation and disrotation under thermal and photochemical condition.]]
|The orbital correlation diagram in Figure 2 shows the simplified version of the MOs observed in reactant, transition structure and product, with their actual HOMO and LUMO displayed in Table 4. The MOs are labelled symmetric (S) or antisymmetric (A) using the persistent symmetry element, C<sub>2</sub>-rotational axis. The type of bonding or antibonding interaction in product is also shown and coloured in orange. The conservation of orbital symmetry introduced by Woodward and Hoffmann states that an orbital of a given symmetry in the reactant is converted smoothly to a product's orbital with the identical symmetry <ref name=":1"> E. V. Anslyn, D. A. Dougherty, ''Modern Physical Organic Chemistry'', University Science Books, Sausalito, United States, 2006.</ref> <ref name=":2"> R. Hoffmann, R. B. Woodward, ''Acc. Chem. Res'', 1968, '''1'''(1), 17-22, DOI: 10.1021/ar50001a003</ref> . Hence, the orbitals in reactant and product can correlate to one another as shown in the diagram on the left. Also, they suggested that the symmetry properties of HOMO in the open-chain conjugated π system control the stereochemical outcome of the electrocyclic reaction <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>.
<br>
The pericyclic reaction calculated using Gussian at PM6 level assumed a thermal reaction condition. By examining the HOMO (MO17) of 1,3-butadiene derivative, under thermal condition, the conrotatory motion (anticlockwise direction) of the methyl groups allows an in-phase and constructive orbital interaction to form a σ bond between the terminal Cs. In contrast, disrotation brings the lobes of of the opposite phases for antibonding formation with a high energy transition structure and hence it is symmetry forbidden reaction path. Hence, under thermal condition, the '''4π electron''' conjugated system reacts with itself '''antarafacially''' via a '''Mobius aromatic transition state''' and is an orbital symmetry allowed process <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>. A C<sub>2</sub> axis of symmetry is preserved during this reaction.
<br>
<br>
On the other hand, under photochemical condition, the electron in MO17 gets excited into MO18, leading to the HOMO to be considered now is MO18. The disrotatory motion of the methyl group on the terminal Cs of 1,3-butadiene derivative brings the lobes of the same phase for bonding interaction and hence it has low activation energy and is an orbital symmetry allowed process <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>. This results in the cis-arrangement of methyl groups in the cyclobut-1ene product. In contrast, the conrotatory motion leads to an antibonding interaction and is an orbital symmetry forbidden pathway <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>.
<br>
<br>
A summary diagram for conrotation of MO17 under thermal condition and disrotation of MO18 under photochemical condition is shown in Figure 3.
|}

==== Log File For IRC Calculation ====
''IRC Calculation of PM6 Optimized TS'': [[File:XLT15SUETS IRC.LOG]]
=== Exercise 1 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_TS
=== Exercise 2 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex3
=== Exercise 3 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex2

=== References in Further Work ===

File:Xlt15cccconndissss.PNG

2018-02-12T21:33:23Z

Xlt15:

Rep:Xlt15 FURTHER

2018-02-12T21:30:38Z

Xlt15: /* Conrotation or Disrotation Analysis Using MO */

=== Further Work: Electrocyclic Reaction ===
[[File:Xlt15reactionscextraa.PNG|frame|center|Figure 1: Reaction scheme of 4π electrocyclic reaction of 1,3-butadiene derivative.]]
A 4π electrocyclic reaction in Figure 1 is investigated as a further work to the computational lab. An electrocyclic reaction is the formation or the breaking of σ bonds across the end of a conjugated π system <ref name=":0"> J. Clayden, N. Greeves, S. Warren, P. Wothers, ''Organic Chemistry'', Oxford University Press Inc., New York, 2001.</ref>. The equilibrium favoured towards left hand side because of the ring strain in the 4-membered ring.
<br>
<br>
''' Method Used In Optimization and Analysis '''
<br>
Method 3 was employed in locating the transition state by which the product, cyclobut-1-ene derivative was drawn and optimized to minimum at PM6 level. With the optimized product, the C-C single bond formed during the pericyclic reaction was deleted, froze at 2.20 Å and optimized to minimum at PM6 level to identify the frozen guess transition state. The guess TS structure was then optimized at PM6 level and the PM6 optimized TS was used to run a IRC calculation. For reactant, 1,3-butadiene derivative, it was obtained from the first frame of IRC calculation and optimized to minimum at PM6 level.
==== Optimized Reactant, Transition State, and Product at PM6 Level ====
{| class="wikitable"
! colspan="3" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 1: Optimized Reactants, Transition State and Product at PM6 Level.
|-
! style="text-align: center;" | 1,3-Butadiene Derivative
! style="text-align: center;" | Transition State
! style="text-align: center;" | 3,4-Dimethylcyclobut-1-ene
|-
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 24</script>
<uploadedFileContents>XLT15REACTANTSUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 100</script>
<uploadedFileContents>XLT15TS SUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 30</script>
<uploadedFileContents>XLT15PRODUCT PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}
The geometry of reactants, transition structure and product are checked to properly converge with their respective stationary points are found in log files. In addition, transition structure has only one imaginary frequency and that imaginary frequency is then visualized to ensure a correct transition state structure is obtained. There is no imaginary frequency obtained in reactants and products.

==== IRC Calculation ====
{| class="wikitable"
! colspan="3" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 3. IRC Calculation of PM6 Optimized Transition Structures
|-
! style="text-align: center;" | Reaction Progress
! style="text-align: center;" | IRC Output
! style="text-align: center;" | Discussion
|-
|[[File:Xlt15sueextra.gif|center]]
|[[File:Xlt15ircpathex1redo.PNG|350px|center]]
| The ring closing process of 1,3-butadiene derivative clearly proceed via conratation where both hydrogens of terminal alkene carbon rotate in the same direction, clockwise as shown in the IRC. This results in the trans-arrangement of the methyl groups in the product.
|}

==== Conrotation or Disrotation Analysis Using MO ====
{| class="wikitable"
! colspan="4" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 4. MO of Reactant, Transition Structure and Product.
|-
! style="text-align: center;" | Molecular Orbital
! style="text-align: center;" | 1,3 Butadiene Derivative
! style="text-align: center;" | Transition Structure
! style="text-align: center;" | 3,4-Dimethylcyclobut-1-ene
|-
!MO18
LUMO
|<jmol>
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|-
!MO17
HOMO
|<jmol>
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</jmolApplet>
</jmol>
|}
{| class="wikitable"
! colspan="2" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 5. Orbital Correlation Diagram of Reactant, TS and Product.
|-
! style="text-align: center;" | Orbital Correlation Diagram
! style="text-align: center;" | Explanation
|-
|[[File:Xlt15correlationdiagra2.PNG|frame|center|Figure 2: Simplied MO of TS and orbital correlation diagram between reactant and product.]]
|The orbital correlation diagram in Table 5 shows the simplified version of the MOs observed in reactant, transition structure and product, with their actual HOMO and LUMO displayed in Table 4. The MOs are labelled symmetric (S) or antisymmetric (A) using the persistent symmetry element, C<sub>2</sub>-rotational axis. The type of bonding or antibonding interaction in product is also shown and coloured in orange. The conservation of orbital symmetry introduced by Woodward and Hoffmann states that an orbital of a given symmetry in the reactant is converted smoothly to a product's orbital with the identical symmetry <ref name=":1"> E. V. Anslyn, D. A. Dougherty, ''Modern Physical Organic Chemistry'', University Science Books, Sausalito, United States, 2006.</ref> <ref name=":2"> R. Hoffmann, R. B. Woodward, ''Acc. Chem. Res'', 1968, '''1'''(1), 17-22, DOI: 10.1021/ar50001a003</ref> . Hence, the orbitals in reactant and product can correlate to one another as shown in the diagram on the left. Also, they suggested that the symmetry properties of HOMO in the open-chain conjugated π system control the stereochemical outcome of the electrocyclic reaction <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>.
<br>
The pericyclic reaction calculated using Gussian at PM6 level assumed a thermal reaction condition. By examining the HOMO (MO17) of 1,3-butadiene derivative, under thermal condition, the conrotatory motion (anticlockwise direction) of the methyl groups allows an in-phase and constructive orbital interaction to form a σ bond between the terminal Cs. In contrast, disrotation brings the lobes of of the opposite phases for antibonding formation with a high energy transition structure and hence it is symmetry forbidden reaction path. Hence, under thermal condition, the '''4π electron''' conjugated system reacts with itself '''antarafacially''' via a '''Mobius aromatic transition state''' and is an orbital symmetry allowed process <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>. A C<sub>2</sub> axis of symmetry is preserved during this reaction.
<br>
<br>
On the other hand, under photochemical condition, the electron in MO17 gets excited into MO18, leading to the HOMO to be considered now is MO18. The disrotatory motion of the methyl group on the terminal Cs of 1,3-butadiene derivative brings the lobes of the same phase for bonding interaction and hence it has low activation energy and is an orbital symmetry allowed process <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>. This results in the cis-arrangement of methyl groups in the cyclobut-1ene product. In contrast, the conrotatory motion leads to an antibonding interaction and is an orbital symmetry forbidden pathway <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>.
<br>
<br>
A summary diagram for conrotation of MO17 under thermal condition and disrotation of MO18 under photochemical condition is shown in Figure 2.
|}
'''Summary Diagram of Conrotation and Disrotation Under Thermal and Photochemical Condition'''
[[File:Xlt15conndis.PNG|frame|left|Figure 3: Conrotation and disrotation under thermal and photochemical condition.]]

==== Log File For IRC Calculation ====
''IRC Calculation of PM6 Optimized TS'': [[File:XLT15SUETS IRC.LOG]]
=== Exercise 1 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_TS
=== Exercise 2 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex3
=== Exercise 3 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex2

=== References in Further Work ===

File:Xlt15conndis.PNG

2018-02-12T21:24:48Z

Xlt15:

File:Xlt15disncon.PNG

2018-02-12T21:24:02Z

Xlt15:

Rep:Xlt15 FURTHER

2018-02-12T21:10:53Z

Xlt15: /* Conrotation or Disrotation Analysis Using MO */

=== Further Work: Electrocyclic Reaction ===
[[File:Xlt15reactionscextraa.PNG|frame|center|Figure 1: Reaction scheme of 4π electrocyclic reaction of 1,3-butadiene derivative.]]
A 4π electrocyclic reaction in Figure 1 is investigated as a further work to the computational lab. An electrocyclic reaction is the formation or the breaking of σ bonds across the end of a conjugated π system <ref name=":0"> J. Clayden, N. Greeves, S. Warren, P. Wothers, ''Organic Chemistry'', Oxford University Press Inc., New York, 2001.</ref>. The equilibrium favoured towards left hand side because of the ring strain in the 4-membered ring.
<br>
<br>
''' Method Used In Optimization and Analysis '''
<br>
Method 3 was employed in locating the transition state by which the product, cyclobut-1-ene derivative was drawn and optimized to minimum at PM6 level. With the optimized product, the C-C single bond formed during the pericyclic reaction was deleted, froze at 2.20 Å and optimized to minimum at PM6 level to identify the frozen guess transition state. The guess TS structure was then optimized at PM6 level and the PM6 optimized TS was used to run a IRC calculation. For reactant, 1,3-butadiene derivative, it was obtained from the first frame of IRC calculation and optimized to minimum at PM6 level.
==== Optimized Reactant, Transition State, and Product at PM6 Level ====
{| class="wikitable"
! colspan="3" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 1: Optimized Reactants, Transition State and Product at PM6 Level.
|-
! style="text-align: center;" | 1,3-Butadiene Derivative
! style="text-align: center;" | Transition State
! style="text-align: center;" | 3,4-Dimethylcyclobut-1-ene
|-
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 24</script>
<uploadedFileContents>XLT15REACTANTSUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 100</script>
<uploadedFileContents>XLT15TS SUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>black</color>
<size>250</size>
<script>frame 30</script>
<uploadedFileContents>XLT15PRODUCT PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}
The geometry of reactants, transition structure and product are checked to properly converge with their respective stationary points are found in log files. In addition, transition structure has only one imaginary frequency and that imaginary frequency is then visualized to ensure a correct transition state structure is obtained. There is no imaginary frequency obtained in reactants and products.

==== IRC Calculation ====
{| class="wikitable"
! colspan="3" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 3. IRC Calculation of PM6 Optimized Transition Structures
|-
! style="text-align: center;" | Reaction Progress
! style="text-align: center;" | IRC Output
! style="text-align: center;" | Discussion
|-
|[[File:Xlt15sueextra.gif|center]]
|[[File:Xlt15ircpathex1redo.PNG|350px|center]]
| The ring closing process of 1,3-butadiene derivative clearly proceed via conratation where both hydrogens of terminal alkene carbon rotate in the same direction, clockwise as shown in the IRC. This results in the trans-arrangement of the methyl groups in the product.
|}

==== Conrotation or Disrotation Analysis Using MO ====
{| class="wikitable"
! colspan="4" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 4. MO of Reactant, Transition Structure and Product.
|-
! style="text-align: center;" | Molecular Orbital
! style="text-align: center;" | 1,3 Butadiene Derivative
! style="text-align: center;" | Transition Structure
! style="text-align: center;" | 3,4-Dimethylcyclobut-1-ene
|-
!MO18
LUMO
|<jmol>
<jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 24; mo 18; mo cutoff 0.01; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>XLT15REACTANTSUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 100; mo 18; mo cutoff 0.02; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>XLT15TS SUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 30; mo 18; mo cutoff 0.02; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>XLT15PRODUCT PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|-
!MO17
HOMO
|<jmol>
<jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 24; mo 17; mo cutoff 0.02; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>XLT15REACTANTSUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 100; mo 17; mo cutoff 0.02; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>XLT15TS SUE.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|<jmol>
<jmolApplet>
<color>white</color>
<size>200</size>
<script>frame 30; mo 17; mo cutoff 0.02; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>XLT15PRODUCT PM6.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}
{| class="wikitable"
! colspan="2" style="text-align: center;" style="background: #0D4F8B; color: white;" | Table 5. Orbital Correlation Diagram of Reactant, TS and Product.
|-
! style="text-align: center;" | Orbital Correlation Diagram
! style="text-align: center;" | Explanation
|-
|[[File:Xlt15correlationdiagra2.PNG|center]]
|The orbital correlation diagram in Table 5 shows the simplified version of the MOs observed in reactant, transition structure and product, with their actual HOMO and LUMO displayed in Table 4. The MOs are labelled symmetric (S) or antisymmetric (A) using the persistent symmetry element, C<sub>2</sub>-rotational axis. The type of bonding or antibonding interaction in product is also shown and coloured in orange. The conservation of orbital symmetry introduced by Woodward and Hoffmann states that an orbital of a given symmetry in the reactant is converted smoothly to a product's orbital with the identical symmetry <ref name=":1"> E. V. Anslyn, D. A. Dougherty, ''Modern Physical Organic Chemistry'', University Science Books, Sausalito, United States, 2006.</ref> <ref name=":2"> R. Hoffmann, R. B. Woodward, ''Acc. Chem. Res'', 1968, '''1'''(1), 17-22, DOI: 10.1021/ar50001a003</ref> . Hence, the orbitals in reactant and product can correlate to one another as shown in the diagram on the left. Also, they suggested that the symmetry properties of HOMO in the open-chain conjugated π system control the stereochemical outcome of the electrocyclic reaction <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>.
<br>
The pericyclic reaction calculated using Gussian at PM6 level assumed a thermal reaction condition. By examining the HOMO (MO17) of 1,3-butadiene derivative, under thermal condition, the conrotatory motion (anticlockwise direction) of the methyl groups allows an in-phase and constructive orbital interaction to form a σ bond between the terminal Cs. In contrast, disrotation brings the lobes of of the opposite phases for antibonding formation with a high energy transition structure and hence it is symmetry forbidden reaction path. Hence, under thermal condition, the '''4π electron''' conjugated system reacts with itself '''antarafacially''' via a '''Mobius aromatic transition state''' and is an orbital symmetry allowed process <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>. A C<sub>2</sub> axis of symmetry is preserved during this reaction.
<br>
<br>
On the other hand, under photochemical condition, the electron in MO17 gets excited into MO18, leading to the HOMO to be considered now is MO18. The disrotatory motion of the methyl group on the terminal Cs of 1,3-butadiene derivative brings the lobes of the same phase for bonding interaction and hence it has low activation energy and is an orbital symmetry allowed process <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>. This results in the cis-arrangement of methyl groups in the cyclobut-1ene product. In contrast, the conrotatory motion leads to an antibonding interaction and is an orbital symmetry forbidden pathway <ref name=":3"> B. Dinda, ''Essentials of Pericyclic and Photochemical Reactions'', Springer International Publishing, Switzerland, 2017.</ref>.
<br>
A summary diagram for conrotation of MO17 under thermal condition and disrotation of MO18 under photochemical condition is shown in Figure 2.
|}

==== Log File For IRC Calculation ====
''IRC Calculation of PM6 Optimized TS'': [[File:XLT15SUETS IRC.LOG]]
=== Exercise 1 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_TS
=== Exercise 2 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex3
=== Exercise 3 ===
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Xlt15_Ex2

=== References in Further Work ===

2018-02-12T18:51:02Z

Xlt15: /* IRC Calculation */

Rep:Xlt15 FURTHER

2018-02-12T18:50:23Z

Xlt15: /* IRC Calculation */

File:Xlt15correlationdiagra1.PNG

2018-02-12T18:25:45Z

Xlt15:

Rep:Xlt15 FURTHER

2018-02-12T18:23:16Z

Xlt15: /* Conrotation or Disrotation Analysis Using MO */

Rep:Xlt15 FURTHER

2018-02-12T16:36:01Z

Xlt15: /* Exercise 2 */