ChemWiki - User contributions [en]

User:Tg2412

2015-01-30T11:58:36Z

Tg2412: /* Cis-butadiene and Ethene */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche3 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gauche_3_tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| C1 || -231.692660 || 0.00
|-align="center"
| anti2 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Anti2 Ci tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| Ci || -231.69253529 || 0.08
|-align="center"
| anti3 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gauche_3_tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| C2h || -231.689069999 || 2.25
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

''' Summary of activation energies (in kcal/mol) '''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''Expt.'''
|-
| ''' '''
| width="125" align="center" | '''at 0 K '''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
|-
| '''ΔE (Chair)'''
| align="center" | 45.70
| align="center" | 44.69
| align="center" | 36.11
| align="center" | 34.93
| align="center" | 33.5 ± 0.5
|-
| '''ΔE (Boat)'''
| align="center" | 55.61
| align="center" | 54.76
| align="center" | 44.37
| align="center" | 43.48
| align="center" | 44.7 ± 2.0
|}

From the Activation energies that calculated above, the HF/21G optimisation result is less actuate than 6-31G* as the activation energy generated from 6-31G* is way closer in both case.

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''HOMO'''
|'''LUMO'''
|-align="center"
|'''butadiene'''
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|-align="center"
|'''ethene'''
|[[Image:HOMO_ethene_tg2412.jpg|350px]]
|[[Image:LUMO_ethene_tg2412.jpg|350px]]
|}
As shown in the graph above, the HOMO and LUMO of cis-butadiene are both symmetrical to the mirror plane. The HOMO transition state is generate from LUMO of butadiene (S)and HOMO ethene(S). The LUMO of TS is generated from LUMO (S)of ditadiene and LUMO+1(AS). It is worth noticing that AS and S can generate symmetrical MO.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency2_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:DA_2_endo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:DA_2_exo_TS_IRC_moive_tg2412.gif]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:DA_2_endo_TS_IRC_moive2_tg2412.gif]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

User:Tg2412

2015-01-30T11:49:59Z

Tg2412: /* Reactants */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche3 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gauche_3_tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| C1 || -231.692660 || 0.00
|-align="center"
| anti2 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Anti2 Ci tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| Ci || -231.69253529 || 0.08
|-align="center"
| anti3 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gauche_3_tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| C2h || -231.689069999 || 2.25
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

''' Summary of activation energies (in kcal/mol) '''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''Expt.'''
|-
| ''' '''
| width="125" align="center" | '''at 0 K '''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
|-
| '''ΔE (Chair)'''
| align="center" | 45.70
| align="center" | 44.69
| align="center" | 36.11
| align="center" | 34.93
| align="center" | 33.5 ± 0.5
|-
| '''ΔE (Boat)'''
| align="center" | 55.61
| align="center" | 54.76
| align="center" | 44.37
| align="center" | 43.48
| align="center" | 44.7 ± 2.0
|}

From the Activation energies that calculated above, the HF/21G optimisation result is less actuate than 6-31G* as the activation energy generated from 6-31G* is way closer in both case.

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|'''butadiene'''
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|-align="center"
|'''ethene'''
|[[Image:HOMO_ethene_tg2412.jpg|350px]]
|[[Image:LUMO_ethene_tg2412.jpg|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency2_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:DA_2_endo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:DA_2_exo_TS_IRC_moive_tg2412.gif]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:DA_2_endo_TS_IRC_moive2_tg2412.gif]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

User:Tg2412

2015-01-30T11:49:19Z

Tg2412: /* Reactants */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche3 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gauche_3_tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| C1 || -231.692660 || 0.00
|-align="center"
| anti2 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Anti2 Ci tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| Ci || -231.69253529 || 0.08
|-align="center"
| anti3 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gauche_3_tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| C2h || Example || Example
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

''' Summary of activation energies (in kcal/mol) '''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''Expt.'''
|-
| ''' '''
| width="125" align="center" | '''at 0 K '''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
|-
| '''ΔE (Chair)'''
| align="center" | 45.70
| align="center" | 44.69
| align="center" | 36.11
| align="center" | 34.93
| align="center" | 33.5 ± 0.5
|-
| '''ΔE (Boat)'''
| align="center" | 55.61
| align="center" | 54.76
| align="center" | 44.37
| align="center" | 43.48
| align="center" | 44.7 ± 2.0
|}

From the Activation energies that calculated above, the HF/21G optimisation result is less actuate than 6-31G* as the activation energy generated from 6-31G* is way closer in both case.

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|'''butadiene'''
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|-align="center"
|'''ethene'''
|[[Image:HOMO_ethene_tg2412.jpg|350px]]
|[[Image:LUMO_ethene_tg2412.jpg|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency2_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:DA_2_endo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:DA_2_exo_TS_IRC_moive_tg2412.gif]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:DA_2_endo_TS_IRC_moive2_tg2412.gif]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

File:Anti3 C2H tg2412.mol

2015-01-30T11:44:40Z

Tg2412:

User:Tg2412

2015-01-30T11:34:57Z

Tg2412: /* Reactants */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche1 || Example || C2 || Example || Example
|-align="center"
| gauche2 || Example || C2 || Example || Example
|-align="center"
| gauche3 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Gauche_3_tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| C1 || -231.692660 || 0.00
|-align="center"
| gauche4 || Example || C2 || Example || Example
|-align="center"
| gauche5 || Example || C1 || Example || Example
|-align="center"
| gauche6 || Example || C1 || Example || Example
|-align="center"
| anti1 || Example || C2 || Example || Example
|-align="center"
| anti2 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Anti2 Ci tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| Ci || -231.69253529 || 0.08
|-align="center"
| anti3 || [[Image:Anti2_Ci_tg2412.PNG|centre|350x350px|Cope rearrangement]] || C2h || Example || Example
|-align="center"
| anti4 || Example || C1 || Example || Example
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

''' Summary of activation energies (in kcal/mol) '''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''Expt.'''
|-
| ''' '''
| width="125" align="center" | '''at 0 K '''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
|-
| '''ΔE (Chair)'''
| align="center" | 45.70
| align="center" | 44.69
| align="center" | 36.11
| align="center" | 34.93
| align="center" | 33.5 ± 0.5
|-
| '''ΔE (Boat)'''
| align="center" | 55.61
| align="center" | 54.76
| align="center" | 44.37
| align="center" | 43.48
| align="center" | 44.7 ± 2.0
|}

From the Activation energies that calculated above, the HF/21G optimisation result is less actuate than 6-31G* as the activation energy generated from 6-31G* is way closer in both case.

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|'''butadiene'''
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|-align="center"
|'''ethene'''
|[[Image:HOMO_ethene_tg2412.jpg|350px]]
|[[Image:LUMO_ethene_tg2412.jpg|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency2_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:DA_2_endo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:DA_2_exo_TS_IRC_moive_tg2412.gif]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:DA_2_endo_TS_IRC_moive2_tg2412.gif]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

File:Gauche 3 tg2412.mol

2015-01-30T11:31:54Z

Tg2412:

File:Gauche 2.mol2

2015-01-30T11:28:19Z

Tg2412: Tg2412 uploaded a new version of "File:Gauche 2.mol2"

User:Tg2412

2015-01-30T11:08:08Z

Tg2412: /* Reactants */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche1 || Example || C2 || Example || Example
|-align="center"
| gauche2 || Example || C2 || Example || Example
|-align="center"
| gauche3 || Example || C1 || Example || Example
|-align="center"
| gauche4 || Example || C2 || Example || Example
|-align="center"
| gauche5 || Example || C1 || Example || Example
|-align="center"
| gauche6 || Example || C1 || Example || Example
|-align="center"
| anti1 || Example || C2 || Example || Example
|-align="center"
| anti2 ||
<jmol><jmolApplet>
<color>white</color>
<size>200</size>
<uploadedFileContents>Anti2 Ci tg2412.mol</uploadedFileContents>
</jmolApplet></jmol>
|| Ci || -231.69253529 || Example
|-align="center"
| anti3 || [[Image:Anti2_Ci_tg2412.PNG|centre|350x350px|Cope rearrangement]] || C2h || Example || Example
|-align="center"
| anti4 || Example || C1 || Example || Example
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

''' Summary of activation energies (in kcal/mol) '''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''Expt.'''
|-
| ''' '''
| width="125" align="center" | '''at 0 K '''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
|-
| '''ΔE (Chair)'''
| align="center" | 45.70
| align="center" | 44.69
| align="center" | 36.11
| align="center" | 34.93
| align="center" | 33.5 ± 0.5
|-
| '''ΔE (Boat)'''
| align="center" | 55.61
| align="center" | 54.76
| align="center" | 44.37
| align="center" | 43.48
| align="center" | 44.7 ± 2.0
|}

From the Activation energies that calculated above, the HF/21G optimisation result is less actuate than 6-31G* as the activation energy generated from 6-31G* is way closer in both case.

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|'''butadiene'''
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|-align="center"
|'''ethene'''
|[[Image:HOMO_ethene_tg2412.jpg|350px]]
|[[Image:LUMO_ethene_tg2412.jpg|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency2_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:DA_2_endo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:DA_2_exo_TS_IRC_moive_tg2412.gif]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:DA_2_endo_TS_IRC_moive2_tg2412.gif]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

File:Anti2 Ci tg2412.mol

2015-01-30T10:49:07Z

Tg2412:

User:Tg2412

2015-01-30T10:45:05Z

Tg2412: /* Reactants */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche1 || Example || C2 || Example || Example
|-align="center"
| gauche2 || Example || C2 || Example || Example
|-align="center"
| gauche3 || Example || C1 || Example || Example
|-align="center"
| gauche4 || Example || C2 || Example || Example
|-align="center"
| gauche5 || Example || C1 || Example || Example
|-align="center"
| gauche6 || Example || C1 || Example || Example
|-align="center"
| anti1 || Example || C2 || Example || Example
|-align="center"
| anti2 || Example || Ci || -231.69253529 || Example
|-align="center"
| anti3 || [[Image:Anti2_Ci_tg2412.PNG|centre|350x350px|Cope rearrangement]] || C2h || Example || Example
|-align="center"
| anti4 || Example || C1 || Example || Example
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

''' Summary of activation energies (in kcal/mol) '''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''Expt.'''
|-
| ''' '''
| width="125" align="center" | '''at 0 K '''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
|-
| '''ΔE (Chair)'''
| align="center" | 45.70
| align="center" | 44.69
| align="center" | 36.11
| align="center" | 34.93
| align="center" | 33.5 ± 0.5
|-
| '''ΔE (Boat)'''
| align="center" | 55.61
| align="center" | 54.76
| align="center" | 44.37
| align="center" | 43.48
| align="center" | 44.7 ± 2.0
|}

From the Activation energies that calculated above, the HF/21G optimisation result is less actuate than 6-31G* as the activation energy generated from 6-31G* is way closer in both case.

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|'''butadiene'''
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|-align="center"
|'''ethene'''
|[[Image:HOMO_ethene_tg2412.jpg|350px]]
|[[Image:LUMO_ethene_tg2412.jpg|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency2_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:DA_2_endo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:DA_2_exo_TS_IRC_moive_tg2412.gif]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:DA_2_endo_TS_IRC_moive2_tg2412.gif]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

User:Tg2412

2015-01-30T10:37:41Z

Tg2412: /* Chair and Boat Transition Structure */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche1 || Example || C2 || Example || Example
|-align="center"
| gauche2 || Example || C2 || Example || Example
|-align="center"
| gauche3 || Example || C1 || Example || Example
|-align="center"
| gauche4 || Example || C2 || Example || Example
|-align="center"
| gauche5 || Example || C1 || Example || Example
|-align="center"
| gauche6 || Example || C1 || Example || Example
|-align="center"
| anti1 || Example || C2 || Example || Example
|-align="center"
| anti2 || Example || Ci || Example || Example
|-align="center"
| anti3 || [[Image:Anti2_Ci_tg2412.PNG|centre|350x350px|Cope rearrangement]] || C2h || Example || Example
|-align="center"
| anti4 || Example || C1 || Example || Example
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

''' Summary of activation energies (in kcal/mol) '''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''Expt.'''
|-
| ''' '''
| width="125" align="center" | '''at 0 K '''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
|-
| '''ΔE (Chair)'''
| align="center" | 45.70
| align="center" | 44.69
| align="center" | 36.11
| align="center" | 34.93
| align="center" | 33.5 ± 0.5
|-
| '''ΔE (Boat)'''
| align="center" | 55.61
| align="center" | 54.76
| align="center" | 44.37
| align="center" | 43.48
| align="center" | 44.7 ± 2.0
|}

From the Activation energies that calculated above, the HF/21G optimisation result is less actuate than 6-31G* as the activation energy generated from 6-31G* is way closer in both case.

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|'''butadiene'''
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|-align="center"
|'''ethene'''
|[[Image:HOMO_ethene_tg2412.jpg|350px]]
|[[Image:LUMO_ethene_tg2412.jpg|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency2_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:DA_2_endo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:DA_2_exo_TS_IRC_moive_tg2412.gif]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:DA_2_endo_TS_IRC_moive2_tg2412.gif]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

User:Tg2412

2015-01-30T10:08:26Z

Tg2412: /* Cis-butadiene and Ethene */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche1 || Example || C2 || Example || Example
|-align="center"
| gauche2 || Example || C2 || Example || Example
|-align="center"
| gauche3 || Example || C1 || Example || Example
|-align="center"
| gauche4 || Example || C2 || Example || Example
|-align="center"
| gauche5 || Example || C1 || Example || Example
|-align="center"
| gauche6 || Example || C1 || Example || Example
|-align="center"
| anti1 || Example || C2 || Example || Example
|-align="center"
| anti2 || Example || Ci || Example || Example
|-align="center"
| anti3 || [[Image:Anti2_Ci_tg2412.PNG|centre|350x350px|Cope rearrangement]] || C2h || Example || Example
|-align="center"
| anti4 || Example || C1 || Example || Example
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|'''butadiene'''
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|-align="center"
|'''ethene'''
|[[Image:HOMO_ethene_tg2412.jpg|350px]]
|[[Image:LUMO_ethene_tg2412.jpg|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency2_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:DA_2_endo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:DA_2_exo_TS_IRC_moive_tg2412.gif]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:DA_2_endo_TS_IRC_moive2_tg2412.gif]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

2015-01-30T09:40:04Z

Tg2412:

File:DA 2 exo TS IRC moive tg2412.gif

2015-01-30T09:33:50Z

Tg2412:

User:Tg2412

2015-01-30T09:25:39Z

Tg2412: /* Endo vs Exo Diels-Alder Reaction */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche1 || Example || C2 || Example || Example
|-align="center"
| gauche2 || Example || C2 || Example || Example
|-align="center"
| gauche3 || Example || C1 || Example || Example
|-align="center"
| gauche4 || Example || C2 || Example || Example
|-align="center"
| gauche5 || Example || C1 || Example || Example
|-align="center"
| gauche6 || Example || C1 || Example || Example
|-align="center"
| anti1 || Example || C2 || Example || Example
|-align="center"
| anti2 || Example || Ci || Example || Example
|-align="center"
| anti3 || [[Image:Anti2_Ci_tg2412.PNG|centre|350x350px|Cope rearrangement]] || C2h || Example || Example
|-align="center"
| anti4 || Example || C1 || Example || Example
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:DA_2_endo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:name.JPG|name.JPG]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:name.JPG|name.JPG]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

User:Tg2412

2015-01-30T09:21:04Z

Tg2412: /* Chair and Boat Transition Structure */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche1 || Example || C2 || Example || Example
|-align="center"
| gauche2 || Example || C2 || Example || Example
|-align="center"
| gauche3 || Example || C1 || Example || Example
|-align="center"
| gauche4 || Example || C2 || Example || Example
|-align="center"
| gauche5 || Example || C1 || Example || Example
|-align="center"
| gauche6 || Example || C1 || Example || Example
|-align="center"
| anti1 || Example || C2 || Example || Example
|-align="center"
| anti2 || Example || Ci || Example || Example
|-align="center"
| anti3 || [[Image:Anti2_Ci_tg2412.PNG|centre|350x350px|Cope rearrangement]] || C2h || Example || Example
|-align="center"
| anti4 || Example || C1 || Example || Example
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of chair TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:JPG]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:name.JPG|name.JPG]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:name.JPG|name.JPG]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

File:DA 2 endo TS vibration tg2412.gif

2015-01-30T09:20:07Z

Tg2412:

User:Tg2412

2015-01-30T08:52:23Z

Tg2412: /* Chair and Boat Transition Structure */

=Module3:Transition states and reactivity=
==Introduction==

==The Cope Rearrangement of 1,5-hexadiene==
The Cope rearrangement of 1,5-hexadiene is a typical [3,3]sigmatropic rearrangement. The mechanism of this reaction is generally believe to go trough 'chair' and 'boat' transition state(TS). During the tutorial, we built both transition structure and found their activation energies.

[[Image:Cope_tg2412.jpg|centre|350x350px|Cope rearrangement]]

===Reactants===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
! Conformer !! Structure !! Point Group !! Energy/Hartrees HF/3-21G !! Relative Energy/kcal/mol
|-align="center"
| gauche1 || Example || C2 || Example || Example
|-align="center"
| gauche2 || Example || C2 || Example || Example
|-align="center"
| gauche3 || Example || C1 || Example || Example
|-align="center"
| gauche4 || Example || C2 || Example || Example
|-align="center"
| gauche5 || Example || C1 || Example || Example
|-align="center"
| gauche6 || Example || C1 || Example || Example
|-align="center"
| anti1 || Example || C2 || Example || Example
|-align="center"
| anti2 || Example || Ci || Example || Example
|-align="center"
| anti3 || [[Image:Anti2_Ci_tg2412.PNG|centre|350x350px|Cope rearrangement]] || C2h || Example || Example
|-align="center"
| anti4 || Example || C1 || Example || Example
|}

=== Chair and Boat Transition Structure===

'''<big>Chair Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Chair_TS_movie_tg2412.gif]]
|}

'''<big>Boat Transition Structure</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of boat TS'''
|-align="center"
|[[Image:Boat_ts_tg2412.gif]]
|}
QTS2 is used to generated to transition structure form the structure of reactant and product. The numbering of atomic from atomic list must be keep the same order.

'''<big>Intrinsic Reaction Coordinate</big>'''

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC for the reaction'''
|'''Energy plot for the IRC '''
|-align="center"
|[[Image:Chair_IRC_real_tg2412.gif]]
|[[Image:IRC_chair_real_tg2412.PNG|700px]]
|}
In this case, IRC is only running in one direction as the reaction is symmetric and the other direction will be exactly the same. Where as for the reaction is not symmetric, it is necessary to run the IRC in both direction(which is used in later past of this wiki page).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 298.15K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -234.391626
| width="125" align="center" | -234.427323
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.461353
| align="center" | -234.405192
| align="center" | -231.450922
| align="center" | -234.392570
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.602802
| align="center" | -234.441291
| align="center" | -231.444349
| align="center" | -234.396006
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.495222
| align="center" | -231.466714
| align="center" | -231.479768
| align="center" | -234.461856
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
|align="center" | '''At 0K '''
!colspan="2"|'''Chair-TS'''
!colspan="2"|'''Boat-TS'''
|-
| ''' '''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
| width="187.5" align="center" | '''HF/3-21G'''
| width="187.5" align="center" | '''B3LYP/6-31G*'''
|-
| '''Sum of electronic and zero-point Energies '''
| width="125" align="center" | -231.466714
| width="125" align="center" | -234.411655
| width="125" align="center" | -231.450922
| width="125" align="center" | -234.398496
|-
| '''Sum of electronic and thermal Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Enthalpies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|-
| ''' Sum of electronic and thermal Free Energies'''
| align="center" | -231.466714
| align="center" | -234.411655
| align="center" | -231.450922
| align="center" | -234.398496
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.466714
| align="center" | -231.466714
| align="center" | -231.461353
| align="center" | -234.54046002
| align="center" | -234.411655
| align="center" | -234.405192
|-
| '''Boat TS'''
| align="center" | -231.60280239
| align="center" | -231.450922
| align="center" | -231.445294
| align="center" | -234.54046002
| align="center" | -234.398497
| align="center" | -234.392570
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

==The Diels Aider Cycloaddition==
===Cis-butadiene and Ethene===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''HOMO of cis-butadiene'''
|'''LUMO of cis-butadiene'''
|-align="center"
|[[Image:DA_reaction_butadiene_HOMO_tg2412.JPG|350px]]
|[[Image:DA_reaction_butadiene_tg2412.JPG|350px]]
|}
As shown in the graph above, the HOMO of cis-butadiene is anti-symmetrical to the mirror plane and LUMO is symmetric to the mirror plane. The transition state is generate from

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Imaginary Frquency of TS'''
|'''HOMO of TS'''
|'''LUMO of TS'''
|-align="center"
|[[Image:DA_1_Imaginary_frquency_tg2412.gif]]
|[[Image:DA_TS_HOMO_tg2412.JPG|400px]]
|[[Image:DA_TS_LUMO_tg2412.JPG|400px]]
|}

===Endo vs Exo Diels-Alder Reaction===

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''Exo TS Imagery frequency'''
|'''Endo TS Imagery frequency'''
|-align="center"
|[[Image:DA_2_exo_TS_vibration_tg2412.gif|DA_2_exo_TS_vibration_tg2412.gif]]
|[[Image:JPG]
|}

'''<big>Exo product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Exo product'''
|'''Energy plot of IRC'''
|-align="center"
|[[Image:name.JPG|name.JPG]]
|[[Image:Exo_TS_IRC_tg2412.PNG|700px]]
|}

'''<big>Endo Product</big>'''
----

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''IRC of Endo product'''
|'''Energy plot of Endo IRC'''
|-align="center"
|[[Image:name.JPG|name.JPG]]
|[[Image:Endo_TS_IRC_tg2412.PNG|700px]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''electronic energy of starting point(hartree)'''
|'''electronic energy of TS(hartree)'''
|'''ΔE(hartree)'''
|-align="center"
|'''exo'''
| -605.651
| -605.610
| 0.041
|-align="center"
|'''endo'''
| -605.652
| -605.604
| 0.048
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|'''activation energy to TS'''
|'''kcal/mol'''
|-align="center"
|'''exo'''
| 30.12
|-align="center"
|'''endo'''
| 25.73
|}
The ICR calculation coverage backward to a local minimum on the both energy plot. Theoretically the backward reaction should not be converge as the reactants will have the minimum energy at infinity. This case we assume it is the energy of reactant as the molecule will approach to each other during the reaction. The different in energy of reactant and transition state is the activation energy.The calculation indicate that exo transition structure have a higher energy transition state(4.39 kcal/mol more than endo). As we know the reaction is driven by kinetics, the major product will endo-prodoct as it has a lower energy transition state.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-align="center"
|''' '''
|'''Endo'''
|'''Exo'''
|-align="center"
|'''LUMO'''
|[[Image:DA2_ENDO_LUMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_LUMO_tg2412.JPG|400px]]
|-align="center"
|'''HOMO'''
|[[Image:DA2_ENDO_HOMO_tg2412.JPG|400px]]
|[[Image:DA2_EXO_HOMO_tg2412.JPG|400px]]
|}
From the molecular orbital of Endo and Exo TS, It is important to see that in the HOMO of Endo-TS the Π orbital on oxygen in -(C=O)-O-(C=O)- fragment can interact and donating electron to the Π* orbital of conjugate double bond orbital in cyclohexa-1,3-diene shown in the LUMO of Exo-TS. This orbital contribution will lower down the overall electronic energy of Endo-TS. This secondary orbital overlap effect is consider to be the main contribution to the lower energy Transition state of endo-product. Where as for the Exo-Ts, there is effect is hard to observe.

User:Tg2412

User:Tg2412

2015-01-30T05:51:52Z

Tg2412: /* Endo vs Exo Diels-Alder Reaction */

User:Tg2412

2015-01-30T05:49:38Z

Tg2412: Undo revision 481043 by Tg2412 (talk)