Rep:Mod:SAITYM954

2014-03-07T13:53:35Z

Ys4111:

=Organic Computational=
==Conformational analysis using Molecular Mechanics==
Cyclopentadiene dimer 1 and 2 and the hydrogenation product of the cyclopentadiene 2, 3 and 4, were modeled on Avagadro and their geometries were optimized using the MMFF94(s) force field option. The energies of the optimized energies are given in Table 1.

{| class="wikitable" border="1"
|+ TABLE 1
! Type of molecule !! Cyclopentadiene dimer 1!! Cyclopentadiene dimer 2!! Hydrogenation product 3!! Hydrogenation product 4
|-
| molecular model ||<jmol><jmolApplet><title>cyclopentadiene dimer 1</title><color>white</color>
<size>150</size><uploadedFileContents>Product1avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>cyclopentadiene dimer 2</title><color>white</color>
<size>150</size><uploadedFileContents>Product2.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>hydrogenation product 3</title><color>white</color>
<size>150</size><uploadedFileContents>Product3avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>hydrogenation product 4</title><color>white</color>
<size>150</size><uploadedFileContents>Product4avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>
|-
| Total bond stretching energy(kcal/mol) || 3.54317 || 3.46793||3.31151|| 2.82308
|-
| Total angle bending energy(kcal/mol) ||30.77258|| 33.18901|| 31.93319|| 24.68545
|-
| Total stretch bending energy(kcal/mol) ||-2.04144|| -2.08220|| -2.10211|| -1.65717
|-
| Total torsional energy(kcal/mol) || -2.73092|| -2.94964|| -1.46866|| -0.37823
|-
| Total out-of-plane bending energy(kcal/mol) || 0.01476|| 0.02183|| 0.01309|| 0.00028
|-
| Total van der Waals energy(kcal/mol) || 12.80160|| 12.35898|| 13.63920|| 10.63705
|-
| Total electrostatic energy(kcal/mol) || 13.01367|| 14.18476|| 5.11950|| 5.14702
|-
| Total energy(kcal/mol) || 55.37342|| 58.19067|| 50.44571|| 41.25749
|}
Although it can be seen that the total energy of the cyclopentadiene dimer 1 is lower than 2, cyclopentadiene dimerises to produce specifically the cyclopentadiene dimer 2. From this information, it can be concluded that although the cyclopentadiene dimer 1 is the more stable product out of the two dimers and therefore the thermodynamic product, the dimerisation of pentadiene is kinetically controlled and therefore favours the kinetic product, cyclopentadiene dimer 2.

The cyclopentadiene dimer 2 can hydrogenate to initially form two products, 3 and 4. Product 3 and 4 have double bonds hydrogenated in the cyclopentene ring and the norbornene ring respectively. Product 4 is seen to be predominantly favored product due to it being the lower energy product as well as the double bond in the norbornene ring reacting with hydrogen approximately 5 times faster than the double bond in the cyclopentene ring.<ref>D. Skála and J. Hanika,Petroleum and Coal,(1968), 45, 105-108</ref> The relative ease of hydrogenation of the respective double bonds can be attributed to the difference in different energies listed in Table 1 between product 3 and 4 and somewhat can be explained by analyzing them. It can be seen that product 4 has substantially lower energy in total angle bending energy, and total van der Waals energy, with a slightly lower energy in total bond stretching energy, relative to product 3, whereas product 3 is only slightly lower in energy in total electrostatic energy and total torsional energy relative to product 4. This explains the big difference in total energy favoring product 4 and also shows that the difference in energy between the two products 3 and 4 is mostly contributed by the difference in total angle bending energy, and total van der Waals energy. The possible explanation why the total angle bending energy, and total van der Waals energy is lower in product 4 is that ,looking at the reactant (cyclopentadiene dimer 2), the hydrogen atom on the unsaturated carbon in the norbornene ring is almost in plane and in closer proximity with the hydrogen atom on the saturated carbon atom adjacent to it than the hydrogen atom on the unsaturated carbon in the cyclopentene ring. The closer proximity of the hydrogen atom in the norbornene ring means that, there is a greater release in strain and therefore lowering of energy especially in total angle bending energy, and total van der Waals energy when the double bond in the norbornene ring is hydrogenated opposed to the cyclopentene ring. This explains why hydrogenation of double bond in the norborene ring, and therefore synthesis of product 4, is favored relative to product 3.
==Atropisomerism in an Intermediate related to the Synthesis of Taxol==
Key intermediate for the synthesis of Taxol, 9 and 10, was modeled on Avagadro and its geometry was optimized using the MMFF94s force-field option. The respective energies of the intermediate are given in Table 2.

{| class="wikitable" border="1"
|+ Table 2
!Type of Molecule !!Intermediate 9(chair) !! Intermediate 10(chair)!! Hydrogenated Intermediate 9!! Hydrogenated Intermediate 10
|-
| Molecular Model || <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_9avagadro2.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_10avagadro2.cml</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_9_hydrogenated_avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_10_hydrogenated.cml</uploadedFileContents>
</jmolApplet></jmol>
|-
| Total bond stretching energy(kcal/mol) || 7.66637|| 7.60691|| 7.06510|| 6.41196
|-
| Total angle bending energy(kcal/mol) || 28.29002|| 18.81375|| 28.68337|| 22.31678
|-
| Total stretch bending energy(kcal/mol) || -0.07465|| -0.14531|| 0.28404|| 0.29516
|-
| Total torsional energy(kcal/mol) || 0.27125|| 0.25598|| 10.40618|| 9.20328
|-
| Total out-of-plane bending energy(kcal/mol) || 0.97178|| 0.84841|| 0.09869|| 0.03531
|-
| Total van der Waals energy(kcal/mol) || 33.11267|| 33.22378|| 33.34614|| 31.27316
|-
| Total electrostatic energy(kcal/mol) || 0.30537|| -0.05004|| 0.00000|| 0.00000
|-
| Total energy(kcal/mol) || 70.54281|| 60.55348|| 79.88353|| 69.53565
|}

{| class="wikitable" border="1"
|+ Table 2 (cont.)
!Type of Molecule !!Intermediate 9(boat) !! Intermediate 10(boat)
|-
| Molecular Model || <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_9avagadro2_boat.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_10avagadro2_boat.cml</uploadedFileContents>
</jmolApplet></jmol>||
|-
| Total bond stretching energy(kcal/mol) || 8.00455|| 7.76754
|-
| Total angle bending energy(kcal/mol) || 30.20403|| 19.02758
|-
| Total stretch bending energy(kcal/mol) || -0.03535|| -0.13479
|-
| Total torsional energy(kcal/mol) || 2.70443|| 3.74744
|-
| Total out-of-plane bending energy(kcal/mol) || 0.94585|| 0.95707
|-
| Total van der Waals energy(kcal/mol) || 35.80197|| 34.99801
|-
| Total electrostatic energy(kcal/mol) || 0.29435|| -0.06080
|-
| Total energy(kcal/mol) || 77.91981|| 66.30205
|}
The intermediate 10 was calculated to be the more thermodynamically stable intermediate relative to intermediate 9. This is mostly due to the difference in total angle bending energy which can be attributed possibly to the position of the O atom which experience less steric repulsion in intermediate 10 than in intermediate 9. The intermediates had lower total energies when the configuration of the 6-membered ring was in a chair configuration rather than a boat configuration. This suggests that the chair configuration is favored over the boat configuration in the 6-membered rings for these intermediates.

The functionalisation of the alkene for these intermediate has been reported to be extremely slow. This can be explained by the the energies listed in Table 2. There is a tendency in polycyclic systems for bridge head atoms to favor sp2 configuration rather than sp3. This is due to the extra stability afforded by these 'cage structures' as well as it being due to the sp2 intermediates having less strain than its parent polycycloalkane configurations.<ref>Wilhelm F. Maier and Paul von RaguC Schleyer, ''J. Am. Chem. SOC.'' 1981, '''103''', 1891-1900 </ref> This effect can be seen in the energy table above where the total torsional energy is significantly lower in energy in the intermediates than their respective hydrogenated product leading to lower total energy in the intermediate.

==Spectroscopic Simulation using Quantum Mechanics==
Molecules 17 and 18 which are derivatives of molecules 8 and 9 were processed in a HPC and its 1H and 13C NMR were calculated . The DOI for the data of the calculations are given in the reference.<ref>{{DOI|10042/27911}}</ref><ref>{{DOI|10042/27912}}</ref><ref>{{DOI|10042/27913}}</ref><ref>{{DOI|10042/27914}}</ref>
{| class="wikitable" border="1"
|+ Table3
! Type of Molecule!!Molecule 17 Chair!! Molecule 17 boat!! Molecule 18 Chair !! Molecule 18 boat
|-
|Molecular model||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>17HPCmol.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>17boatHPCmol.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>HPC18mol.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>18HPCboatmol.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Sum of electronic and thermal Free Energies||-1651.440152||-1651.437358||-1651.464202||-1651.462786
|}
The Sum of electronic and thermal Free Energies, is the free energy, ΔG , of the molecule and can be used to comapre relative energies of these molecules. It can be sen that molecule 18 is generally favoured. however contrary to molecules 9 and 10, the molecule with the 6-membered ring in the boat configuration has lower relative energies and is favored.
The 1H and 13C NMR for both molecule 17 and 18 are as follows
{| class="wikitable" border="1"
|+ NMR of molecule 17(boat)
! 1H !! 13C!! NMR atom labels!! NMR atom labels 2
|-
| [[File:NMR17.svg|thumb|center|click to expand]] || [[File:NMR13C_17.svg|thumb|center|click to expand]]|| [[File:Labels17.jpg|thumb|center|click to expand]]|| [[File:Labels17_2.jpg|thumb|center|click to expand]]
|}

{| class="wikitable" border="1"
|+ NMR of molecule 18(boat)
! 1H !! 13C!! NMR atom labels!! NMR atom labels 2
|-
| [[File:NMRH1_18.svg|thumb|center|click to expand]] || [[File:NMRC13_18.svg|thumb|center|click to expand]]|| [[File:Labels18.jpg|thumb|center|click to expand]]|| [[File:Labels18_2.jpg|thumb|center|click to expand]]
|}

{| class="wikitable" border="1"
|+ NMR assignments
! 1H 17 !! 13C 17!!1H 18!!13C 18
|-
| [[File:HNMRsummary_17.jpg|thumb|center|click to expand]] || [[File:CNMRsummary_17.jpg|thumb|center|click to expand]]|| [[File:HNMRsummary_18.jpg|thumb|center|click to expand]]|| [[File:CNMRsummary_18.jpg|thumb|center|click to expand]]
|}
{| class="wikitable" border="1"
|+ Comaprison between literature and calculated NMR<ref>''Leo A. Paquette,* Neil A. Pegg, Dana Toops,’ George D. Maynard, and
Robin D. Rogers*, J. Am. Chem. Soc.'',(1990),'''112''',277 </ref>
! 1H 17 !! 13C 17!!1H 18!!13C 18
|-
| [[File:HNMR_boat_17_excel.jpg|thumb|center|click to expand]] || [[File:CNMR_boat_17_excel.jpg|thumb|center|click to expand]]|| [[File:HNMR_boat_18_excel.jpg|thumb|center|click to expand]]|| [[File:CNMR_boat_18_excel.jpg|thumb|center|click to expand]]
|}
The calculated NMRs were generally in agreement with literature. The 1H NMRs did not show great agreement with literature but chemical shift values were generally in the right place. On the other hand 13C NMRs showed good agreement with literature values. The calculated NMRs shifts tended to be higher than the chemical shifts in literature but this is thought to be due to lack of precise correction. The NMRs of the chair conformations were also calculated and these NMR generally tended to have chemical shifts at lower magnetic field relative to NMRs of the molecules with boat conformations. The NMR chemical shift of the carbon atoms attached to the sulfur atom must be corrected due to spin-orbit coupling errors. This explains the large deviation of chemical shift of C-12 and a possible small deviation at C-17 and C-18. However the literature for spin-orbit coupling error for the C-S bond could not be found and therefore the chemical shift values were left uncorrected on the presented data but is expected to be around -6ppm correction for each C-S bond.
==Analysis of the properties of the synthesised alkene epoxides==
The alkenes styrene and trans-Stilbene were chosen, and its epoxide derivatives were analysed.
===Crystal structures of the two catalyst for epoxidation 21 and 23===
The Shi asymmetric Fructose catalyst and the Jacobsen asymmetric catalyst which are labelled as catalyst 21 and 23 respectively are the stable precursors of the catalyst and are used in catalysing the epoxidation of alkenes. Its structures are shown below.
{| class="wikitable" border="1"
|+ Catalysts 21 and 23
! catalyst 21 !! catalyst 23!! anomeric centre of catalyst 21!!Stereoisomer A and B of catalyst 21
|-
| [[File:Catalyst21.jpg|thumb|center|The Shi asymmetric Fructose catalyst ]] || [[File:Catalyst_23.jpg|thumb|center|The Jacobsen asymmetric catalyst ]]|| [[File:Catalyst21_anomer.jpg|thumb|center|alpha and beta anomers of catalyst 21 (click to expand) ]]|| [[File:Catalyst21_isomer.jpg|thumb|center|Stereoisomer A and B of catalyst 21 (click to expand) ]]
|}

{| class="wikitable" border="1"
|+ crystal structures of catalyst 21 and 23
! catalyst 21 !! catalyst 23
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>250</size><uploadedFileContents>Catalyst_21_mercury.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>250</size><uploadedFileContents>Catalyst23mercury.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Labels on Atoms
! catalyst 21!! catalyst 23
|-
| [[File:Labels21.jpg|thumb|center|The Shi asymmetric Fructose catalyst ]] || [[File:Labels23.jpg|thumb|center|The Jacobsen asymmetric catalyst ]]
|}

Catalyst 21, forms a crystal structure stabilized by hydrogen bonding between the hydrogen atoms on carbon C8,C9 and C6 and oxygen atoms O1 and O2. Two stereoisomer, A and B, exist for catalyst 21 and in the crystal structure, the A isomer forms infinite zig-zag chain connected by hydrogen bonding with B isomer further stabilizing the crystal sturcture as side-chains. The C-O bond of the anomeric center, located on C2, has unusual properties. It can be seen that oxygen atoms bonded to C2, O6 and O2, have unusually short C-O bond lengths 1.403A. Looking at the average C-O bond length which is 1.43, there is a big difference in bond length. This shortened C-O bond length could be accounted for by the anomeric effect where there are stabilizing interaction between the bonding orbitals of oxygen and anti-bonding orbital of carbon. This effect also explains why the C2-C3 and C2-C1 are one of the longest C-C bonds in the molecule.<ref>M.Durik, V.Langer, D.Gyepesova, J.Micova, B.Steiner, M.Koos, ''Acta Crystallogr'', (2001). '''E57''', o672-o674</ref>

Catalyst 23 form crystal structures where the catalyst assume an asymmetric position shown above. The crystal structure consists only of Van der Waal's interactions. The tert-butyl group present in the molecule gives the bent shape that is present in the molecule due to steric repulsion and it has been found that when these tert-butyl groups present in positions C17 and C4 were substituted for triisopropylsiloxyl groups, the molecule took a flat shape instead of a bent shape as previously seen.<ref>JAE WOONG YOON, TAE-SUNO YOON, SOON WON LEE AND WHANCHUL SHIN, ''Acta Cryst.'' (1999). '''C55''', 1766-1769 </ref>
===NMR analysis of the epoxide products===
The DOI for the data of the calculations for these epoxides are given in the reference.<ref>{{DOI|10042/27915}}</ref><ref>{{DOI|10042/27916}}</ref><ref>{{DOI|10042/27917}}</ref><ref>{{DOI|10042/27918}}</ref>

{| class="wikitable" border="1"
|+ Calculated NMR of styrene oxide
! 1H styrene oxide !! 13C styrene oxide!!labels on atoms!!NMR atom assignment
|-
| [[File:HNMRHPC_styrene.svg|thumb|center|'' ]] || [[File:CNMRHPC_styrene.svg|thumb|center|'' ]]|| [[File:Labels_styrene.jpg|thumb|center|'' ]]|| [[File:CandHNMR_styrene.jpg|thumb|center|'' ]]
|}

{| class="wikitable" border="1"
|+ Calculated NMR of trans-Stilbene oxide
! 1H trans-Stilbene oxide!!13C trans-Stilbene !! labels on atoms!!NMR atom assignment
|-
| [[File:HNMRHPC_stilbene.svg|thumb|center|'' ]] || [[File:CNMRHPC_stilbene.svg|thumb|center|'' ]]|| [[File:Labels_stilbene.jpg|thumb|center|'' ]]|| [[File:HandCNMR_stillbene.jpg|thumb|center|'' ]]
|}

{| class="wikitable" border="1"
|+ NMR chemical shift data and comparison with literature<ref>Charlotte Wiles*, Marcus J. Hammond1 and Paul Watts*,''Beilstein Journal of Organic Chemistry'', (2009), '''5''', 1-12</ref>
! 1H styrene oxide !! 13C styrene oxide!!1H trans-Stilbene oxide!!13C trans-Stilbene
|-
| [[File:Styrene_oxide_HNMR.jpg|thumb|center|'' ]] || [[File:Styrene_oxide_CNMR.jpg|thumb|center|'' ]] ||[[File:Trans-stilbene_oxide_HNMR.jpg|thumb|center|'' ]]||[[File:Trans-stilbene_oxide_CNMR.jpg|thumb|center|'' ]]
|}
The calculated NMRs showed very good agreement with literature, and shows that these computated epoxide models can be used to predict properties of real molecules with a relatively good accuracy. As expected, the NMR values of enantiomers and diastereoisomers of the epoxides were the same.
===Assigning the absolute configuration of the product===
====Calculated and reported literature for the epoxides, styrene oxide and trans-stilbene oxide====
The reported and calculated optical rotations are shown in the table below.

{| class="wikitable" border="1"
|+ optical rotations of epoxides at 598nm
! ''!!(R)-styrene oxide !! ''!! (S)-styrene oxide!! ''!!(R,R)-trans-stilbene oxide!!''!!(S,S)-trans-stilbene oxide!!''
|-
| '' || calculated|| literature|| calculated|| literature|| calculated|| literature|| calculated|| literature
|-
| optical rotation (598nm)/degrees || -30.43<ref>{{DOI|10042/27922}}</ref> ||-33.3<ref>Frederick R. Jensen* and Ronald C. Kiskis*,''Journal of the American Chemical Society'',1975,'''97.20''',5825</ref>|| 30.10<ref>{{DOI|10042/27921}}</ref> || 32.1<ref>Hui Lin a,b, Yan Liu a, Zhong-Liu Wua,''Tetrahedron: Asymmetry'' ,(2011),'''22''' 134–137</ref>|| 297.90<ref>{{DOI|10042/27919}}</ref> || 310<ref>Rukhsana I. Kureshy,* Surendra Singh, Noor-ul H. Khan, Sayed H. R. Abdi,
Santosh Agrawal and Raksh V. Jasra,''Tetrahedron: Asymmetry'' (2006),'''17''', 1638–1643 </ref>|| -297.67<ref>{{DOI|10042/27920}}</ref> || no literature found
|}
The optical rotations are in good agreement with the reported literature values. Although the literature value for the optical rotation for (S,S)-trans stilbene oxide could not be found, assuming that the value of the optical rotation for (R,R)-trans stilbene oxide, which has good agreement with reported literature value , is accurate, it can also be assumed that the computed value of (S,S)-trans stilbene is also correct as they are diasteroisomers of each other and the optical rotation of diastereoisomers should be equal but opposite which it very nearly is. Optical rotations of less than a 100 degrees, cannot usually be calculated accurately using this computational methods, but it seems as though the optical rotation of styrene has been calculated relatively accurately. This could be due to styrene being a relatively simple molecule. The sign of optical rotation cannot be used to predict the absolute configuration S or R, due to the direction of the optical rotation being completely random depending on the molecule for R and S. This can be seen in the computed values of optical rotation where R and S configurations have both direction of optical rotation assigned between the two molecules.

====Using the calculated properties of transition state for the reaction====
The calculated energies of transition state for the epoxidation of the chosen alkenes were used to assign the absolute configuration of epoxides, styrene oxide and trans-stilbene oxide. The energy calculation were provided by the Imperial College Chemistry department. The label R or S of the transition state refers to the face of the alkene that the catalsyt react to and therefore R and S of the same number are enantiomers of each other. Below the difference in free energy ΔG is calculated and the equilibrium constant, K, which refers to the ratio of R and S produced is calculated by the equation ΔG=-RTlnK. The calculated K is then used to work out the enantiomeric excess for either R or S. For example if K=0.6149, in this case it means that for every mole of S enantiomer produced, 0.6149 moles of R enatiomer is produced. ee=((R-S)/(R+S))x100%, where R+S =1, and therefore ee= ((1/1.6146)-(0.6149/1.6149)/(1))x100%= 23.84% ee for S.
=====Styrene transition state=====
=====Shi epoxidation of styrene=====
For the epoxidation of styrene using Shi's catalyst. 8 possible transition states can be envisaged

{| class="wikitable" border="1"
|+ structures of transiton state (R)
! R1 !! R2!! R3!! R4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R1 yuki.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ structures of transiton state (S)
! S1 !! S2!! S3!! S4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S1.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for styrene transition state (R and S)(Shi epoxidation) 2625.5
! Type of transition !! S1!! S2!! S3!! S4
|-
| Sum of electronic and thermal Free Energies || -1303.733828|| -1303.724178|| -1303.727673|| -1303.738503
|-
!Type of transition!! R1!! R2!! R3!! R4
|-
| Sum of electronic and thermal Free Energies||-1303.730703|| -1303.730238||-1303.736813|| -1303.738044
|-
!''!!R1-S1!! S2-R2!! S3-R3!! R4-S4
|-
|Difference in Free energy(hartree) || 0.003125|| 0.00606|| 0.00914|| 0.000459
|-
|Difference in Free energy(kJ/mol) || 8.205|| 15.911|| 23.997|| 1.205
|-
|Equlibrium constant(K)|| 0.0365|| 0.001629|| 0.0000624|| 0.6149
|-
|Enantimeric excess of (R or S)|| 92.9%(S)|| 99.8%(R)|| 99.9%(R)|| 23.84%(S)
|}
Literature for this reaction have reported to give the enatiomeric excess to the R enantiomer at 81%. It is therefore very likely that the approach and orientation of the catalyst will be either 2 or 3. <ref>Hongqi Tian, Xuegong She, Jiaxi Xu, and Yian Shi*,''Org. Lett.'',(2001),'''3''',1929-1931</ref>

=====Jacobsen epoxidation of styrene=====
{| class="wikitable" border="1"
|+ structures of transiton state
! R5 !! R6!! S5!! S6
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R1_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R2_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S1_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S2_J.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for styrene transition state (Jacobsen epoxidation)
! Type of transition !! S5!! S6
|-
|Sum of electronic and thermal Free Energies ||-3343.969197|| -3343.963191
|-
!Type of transition !! R5!! R6
|-
| Sum of electronic and thermal Free Energies || -3343.960889|| -3343.962162
|-
!''!!R1-S1!! R2-S2
|-
|Difference in Free energy(hartree) || 0.008308|| 0.001029
|-
|Difference in Free energy(kJ/mol) || 21.812654|| 2.7016395
|-
|Equlibrium constant|| 0.000125|| 0.32866
|-
|Enantimeric excess(ee) of (R or S)|| 99.9%(S)|| 50.5%(S)
|}
Literature for this epoxidation has reported ee of 46% favoring S enantiomer. This is in good agreement with the second transition state and therefore the catalyst is likely to be orientated as such.<ref>Michael Palucki, Paul J. Pospisil, Wei Zhang, and
Eric N. Jacobsen,''J. Am. Chem. SOC.'' 1994,'''116''', 9333-9334 </ref>
=====Trans-Stilbene transition state=====
Similar to the styrene transition state, the energies of the trans-stilbene transition states were analysed. There are 8 possible transition state that can be envisaged for this reaction
=====Shi epoxidation of trans-stilbene=====
{| class="wikitable" border="1"
|+ structures of transiton state (R)
! RR1 !! RR2!! RR3!! RR4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR1.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ structures of transiton state (S)
! SS1 !! SS2!! SS3!! SS4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS1.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for tans-stilbene transition state (R and S)(Shi epoxidation) 2625.5
! Type of transition !! SS1!! SS2!! SS3!! SS4
|-
| Sum of electronic and thermal Free Energies || -1534.683440||-1534.685089||-1534.693818|| -1534.691858
|-
!Type of transition!! RR1!! RR2!! RR3!! RR4
|-
| Sum of electronic and thermal Free Energies||-1534.687808|| -1534.687252||-1534.700037|| -1534.699901
|-
!''!!SS1-RR1!! SS2-RR2!! SS3-RR3!! SS4-RR4
|-
|Difference in Free energy(hartree) || 0.004368|| 0.002163|| 0.006219|| 0.008043
|-
|Difference in Free energy(kJ/mol) || 11.4681|| 5.6789|| 16.3279|| 21.1169
|-
|Equlibrium constant(K)|| 0.009784|| 0.1011|| 0.001377|| 0.0001994
|-
|Enantimeric excess of (RR or SS)|| 98.1%(RR)|| 81.6%(RR)|| 99.7%(RR)|| 99.9%(RR)
|}
Literature for this epoxidation has reported ee>95% favouring RR configuration which is in good agreement with transition states 1,3 and 4. This epoxidation is therefore likely to take any of the transition, 1,3 and 4, as the transiton state for this reaction.<ref>Yong Tu, Zhi-Xian Wang, and Yian Shi*,''J. Am. Chem. Soc.'' 1996, '''118''', 9806-9807</ref>
=====Jacobson epoxidation of trans-stilbene=====
{| class="wikitable" border="1"
|+ structures of transiton state
! RR5 !! SS5
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR1_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS1_J.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for trans-stilbene transition state (Jacobsen epoxidation)
! Type of transition !! SS5
|-
|Sum of electronic and thermal Free Energies ||-3574.923087
|-
!Type of transition !! RR5
|-
| Sum of electronic and thermal Free Energies || -3574.921174
|-
!''!!RR5-SS5
|-
|Difference in Free energy(hartree) || 0.001913
|-
|Difference in Free energy(kJ/mol) || 5.0225
|-
|Equlibrium constant|| 0.1318
|-
|Enantimeric excess(ee) of (RR or SS)|| 76.7%(SS)
|}
Literature for this epoxidation reported ee of 25% favouring the SS configuration.<ref>Bridget D. Brandes and Eric N. Jacobsen,''J. Org. Chem.'' 1994,'''59''', 4378-4380</ref> Although computed energies predicted the SS configuration to be favored, there is a big difference in the value of ee. This could be due to error in experimental data, or lack of accuracy in the computational data and therefore further analysis maybe needed to clarify this.

Overall it can be concluded that the predictions for the absolute configuration of these epoxide reactions using different catalyst via computational methods are relatively accurate, as can be seen by the good agreement with literature values.

====Investigating the non-covalent interactions in the active-site of the reaction transition state====
NCI ananlysis was done on both R2 and S2 transitions for comparison.

{| class="wikitable" border="1"
|+ Molecular model showing NCI
! R2 !! S2
|-
| [[File:Styrene_R2_2.jpg|thumb|center|250px|'' ]] || [[File:Styrene_S2.jpg|thumb|center|250px|'' ]]
|}
The second transition state heavily favours the R enantiomer with an ee=99.8%(R), The R2 transition has a large mildly attractive surface of interaction almost completely surrounding the double bond of the styrene, which is the reaction site. The S2 transition in comaprison has a smaller midly attractive NCI surface relative to R around the double bond and has a cone like NCI interaction above the phenyl group which could become mildly repulsive upon closer approach of the catalyst to styrene which could suggest slight steric hinderance in S2. This difference in the magnitude of NCI interaction around the double bond could explain why R2 is so favored relative to the S2.
====Investigating the Electronic topology (QTAIM) in the active-site of the reaction transition state====
The QTAIM of R2 only was analyzed this time.

==reference==
<references/>

Rep:Mod:SAITYM954

2014-03-07T13:31:23Z

Ys4111:

=Organic Computational=
==Conformational analysis using Molecular Mechanics==
Cyclopentadiene dimer 1 and 2 and the hydrogenation product of the cyclopentadiene 2, 3 and 4, were modeled on Avagadro and their geometries were optimized using the MMFF94(s) force field option. The energies of the optimized energies are given in Table 1.

{| class="wikitable" border="1"
|+ TABLE 1
! Type of molecule !! Cyclopentadiene dimer 1!! Cyclopentadiene dimer 2!! Hydrogenation product 3!! Hydrogenation product 4
|-
| molecular model ||<jmol><jmolApplet><title>cyclopentadiene dimer 1</title><color>white</color>
<size>150</size><uploadedFileContents>Product1avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>cyclopentadiene dimer 2</title><color>white</color>
<size>150</size><uploadedFileContents>Product2.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>hydrogenation product 3</title><color>white</color>
<size>150</size><uploadedFileContents>Product3avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>hydrogenation product 4</title><color>white</color>
<size>150</size><uploadedFileContents>Product4avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>
|-
| Total bond stretching energy(kcal/mol) || 3.54317 || 3.46793||3.31151|| 2.82308
|-
| Total angle bending energy(kcal/mol) ||30.77258|| 33.18901|| 31.93319|| 24.68545
|-
| Total stretch bending energy(kcal/mol) ||-2.04144|| -2.08220|| -2.10211|| -1.65717
|-
| Total torsional energy(kcal/mol) || -2.73092|| -2.94964|| -1.46866|| -0.37823
|-
| Total out-of-plane bending energy(kcal/mol) || 0.01476|| 0.02183|| 0.01309|| 0.00028
|-
| Total van der Waals energy(kcal/mol) || 12.80160|| 12.35898|| 13.63920|| 10.63705
|-
| Total electrostatic energy(kcal/mol) || 13.01367|| 14.18476|| 5.11950|| 5.14702
|-
| Total energy(kcal/mol) || 55.37342|| 58.19067|| 50.44571|| 41.25749
|}
Although it can be seen that the total energy of the cyclopentadiene dimer 1 is lower than 2, cyclopentadiene dimerises to produce specifically the cyclopentadiene dimer 2. From this information, it can be concluded that although the cyclopentadiene dimer 1 is the more stable product out of the two dimers and therefore the thermodynamic product, the dimerisation of pentadiene is kinetically controlled and therefore favours the kinetic product, cyclopentadiene dimer 2.

The cyclopentadiene dimer 2 can hydrogenate to initially form two products, 3 and 4. Product 3 and 4 have double bonds hydrogenated in the cyclopentene ring and the norbornene ring respectively. Product 4 is seen to be predominantly favored product due to it being the lower energy product as well as the double bond in the norbornene ring reacting with hydrogen approximately 5 times faster than the double bond in the cyclopentene ring.<ref>D. Skála and J. Hanika,Petroleum and Coal,(1968), 45, 105-108</ref> The relative ease of hydrogenation of the respective double bonds can be attributed to the difference in different energies listed in Table 1 between product 3 and 4 and somewhat can be explained by analyzing them. It can be seen that product 4 has substantially lower energy in total angle bending energy, and total van der Waals energy, with a slightly lower energy in total bond stretching energy, relative to product 3, whereas product 3 is only slightly lower in energy in total electrostatic energy and total torsional energy relative to product 4. This explains the big difference in total energy favoring product 4 and also shows that the difference in energy between the two products 3 and 4 is mostly contributed by the difference in total angle bending energy, and total van der Waals energy. The possible explanation why the total angle bending energy, and total van der Waals energy is lower in product 4 is that ,looking at the reactant (cyclopentadiene dimer 2), the hydrogen atom on the unsaturated carbon in the norbornene ring is almost in plane and in closer proximity with the hydrogen atom on the saturated carbon atom adjacent to it than the hydrogen atom on the unsaturated carbon in the cyclopentene ring. The closer proximity of the hydrogen atom in the norbornene ring means that, there is a greater release in strain and therefore lowering of energy especially in total angle bending energy, and total van der Waals energy when the double bond in the norbornene ring is hydrogenated opposed to the cyclopentene ring. This explains why hydrogenation of double bond in the norborene ring, and therefore synthesis of product 4, is favored relative to product 3.
==Atropisomerism in an Intermediate related to the Synthesis of Taxol==
Key intermediate for the synthesis of Taxol, 9 and 10, was modeled on Avagadro and its geometry was optimized using the MMFF94s force-field option. The respective energies of the intermediate are given in Table 2.

{| class="wikitable" border="1"
|+ Table 2
!Type of Molecule !!Intermediate 9(chair) !! Intermediate 10(chair)!! Hydrogenated Intermediate 9!! Hydrogenated Intermediate 10
|-
| Molecular Model || <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_9avagadro2.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_10avagadro2.cml</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_9_hydrogenated_avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_10_hydrogenated.cml</uploadedFileContents>
</jmolApplet></jmol>
|-
| Total bond stretching energy(kcal/mol) || 7.66637|| 7.60691|| 7.06510|| 6.41196
|-
| Total angle bending energy(kcal/mol) || 28.29002|| 18.81375|| 28.68337|| 22.31678
|-
| Total stretch bending energy(kcal/mol) || -0.07465|| -0.14531|| 0.28404|| 0.29516
|-
| Total torsional energy(kcal/mol) || 0.27125|| 0.25598|| 10.40618|| 9.20328
|-
| Total out-of-plane bending energy(kcal/mol) || 0.97178|| 0.84841|| 0.09869|| 0.03531
|-
| Total van der Waals energy(kcal/mol) || 33.11267|| 33.22378|| 33.34614|| 31.27316
|-
| Total electrostatic energy(kcal/mol) || 0.30537|| -0.05004|| 0.00000|| 0.00000
|-
| Total energy(kcal/mol) || 70.54281|| 60.55348|| 79.88353|| 69.53565
|}

{| class="wikitable" border="1"
|+ Table 2 (cont.)
!Type of Molecule !!Intermediate 9(boat) !! Intermediate 10(boat)
|-
| Molecular Model || <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_9avagadro2_boat.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_10avagadro2_boat.cml</uploadedFileContents>
</jmolApplet></jmol>||
|-
| Total bond stretching energy(kcal/mol) || 8.00455|| 7.76754
|-
| Total angle bending energy(kcal/mol) || 30.20403|| 19.02758
|-
| Total stretch bending energy(kcal/mol) || -0.03535|| -0.13479
|-
| Total torsional energy(kcal/mol) || 2.70443|| 3.74744
|-
| Total out-of-plane bending energy(kcal/mol) || 0.94585|| 0.95707
|-
| Total van der Waals energy(kcal/mol) || 35.80197|| 34.99801
|-
| Total electrostatic energy(kcal/mol) || 0.29435|| -0.06080
|-
| Total energy(kcal/mol) || 77.91981|| 66.30205
|}
The intermediate 10 was calculated to be the more thermodynamically stable intermediate relative to intermediate 9. This is mostly due to the difference in total angle bending energy which can be attributed possibly to the position of the O atom which experience less steric repulsion in intermediate 10 than in intermediate 9. The intermediates had lower total energies when the configuration of the 6-membered ring was in a chair configuration rather than a boat configuration. This suggests that the chair configuration is favored over the boat configuration in the 6-membered rings for these intermediates.

The functionalisation of the alkene for these intermediate has been reported to be extremely slow. This can be explained by the the energies listed in Table 2. There is a tendency in polycyclic systems for bridge head atoms to favor sp2 configuration rather than sp3. This is due to the extra stability afforded by these 'cage structures' as well as it being due to the sp2 intermediates having less strain than its parent polycycloalkane configurations.<ref>Wilhelm F. Maier and Paul von RaguC Schleyer, ''J. Am. Chem. SOC.'' 1981, '''103''', 1891-1900 </ref> This effect can be seen in the energy table above where the total torsional energy is significantly lower in energy in the intermediates than their respective hydrogenated product leading to lower total energy in the intermediate.

==Spectroscopic Simulation using Quantum Mechanics==
Molecules 17 and 18 which are derivatives of molecules 8 and 9 were processed in a HPC and its 1H and 13C NMR were calculated . The DOI for the data of the calculations are given in the reference.<ref>{{DOI|10042/27911}}</ref><ref>{{DOI|10042/27912}}</ref><ref>{{DOI|10042/27913}}</ref><ref>{{DOI|10042/27914}}</ref>
{| class="wikitable" border="1"
|+ Table3
! Type of Molecule!!Molecule 17 Chair!! Molecule 17 boat!! Molecule 18 Chair !! Molecule 18 boat
|-
|Molecular model||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>17HPCmol.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>17boatHPCmol.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>HPC18mol.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>18HPCboatmol.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Sum of electronic and thermal Free Energies||-1651.440152||-1651.437358||-1651.464202||-1651.462786
|}
The Sum of electronic and thermal Free Energies, is the free energy, ΔG , of the molecule and can be used to comapre relative energies of these molecules. It can be sen that molecule 18 is generally favoured. however contrary to molecules 9 and 10, the molecule with the 6-membered ring in the boat configuration has lower relative energies and is favored.
The 1H and 13C NMR for both molecule 17 and 18 are as follows
{| class="wikitable" border="1"
|+ NMR of molecule 17(boat)
! 1H !! 13C!! NMR atom labels!! NMR atom labels 2
|-
| [[File:NMR17.svg|thumb|center|click to expand]] || [[File:NMR13C_17.svg|thumb|center|click to expand]]|| [[File:Labels17.jpg|thumb|center|click to expand]]|| [[File:Labels17_2.jpg|thumb|center|click to expand]]
|}

{| class="wikitable" border="1"
|+ NMR of molecule 18(boat)
! 1H !! 13C!! NMR atom labels!! NMR atom labels 2
|-
| [[File:NMRH1_18.svg|thumb|center|click to expand]] || [[File:NMRC13_18.svg|thumb|center|click to expand]]|| [[File:Labels18.jpg|thumb|center|click to expand]]|| [[File:Labels18_2.jpg|thumb|center|click to expand]]
|}

{| class="wikitable" border="1"
|+ NMR assignments
! 1H 17 !! 13C 17!!1H 18!!13C 18
|-
| [[File:HNMRsummary_17.jpg|thumb|center|click to expand]] || [[File:CNMRsummary_17.jpg|thumb|center|click to expand]]|| [[File:HNMRsummary_18.jpg|thumb|center|click to expand]]|| [[File:CNMRsummary_18.jpg|thumb|center|click to expand]]
|}
{| class="wikitable" border="1"
|+ Comaprison between literature and calculated NMR<ref>''Leo A. Paquette,* Neil A. Pegg, Dana Toops,’ George D. Maynard, and
Robin D. Rogers*, J. Am. Chem. Soc.'',(1990),'''112''',277 </ref>
! 1H 17 !! 13C 17!!1H 18!!13C 18
|-
| [[File:HNMR_boat_17_excel.jpg|thumb|center|click to expand]] || [[File:CNMR_boat_17_excel.jpg|thumb|center|click to expand]]|| [[File:HNMR_boat_18_excel.jpg|thumb|center|click to expand]]|| [[File:CNMR_boat_18_excel.jpg|thumb|center|click to expand]]
|}
The calculated NMRs were generally in agreement with literature. The 1H NMRs did not show great agreement with literature but chemical shift values were generally in the right place. On the other hand 13C NMRs showed good agreement with literature values. The calculated NMRs shifts tended to be higher than the chemical shifts in literature but this is thought to be due to lack of precise correction. The NMRs of the chair conformations were also calculated and these NMR generally tended to have chemical shifts at lower magnetic field relative to NMRs of the molecules with boat conformations. The NMR chemical shift of the carbon atoms attached to the sulfur atom must be corrected due to spin-orbit coupling errors. This explains the large deviation of chemical shift of C-12 and a possible small deviation at C-17 and C-18. However the literature for spin-orbit coupling error for the C-S bond could not be found and therefore the chemical shift values were left uncorrected on the presented data but is expected to be around -6ppm correction for each C-S bond.
==Analysis of the properties of the synthesised alkene epoxides==
The alkenes styrene and trans-Stilbene were chosen, and its epoxide derivatives were analysed.
===Crystal structures of the two catalyst for epoxidation 21 and 23===
The Shi asymmetric Fructose catalyst and the Jacobsen asymmetric catalyst which are labelled as catalyst 21 and 23 respectively are the stable precursors of the catalyst and are used in catalysing the epoxidation of alkenes. Its structures are shown below.
{| class="wikitable" border="1"
|+ Catalysts 21 and 23
! catalyst 21 !! catalyst 23!! anomeric centre of catalyst 21!!Stereoisomer A and B of catalyst 21
|-
| [[File:Catalyst21.jpg|thumb|center|The Shi asymmetric Fructose catalyst ]] || [[File:Catalyst_23.jpg|thumb|center|The Jacobsen asymmetric catalyst ]]|| [[File:Catalyst21_anomer.jpg|thumb|center|alpha and beta anomers of catalyst 21 (click to expand) ]]|| [[File:Catalyst21_isomer.jpg|thumb|center|Stereoisomer A and B of catalyst 21 (click to expand) ]]
|}

{| class="wikitable" border="1"
|+ crystal structures of catalyst 21 and 23
! catalyst 21 !! catalyst 23
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>250</size><uploadedFileContents>Catalyst_21_mercury.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>250</size><uploadedFileContents>Catalyst23mercury.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Labels on Atoms
! catalyst 21!! catalyst 23
|-
| [[File:Labels21.jpg|thumb|center|The Shi asymmetric Fructose catalyst ]] || [[File:Labels23.jpg|thumb|center|The Jacobsen asymmetric catalyst ]]
|}

Catalyst 21, forms a crystal structure stabilized by hydrogen bonding between the hydrogen atoms on carbon C8,C9 and C6 and oxygen atoms O1 and O2. Two stereoisomer, A and B, exist for catalyst 21 and in the crystal structure, the A isomer forms infinite zig-zag chain connected by hydrogen bonding with B isomer further stabilizing the crystal sturcture as side-chains. The C-O bond of the anomeric center, located on C2, has unusual properties. It can be seen that oxygen atoms bonded to C2, O6 and O2, have unusually short C-O bond lengths 1.403A. Looking at the average C-O bond length which is 1.43, there is a big difference in bond length. This shortened C-O bond length could be accounted for by the anomeric effect where there are stabilizing interaction between the bonding orbitals of oxygen and anti-bonding orbital of carbon. This effect also explains why the C2-C3 and C2-C1 are one of the longest C-C bonds in the molecule.<ref>M.Durik, V.Langer, D.Gyepesova, J.Micova, B.Steiner, M.Koos, ''Acta Crystallogr'', (2001). '''E57''', o672-o674</ref>

Catalyst 23 form crystal structures where the catalyst assume an asymmetric position shown above. The crystal structure consists only of Van der Waal's interactions. The tert-butyl group present in the molecule gives the bent shape that is present in the molecule due to steric repulsion and it has been found that when these tert-butyl groups present in positions C17 and C4 were substituted for triisopropylsiloxyl groups, the molecule took a flat shape instead of a bent shape as previously seen.<ref>JAE WOONG YOON, TAE-SUNO YOON, SOON WON LEE AND WHANCHUL SHIN, ''Acta Cryst.'' (1999). '''C55''', 1766-1769 </ref>
===NMR analysis of the epoxide products===
The DOI for the data of the calculations for these epoxides are given in the reference.<ref>{{DOI|10042/27915}}</ref><ref>{{DOI|10042/27916}}</ref><ref>{{DOI|10042/27917}}</ref><ref>{{DOI|10042/27918}}</ref>

{| class="wikitable" border="1"
|+ Calculated NMR of styrene oxide
! 1H styrene oxide !! 13C styrene oxide!!labels on atoms!!NMR atom assignment
|-
| [[File:HNMRHPC_styrene.svg|thumb|center|'' ]] || [[File:CNMRHPC_styrene.svg|thumb|center|'' ]]|| [[File:Labels_styrene.jpg|thumb|center|'' ]]|| [[File:CandHNMR_styrene.jpg|thumb|center|'' ]]
|}

{| class="wikitable" border="1"
|+ Calculated NMR of trans-Stilbene oxide
! 1H trans-Stilbene oxide!!13C trans-Stilbene !! labels on atoms!!NMR atom assignment
|-
| [[File:HNMRHPC_stilbene.svg|thumb|center|'' ]] || [[File:CNMRHPC_stilbene.svg|thumb|center|'' ]]|| [[File:Labels_stilbene.jpg|thumb|center|'' ]]|| [[File:HandCNMR_stillbene.jpg|thumb|center|'' ]]
|}

{| class="wikitable" border="1"
|+ NMR chemical shift data and comparison with literature<ref>Charlotte Wiles*, Marcus J. Hammond1 and Paul Watts*,''Beilstein Journal of Organic Chemistry'', (2009), '''5''', 1-12</ref>
! 1H styrene oxide !! 13C styrene oxide!!1H trans-Stilbene oxide!!13C trans-Stilbene
|-
| [[File:Styrene_oxide_HNMR.jpg|thumb|center|'' ]] || [[File:Styrene_oxide_CNMR.jpg|thumb|center|'' ]] ||[[File:Trans-stilbene_oxide_HNMR.jpg|thumb|center|'' ]]||[[File:Trans-stilbene_oxide_CNMR.jpg|thumb|center|'' ]]
|}
The calculated NMRs showed very good agreement with literature, and shows that these computated epoxide models can be used to predict properties of real molecules with a relatively good accuracy. As expected, the NMR values of enantiomers and diastereoisomers of the epoxides were the same.
===Assigning the absolute configuration of the product===
====Calculated and reported literature for the epoxides, styrene oxide and trans-stilbene oxide====
The reported and calculated optical rotations are shown in the table below.

{| class="wikitable" border="1"
|+ optical rotations of epoxides at 598nm
! ''!!(R)-styrene oxide !! ''!! (S)-styrene oxide!! ''!!(R,R)-trans-stilbene oxide!!''!!(S,S)-trans-stilbene oxide!!''
|-
| '' || calculated|| literature|| calculated|| literature|| calculated|| literature|| calculated|| literature
|-
| optical rotation (598nm)/degrees || -30.43<ref>{{DOI|10042/27922}}</ref> ||-33.3<ref>Frederick R. Jensen* and Ronald C. Kiskis*,''Journal of the American Chemical Society'',1975,'''97.20''',5825</ref>|| 30.10<ref>{{DOI|10042/27921}}</ref> || 32.1<ref>Hui Lin a,b, Yan Liu a, Zhong-Liu Wua,''Tetrahedron: Asymmetry'' ,(2011),'''22''' 134–137</ref>|| 297.90<ref>{{DOI|10042/27919}}</ref> || 310<ref>Rukhsana I. Kureshy,* Surendra Singh, Noor-ul H. Khan, Sayed H. R. Abdi,
Santosh Agrawal and Raksh V. Jasra,''Tetrahedron: Asymmetry'' (2006),'''17''', 1638–1643 </ref>|| -297.67<ref>{{DOI|10042/27920}}</ref> || no literature found
|}
The optical rotations are in good agreement with the reported literature values. Although the literature value for the optical rotation for (S,S)-trans stilbene oxide could not be found, assuming that the value of the optical rotation for (R,R)-trans stilbene oxide, which has good agreement with reported literature value , is accurate, it can also be assumed that the computed value of (S,S)-trans stilbene is also correct as they are diasteroisomers of each other and the optical rotation of diastereoisomers should be equal but opposite which it very nearly is. Optical rotations of less than a 100 degrees, cannot usually be calculated accurately using this computational methods, but it seems as though the optical rotation of styrene has been calculated relatively accurately. This could be due to styrene being a relatively simple molecule. The sign of optical rotation cannot be used to predict the absolute configuration S or R, due to the direction of the optical rotation being completely random depending on the molecule for R and S. This can be seen in the computed values of optical rotation where R and S configurations have both direction of optical rotation assigned between the two molecules.

====Using the calculated properties of transition state for the reaction====
The calculated energies of transition state for the epoxidation of the chosen alkenes were used to assign the absolute configuration of epoxides, styrene oxide and trans-stilbene oxide. The energy calculation were provided by the Imperial College Chemistry department. The label R or S of the transition state refers to the face of the alkene that the catalsyt react to and therefore R and S of the same number are enantiomers of each other. Below the difference in free energy ΔG is calculated and the equilibrium constant, K, which refers to the ratio of R and S produced is calculated by the equation ΔG=-RTlnK. The calculated K is then used to work out the enantiomeric excess for either R or S. For example if K=0.6149, in this case it means that for every mole of S enantiomer produced, 0.6149 moles of R enatiomer is produced. ee=((R-S)/(R+S))x100%, where R+S =1, and therefore ee= ((1/1.6146)-(0.6149/1.6149)/(1))x100%= 23.84% ee for S.
=====Styrene transition state=====
=====Shi epoxidation of styrene=====
For the epoxidation of styrene using Shi's catalyst. 8 possible transition states can be envisaged

{| class="wikitable" border="1"
|+ structures of transiton state (R)
! R1 !! R2!! R3!! R4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R1 yuki.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ structures of transiton state (S)
! S1 !! S2!! S3!! S4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S1.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for styrene transition state (R and S)(Shi epoxidation) 2625.5
! Type of transition !! S1!! S2!! S3!! S4
|-
| Sum of electronic and thermal Free Energies || -1303.733828|| -1303.724178|| -1303.727673|| -1303.738503
|-
!Type of transition!! R1!! R2!! R3!! R4
|-
| Sum of electronic and thermal Free Energies||-1303.730703|| -1303.730238||-1303.736813|| -1303.738044
|-
!''!!R1-S1!! S2-R2!! S3-R3!! R4-S4
|-
|Difference in Free energy(hartree) || 0.003125|| 0.00606|| 0.00914|| 0.000459
|-
|Difference in Free energy(kJ/mol) || 8.205|| 15.911|| 23.997|| 1.205
|-
|Equlibrium constant(K)|| 0.0365|| 0.001629|| 0.0000624|| 0.6149
|-
|Enantimeric excess of (R or S)|| 92.9%(S)|| 99.8%(R)|| 99.9%(R)|| 23.84%(S)
|}
Literature for this reaction have reported to give the enatiomeric excess to the R enantiomer at 81%. It is therefore very likely that the approach and orientation of the catalyst will be either 2 or 3. <ref>Hongqi Tian, Xuegong She, Jiaxi Xu, and Yian Shi*,''Org. Lett.'',(2001),'''3''',1929-1931</ref>

=====Jacobsen epoxidation of styrene=====
{| class="wikitable" border="1"
|+ structures of transiton state
! R5 !! R6!! S5!! S6
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R1_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R2_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S1_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S2_J.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for styrene transition state (Jacobsen epoxidation)
! Type of transition !! S5!! S6
|-
|Sum of electronic and thermal Free Energies ||-3343.969197|| -3343.963191
|-
!Type of transition !! R5!! R6
|-
| Sum of electronic and thermal Free Energies || -3343.960889|| -3343.962162
|-
!''!!R1-S1!! R2-S2
|-
|Difference in Free energy(hartree) || 0.008308|| 0.001029
|-
|Difference in Free energy(kJ/mol) || 21.812654|| 2.7016395
|-
|Equlibrium constant|| 0.000125|| 0.32866
|-
|Enantimeric excess(ee) of (R or S)|| 99.9%(S)|| 50.5%(S)
|}
Literature for this epoxidation has reported ee of 46% favoring S enantiomer. This is in good agreement with the second transition state and therefore the catalyst is likely to be orientated as such.<ref>Michael Palucki, Paul J. Pospisil, Wei Zhang, and
Eric N. Jacobsen,''J. Am. Chem. SOC.'' 1994,'''116''', 9333-9334 </ref>
=====Trans-Stilbene transition state=====
Similar to the styrene transition state, the energies of the trans-stilbene transition states were analysed. There are 8 possible transition state that can be envisaged for this reaction
=====Shi epoxidation of trans-stilbene=====
{| class="wikitable" border="1"
|+ structures of transiton state (R)
! RR1 !! RR2!! RR3!! RR4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR1.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ structures of transiton state (S)
! SS1 !! SS2!! SS3!! SS4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS1.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for tans-stilbene transition state (R and S)(Shi epoxidation) 2625.5
! Type of transition !! SS1!! SS2!! SS3!! SS4
|-
| Sum of electronic and thermal Free Energies || -1534.683440||-1534.685089||-1534.693818|| -1534.691858
|-
!Type of transition!! RR1!! RR2!! RR3!! RR4
|-
| Sum of electronic and thermal Free Energies||-1534.687808|| -1534.687252||-1534.700037|| -1534.699901
|-
!''!!SS1-RR1!! SS2-RR2!! SS3-RR3!! SS4-RR4
|-
|Difference in Free energy(hartree) || 0.004368|| 0.002163|| 0.006219|| 0.008043
|-
|Difference in Free energy(kJ/mol) || 11.4681|| 5.6789|| 16.3279|| 21.1169
|-
|Equlibrium constant(K)|| 0.009784|| 0.1011|| 0.001377|| 0.0001994
|-
|Enantimeric excess of (RR or SS)|| 98.1%(RR)|| 81.6%(RR)|| 99.7%(RR)|| 99.9%(RR)
|}
Literature for this epoxidation has reported ee>95% favouring RR configuration which is in good agreement with transition states 1,3 and 4. This epoxidation is therefore likely to take any of the transition, 1,3 and 4, as the transiton state for this reaction.<ref>Yong Tu, Zhi-Xian Wang, and Yian Shi*,''J. Am. Chem. Soc.'' 1996, '''118''', 9806-9807</ref>
=====Jacobson epoxidation of trans-stilbene=====
{| class="wikitable" border="1"
|+ structures of transiton state
! RR5 !! SS5
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR1_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS1_J.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for trans-stilbene transition state (Jacobsen epoxidation)
! Type of transition !! SS5
|-
|Sum of electronic and thermal Free Energies ||-3574.923087
|-
!Type of transition !! RR5
|-
| Sum of electronic and thermal Free Energies || -3574.921174
|-
!''!!RR5-SS5
|-
|Difference in Free energy(hartree) || 0.001913
|-
|Difference in Free energy(kJ/mol) || 5.0225
|-
|Equlibrium constant|| 0.1318
|-
|Enantimeric excess(ee) of (RR or SS)|| 76.7%(SS)
|}
Literature for this epoxidation reported ee of 25% favouring the SS configuration.<ref>Bridget D. Brandes and Eric N. Jacobsen,''J. Org. Chem.'' 1994,'''59''', 4378-4380</ref> Although computed energies predicted the SS configuration to be favored, there is a big difference in the value of ee. This could be due to error in experimental data, or lack of accuracy in the computational data and therefore further analysis maybe needed to clarify this.

Overall it can be concluded that the predictions for the absolute configuration of these epoxide reactions using different catalyst via computational methods are relatively accurate, as can be seen by the good agreement with literature values.

====Investigating the non-covalent interactions in the active-site of the reaction transition state====
NCI ananlysis was done on both R2 and S2 transitions for comparison.

{| class="wikitable" border="1"
|+ Molecular model showing NCI
! R2 !! S2
|-
| [[File:Styrene_R2_2.jpg|thumb|center|'' ]] || [[File:Styrene_S2.jpg|thumb|center|'' ]]
|}
The second transition state heavily favours the R enantiomer with an ee=99.8%(R), The R2 transition has a large mildly attractive surface of interaction almost completely surrounding the double bond of the styrene, which is the reaction site. The S2 transition in comaprison has a small midly attractive NCI surface relative to R and has a mildly replusive interaction in the center of the cone above the phenyl group. The difference in NCI interaction around the double bond, explains why R2 is so favored relative to the S2.

==reference==
<references/>

File:Styrene R2 2.jpg

2014-03-07T13:08:15Z

Ys4111: uploaded a new version of "File:Styrene R2 2.jpg"

Rep:Mod:SAITYM954

2014-03-07T13:06:09Z

Ys4111:

=Organic Computational=
==Conformational analysis using Molecular Mechanics==
Cyclopentadiene dimer 1 and 2 and the hydrogenation product of the cyclopentadiene 2, 3 and 4, were modeled on Avagadro and their geometries were optimized using the MMFF94(s) force field option. The energies of the optimized energies are given in Table 1.

{| class="wikitable" border="1"
|+ TABLE 1
! Type of molecule !! Cyclopentadiene dimer 1!! Cyclopentadiene dimer 2!! Hydrogenation product 3!! Hydrogenation product 4
|-
| molecular model ||<jmol><jmolApplet><title>cyclopentadiene dimer 1</title><color>white</color>
<size>150</size><uploadedFileContents>Product1avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>cyclopentadiene dimer 2</title><color>white</color>
<size>150</size><uploadedFileContents>Product2.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>hydrogenation product 3</title><color>white</color>
<size>150</size><uploadedFileContents>Product3avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>hydrogenation product 4</title><color>white</color>
<size>150</size><uploadedFileContents>Product4avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>
|-
| Total bond stretching energy(kcal/mol) || 3.54317 || 3.46793||3.31151|| 2.82308
|-
| Total angle bending energy(kcal/mol) ||30.77258|| 33.18901|| 31.93319|| 24.68545
|-
| Total stretch bending energy(kcal/mol) ||-2.04144|| -2.08220|| -2.10211|| -1.65717
|-
| Total torsional energy(kcal/mol) || -2.73092|| -2.94964|| -1.46866|| -0.37823
|-
| Total out-of-plane bending energy(kcal/mol) || 0.01476|| 0.02183|| 0.01309|| 0.00028
|-
| Total van der Waals energy(kcal/mol) || 12.80160|| 12.35898|| 13.63920|| 10.63705
|-
| Total electrostatic energy(kcal/mol) || 13.01367|| 14.18476|| 5.11950|| 5.14702
|-
| Total energy(kcal/mol) || 55.37342|| 58.19067|| 50.44571|| 41.25749
|}
Although it can be seen that the total energy of the cyclopentadiene dimer 1 is lower than 2, cyclopentadiene dimerises to produce specifically the cyclopentadiene dimer 2. From this information, it can be concluded that although the cyclopentadiene dimer 1 is the more stable product out of the two dimers and therefore the thermodynamic product, the dimerisation of pentadiene is kinetically controlled and therefore favours the kinetic product, cyclopentadiene dimer 2.

The cyclopentadiene dimer 2 can hydrogenate to initially form two products, 3 and 4. Product 3 and 4 have double bonds hydrogenated in the cyclopentene ring and the norbornene ring respectively. Product 4 is seen to be predominantly favored product due to it being the lower energy product as well as the double bond in the norbornene ring reacting with hydrogen approximately 5 times faster than the double bond in the cyclopentene ring.<ref>D. Skála and J. Hanika,Petroleum and Coal,(1968), 45, 105-108</ref> The relative ease of hydrogenation of the respective double bonds can be attributed to the difference in different energies listed in Table 1 between product 3 and 4 and somewhat can be explained by analyzing them. It can be seen that product 4 has substantially lower energy in total angle bending energy, and total van der Waals energy, with a slightly lower energy in total bond stretching energy, relative to product 3, whereas product 3 is only slightly lower in energy in total electrostatic energy and total torsional energy relative to product 4. This explains the big difference in total energy favoring product 4 and also shows that the difference in energy between the two products 3 and 4 is mostly contributed by the difference in total angle bending energy, and total van der Waals energy. The possible explanation why the total angle bending energy, and total van der Waals energy is lower in product 4 is that ,looking at the reactant (cyclopentadiene dimer 2), the hydrogen atom on the unsaturated carbon in the norbornene ring is almost in plane and in closer proximity with the hydrogen atom on the saturated carbon atom adjacent to it than the hydrogen atom on the unsaturated carbon in the cyclopentene ring. The closer proximity of the hydrogen atom in the norbornene ring means that, there is a greater release in strain and therefore lowering of energy especially in total angle bending energy, and total van der Waals energy when the double bond in the norbornene ring is hydrogenated opposed to the cyclopentene ring. This explains why hydrogenation of double bond in the norborene ring, and therefore synthesis of product 4, is favored relative to product 3.
==Atropisomerism in an Intermediate related to the Synthesis of Taxol==
Key intermediate for the synthesis of Taxol, 9 and 10, was modeled on Avagadro and its geometry was optimized using the MMFF94s force-field option. The respective energies of the intermediate are given in Table 2.

{| class="wikitable" border="1"
|+ Table 2
!Type of Molecule !!Intermediate 9(chair) !! Intermediate 10(chair)!! Hydrogenated Intermediate 9!! Hydrogenated Intermediate 10
|-
| Molecular Model || <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_9avagadro2.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_10avagadro2.cml</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_9_hydrogenated_avagadro.cml</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_10_hydrogenated.cml</uploadedFileContents>
</jmolApplet></jmol>
|-
| Total bond stretching energy(kcal/mol) || 7.66637|| 7.60691|| 7.06510|| 6.41196
|-
| Total angle bending energy(kcal/mol) || 28.29002|| 18.81375|| 28.68337|| 22.31678
|-
| Total stretch bending energy(kcal/mol) || -0.07465|| -0.14531|| 0.28404|| 0.29516
|-
| Total torsional energy(kcal/mol) || 0.27125|| 0.25598|| 10.40618|| 9.20328
|-
| Total out-of-plane bending energy(kcal/mol) || 0.97178|| 0.84841|| 0.09869|| 0.03531
|-
| Total van der Waals energy(kcal/mol) || 33.11267|| 33.22378|| 33.34614|| 31.27316
|-
| Total electrostatic energy(kcal/mol) || 0.30537|| -0.05004|| 0.00000|| 0.00000
|-
| Total energy(kcal/mol) || 70.54281|| 60.55348|| 79.88353|| 69.53565
|}

{| class="wikitable" border="1"
|+ Table 2 (cont.)
!Type of Molecule !!Intermediate 9(boat) !! Intermediate 10(boat)
|-
| Molecular Model || <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_9avagadro2_boat.cml</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>Taxol_10avagadro2_boat.cml</uploadedFileContents>
</jmolApplet></jmol>||
|-
| Total bond stretching energy(kcal/mol) || 8.00455|| 7.76754
|-
| Total angle bending energy(kcal/mol) || 30.20403|| 19.02758
|-
| Total stretch bending energy(kcal/mol) || -0.03535|| -0.13479
|-
| Total torsional energy(kcal/mol) || 2.70443|| 3.74744
|-
| Total out-of-plane bending energy(kcal/mol) || 0.94585|| 0.95707
|-
| Total van der Waals energy(kcal/mol) || 35.80197|| 34.99801
|-
| Total electrostatic energy(kcal/mol) || 0.29435|| -0.06080
|-
| Total energy(kcal/mol) || 77.91981|| 66.30205
|}
The intermediate 10 was calculated to be the more thermodynamically stable intermediate relative to intermediate 9. This is mostly due to the difference in total angle bending energy which can be attributed possibly to the position of the O atom which experience less steric repulsion in intermediate 10 than in intermediate 9. The intermediates had lower total energies when the configuration of the 6-membered ring was in a chair configuration rather than a boat configuration. This suggests that the chair configuration is favored over the boat configuration in the 6-membered rings for these intermediates.

The functionalisation of the alkene for these intermediate has been reported to be extremely slow. This can be explained by the the energies listed in Table 2. There is a tendency in polycyclic systems for bridge head atoms to favor sp2 configuration rather than sp3. This is due to the extra stability afforded by these 'cage structures' as well as it being due to the sp2 intermediates having less strain than its parent polycycloalkane configurations.<ref>Wilhelm F. Maier and Paul von RaguC Schleyer, ''J. Am. Chem. SOC.'' 1981, '''103''', 1891-1900 </ref> This effect can be seen in the energy table above where the total torsional energy is significantly lower in energy in the intermediates than their respective hydrogenated product leading to lower total energy in the intermediate.

==Spectroscopic Simulation using Quantum Mechanics==
Molecules 17 and 18 which are derivatives of molecules 8 and 9 were processed in a HPC and its 1H and 13C NMR were calculated . The DOI for the data of the calculations are given in the reference.<ref>{{DOI|10042/27911}}</ref><ref>{{DOI|10042/27912}}</ref><ref>{{DOI|10042/27913}}</ref><ref>{{DOI|10042/27914}}</ref>
{| class="wikitable" border="1"
|+ Table3
! Type of Molecule!!Molecule 17 Chair!! Molecule 17 boat!! Molecule 18 Chair !! Molecule 18 boat
|-
|Molecular model||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>17HPCmol.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>17boatHPCmol.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>HPC18mol.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>18HPCboatmol.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Sum of electronic and thermal Free Energies||-1651.440152||-1651.437358||-1651.464202||-1651.462786
|}
The Sum of electronic and thermal Free Energies, is the free energy, ΔG , of the molecule and can be used to comapre relative energies of these molecules. It can be sen that molecule 18 is generally favoured. however contrary to molecules 9 and 10, the molecule with the 6-membered ring in the boat configuration has lower relative energies and is favored.
The 1H and 13C NMR for both molecule 17 and 18 are as follows
{| class="wikitable" border="1"
|+ NMR of molecule 17(boat)
! 1H !! 13C!! NMR atom labels!! NMR atom labels 2
|-
| [[File:NMR17.svg|thumb|center|click to expand]] || [[File:NMR13C_17.svg|thumb|center|click to expand]]|| [[File:Labels17.jpg|thumb|center|click to expand]]|| [[File:Labels17_2.jpg|thumb|center|click to expand]]
|}

{| class="wikitable" border="1"
|+ NMR of molecule 18(boat)
! 1H !! 13C!! NMR atom labels!! NMR atom labels 2
|-
| [[File:NMRH1_18.svg|thumb|center|click to expand]] || [[File:NMRC13_18.svg|thumb|center|click to expand]]|| [[File:Labels18.jpg|thumb|center|click to expand]]|| [[File:Labels18_2.jpg|thumb|center|click to expand]]
|}

{| class="wikitable" border="1"
|+ NMR assignments
! 1H 17 !! 13C 17!!1H 18!!13C 18
|-
| [[File:HNMRsummary_17.jpg|thumb|center|click to expand]] || [[File:CNMRsummary_17.jpg|thumb|center|click to expand]]|| [[File:HNMRsummary_18.jpg|thumb|center|click to expand]]|| [[File:CNMRsummary_18.jpg|thumb|center|click to expand]]
|}
{| class="wikitable" border="1"
|+ Comaprison between literature and calculated NMR<ref>''Leo A. Paquette,* Neil A. Pegg, Dana Toops,’ George D. Maynard, and
Robin D. Rogers*, J. Am. Chem. Soc.'',(1990),'''112''',277 </ref>
! 1H 17 !! 13C 17!!1H 18!!13C 18
|-
| [[File:HNMR_boat_17_excel.jpg|thumb|center|click to expand]] || [[File:CNMR_boat_17_excel.jpg|thumb|center|click to expand]]|| [[File:HNMR_boat_18_excel.jpg|thumb|center|click to expand]]|| [[File:CNMR_boat_18_excel.jpg|thumb|center|click to expand]]
|}
The calculated NMRs were generally in agreement with literature. The 1H NMRs did not show great agreement with literature but chemical shift values were generally in the right place. On the other hand 13C NMRs showed good agreement with literature values. The calculated NMRs shifts tended to be higher than the chemical shifts in literature but this is thought to be due to lack of precise correction. The NMRs of the chair conformations were also calculated and these NMR generally tended to have chemical shifts at lower magnetic field relative to NMRs of the molecules with boat conformations. The NMR chemical shift of the carbon atoms attached to the sulfur atom must be corrected due to spin-orbit coupling errors. This explains the large deviation of chemical shift of C-12 and a possible small deviation at C-17 and C-18. However the literature for spin-orbit coupling error for the C-S bond could not be found and therefore the chemical shift values were left uncorrected on the presented data but is expected to be around -6ppm correction for each C-S bond.
==Analysis of the properties of the synthesised alkene epoxides==
The alkenes styrene and trans-Stilbene were chosen, and its epoxide derivatives were analysed.
===Crystal structures of the two catalyst for epoxidation 21 and 23===
The Shi asymmetric Fructose catalyst and the Jacobsen asymmetric catalyst which are labelled as catalyst 21 and 23 respectively are the stable precursors of the catalyst and are used in catalysing the epoxidation of alkenes. Its structures are shown below.
{| class="wikitable" border="1"
|+ Catalysts 21 and 23
! catalyst 21 !! catalyst 23!! anomeric centre of catalyst 21!!Stereoisomer A and B of catalyst 21
|-
| [[File:Catalyst21.jpg|thumb|center|The Shi asymmetric Fructose catalyst ]] || [[File:Catalyst_23.jpg|thumb|center|The Jacobsen asymmetric catalyst ]]|| [[File:Catalyst21_anomer.jpg|thumb|center|alpha and beta anomers of catalyst 21 (click to expand) ]]|| [[File:Catalyst21_isomer.jpg|thumb|center|Stereoisomer A and B of catalyst 21 (click to expand) ]]
|}

{| class="wikitable" border="1"
|+ crystal structures of catalyst 21 and 23
! catalyst 21 !! catalyst 23
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>250</size><uploadedFileContents>Catalyst_21_mercury.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>250</size><uploadedFileContents>Catalyst23mercury.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Labels on Atoms
! catalyst 21!! catalyst 23
|-
| [[File:Labels21.jpg|thumb|center|The Shi asymmetric Fructose catalyst ]] || [[File:Labels23.jpg|thumb|center|The Jacobsen asymmetric catalyst ]]
|}

Catalyst 21, forms a crystal structure stabilized by hydrogen bonding between the hydrogen atoms on carbon C8,C9 and C6 and oxygen atoms O1 and O2. Two stereoisomer, A and B, exist for catalyst 21 and in the crystal structure, the A isomer forms infinite zig-zag chain connected by hydrogen bonding with B isomer further stabilizing the crystal sturcture as side-chains. The C-O bond of the anomeric center, located on C2, has unusual properties. It can be seen that oxygen atoms bonded to C2, O6 and O2, have unusually short C-O bond lengths 1.403A. Looking at the average C-O bond length which is 1.43, there is a big difference in bond length. This shortened C-O bond length could be accounted for by the anomeric effect where there are stabilizing interaction between the bonding orbitals of oxygen and anti-bonding orbital of carbon. This effect also explains why the C2-C3 and C2-C1 are one of the longest C-C bonds in the molecule.<ref>M.Durik, V.Langer, D.Gyepesova, J.Micova, B.Steiner, M.Koos, ''Acta Crystallogr'', (2001). '''E57''', o672-o674</ref>

Catalyst 23 form crystal structures where the catalyst assume an asymmetric position shown above. The crystal structure consists only of Van der Waal's interactions. The tert-butyl group present in the molecule gives the bent shape that is present in the molecule due to steric repulsion and it has been found that when these tert-butyl groups present in positions C17 and C4 were substituted for triisopropylsiloxyl groups, the molecule took a flat shape instead of a bent shape as previously seen.<ref>JAE WOONG YOON, TAE-SUNO YOON, SOON WON LEE AND WHANCHUL SHIN, ''Acta Cryst.'' (1999). '''C55''', 1766-1769 </ref>
===NMR analysis of the epoxide products===
The DOI for the data of the calculations for these epoxides are given in the reference.<ref>{{DOI|10042/27915}}</ref><ref>{{DOI|10042/27916}}</ref><ref>{{DOI|10042/27917}}</ref><ref>{{DOI|10042/27918}}</ref>

{| class="wikitable" border="1"
|+ Calculated NMR of styrene oxide
! 1H styrene oxide !! 13C styrene oxide!!labels on atoms!!NMR atom assignment
|-
| [[File:HNMRHPC_styrene.svg|thumb|center|'' ]] || [[File:CNMRHPC_styrene.svg|thumb|center|'' ]]|| [[File:Labels_styrene.jpg|thumb|center|'' ]]|| [[File:CandHNMR_styrene.jpg|thumb|center|'' ]]
|}

{| class="wikitable" border="1"
|+ Calculated NMR of trans-Stilbene oxide
! 1H trans-Stilbene oxide!!13C trans-Stilbene !! labels on atoms!!NMR atom assignment
|-
| [[File:HNMRHPC_stilbene.svg|thumb|center|'' ]] || [[File:CNMRHPC_stilbene.svg|thumb|center|'' ]]|| [[File:Labels_stilbene.jpg|thumb|center|'' ]]|| [[File:HandCNMR_stillbene.jpg|thumb|center|'' ]]
|}

{| class="wikitable" border="1"
|+ NMR chemical shift data and comparison with literature<ref>Charlotte Wiles*, Marcus J. Hammond1 and Paul Watts*,''Beilstein Journal of Organic Chemistry'', (2009), '''5''', 1-12</ref>
! 1H styrene oxide !! 13C styrene oxide!!1H trans-Stilbene oxide!!13C trans-Stilbene
|-
| [[File:Styrene_oxide_HNMR.jpg|thumb|center|'' ]] || [[File:Styrene_oxide_CNMR.jpg|thumb|center|'' ]] ||[[File:Trans-stilbene_oxide_HNMR.jpg|thumb|center|'' ]]||[[File:Trans-stilbene_oxide_CNMR.jpg|thumb|center|'' ]]
|}
The calculated NMRs showed very good agreement with literature, and shows that these computated epoxide models can be used to predict properties of real molecules with a relatively good accuracy. As expected, the NMR values of enantiomers and diastereoisomers of the epoxides were the same.
===Assigning the absolute configuration of the product===
====Calculated and reported literature for the epoxides, styrene oxide and trans-stilbene oxide====
The reported and calculated optical rotations are shown in the table below.

{| class="wikitable" border="1"
|+ optical rotations of epoxides at 598nm
! ''!!(R)-styrene oxide !! ''!! (S)-styrene oxide!! ''!!(R,R)-trans-stilbene oxide!!''!!(S,S)-trans-stilbene oxide!!''
|-
| '' || calculated|| literature|| calculated|| literature|| calculated|| literature|| calculated|| literature
|-
| optical rotation (598nm)/degrees || -30.43<ref>{{DOI|10042/27922}}</ref> ||-33.3<ref>Frederick R. Jensen* and Ronald C. Kiskis*,''Journal of the American Chemical Society'',1975,'''97.20''',5825</ref>|| 30.10<ref>{{DOI|10042/27921}}</ref> || 32.1<ref>Hui Lin a,b, Yan Liu a, Zhong-Liu Wua,''Tetrahedron: Asymmetry'' ,(2011),'''22''' 134–137</ref>|| 297.90<ref>{{DOI|10042/27919}}</ref> || 310<ref>Rukhsana I. Kureshy,* Surendra Singh, Noor-ul H. Khan, Sayed H. R. Abdi,
Santosh Agrawal and Raksh V. Jasra,''Tetrahedron: Asymmetry'' (2006),'''17''', 1638–1643 </ref>|| -297.67<ref>{{DOI|10042/27920}}</ref> || no literature found
|}
The optical rotations are in good agreement with the reported literature values. Although the literature value for the optical rotation for (S,S)-trans stilbene oxide could not be found, assuming that the value of the optical rotation for (R,R)-trans stilbene oxide, which has good agreement with reported literature value , is accurate, it can also be assumed that the computed value of (S,S)-trans stilbene is also correct as they are diasteroisomers of each other and the optical rotation of diastereoisomers should be equal but opposite which it very nearly is. Optical rotations of less than a 100 degrees, cannot usually be calculated accurately using this computational methods, but it seems as though the optical rotation of styrene has been calculated relatively accurately. This could be due to styrene being a relatively simple molecule. The sign of optical rotation cannot be used to predict the absolute configuration S or R, due to the direction of the optical rotation being completely random depending on the molecule for R and S. This can be seen in the computed values of optical rotation where R and S configurations have both direction of optical rotation assigned between the two molecules.

====Using the calculated properties of transition state for the reaction====
The calculated energies of transition state for the epoxidation of the chosen alkenes were used to assign the absolute configuration of epoxides, styrene oxide and trans-stilbene oxide. The energy calculation were provided by the Imperial College Chemistry department. The label R or S of the transition state refers to the face of the alkene that the catalsyt react to and therefore R and S of the same number are enantiomers of each other. Below the difference in free energy ΔG is calculated and the equilibrium constant, K, which refers to the ratio of R and S produced is calculated by the equation ΔG=-RTlnK. The calculated K is then used to work out the enantiomeric excess for either R or S. For example if K=0.6149, in this case it means that for every mole of S enantiomer produced, 0.6149 moles of R enatiomer is produced. ee=((R-S)/(R+S))x100%, where R+S =1, and therefore ee= ((1/1.6146)-(0.6149/1.6149)/(1))x100%= 23.84% ee for S.
=====Styrene transition state=====
=====Shi epoxidation of styrene=====
For the epoxidation of styrene using Shi's catalyst. 8 possible transition states can be envisaged

{| class="wikitable" border="1"
|+ structures of transiton state (R)
! R1 !! R2!! R3!! R4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R1 yuki.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ structures of transiton state (S)
! S1 !! S2!! S3!! S4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S1.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for styrene transition state (R and S)(Shi epoxidation) 2625.5
! Type of transition !! S1!! S2!! S3!! S4
|-
| Sum of electronic and thermal Free Energies || -1303.733828|| -1303.724178|| -1303.727673|| -1303.738503
|-
!Type of transition!! R1!! R2!! R3!! R4
|-
| Sum of electronic and thermal Free Energies||-1303.730703|| -1303.730238||-1303.736813|| -1303.738044
|-
!''!!R1-S1!! S2-R2!! S3-R3!! R4-S4
|-
|Difference in Free energy(hartree) || 0.003125|| 0.00606|| 0.00914|| 0.000459
|-
|Difference in Free energy(kJ/mol) || 8.205|| 15.911|| 23.997|| 1.205
|-
|Equlibrium constant(K)|| 0.0365|| 0.001629|| 0.0000624|| 0.6149
|-
|Enantimeric excess of (R or S)|| 92.9%(S)|| 99.8%(R)|| 99.9%(R)|| 23.84%(S)
|}
Literature for this reaction have reported to give the enatiomeric excess to the R enantiomer at 81%. It is therefore very likely that the approach and orientation of the catalyst will be either 2 or 3. <ref>Hongqi Tian, Xuegong She, Jiaxi Xu, and Yian Shi*,''Org. Lett.'',(2001),'''3''',1929-1931</ref>

=====Jacobsen epoxidation of styrene=====
{| class="wikitable" border="1"
|+ structures of transiton state
! R5 !! R6!! S5!! S6
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R1_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>R2_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S1_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>S2_J.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for styrene transition state (Jacobsen epoxidation)
! Type of transition !! S5!! S6
|-
|Sum of electronic and thermal Free Energies ||-3343.969197|| -3343.963191
|-
!Type of transition !! R5!! R6
|-
| Sum of electronic and thermal Free Energies || -3343.960889|| -3343.962162
|-
!''!!R1-S1!! R2-S2
|-
|Difference in Free energy(hartree) || 0.008308|| 0.001029
|-
|Difference in Free energy(kJ/mol) || 21.812654|| 2.7016395
|-
|Equlibrium constant|| 0.000125|| 0.32866
|-
|Enantimeric excess(ee) of (R or S)|| 99.9%(S)|| 50.5%(S)
|}
Literature for this epoxidation has reported ee of 46% favoring S enantiomer. This is in good agreement with the second transition state and therefore the catalyst is likely to be orientated as such.<ref>Michael Palucki, Paul J. Pospisil, Wei Zhang, and
Eric N. Jacobsen,''J. Am. Chem. SOC.'' 1994,'''116''', 9333-9334 </ref>
=====Trans-Stilbene transition state=====
Similar to the styrene transition state, the energies of the trans-stilbene transition states were analysed. There are 8 possible transition state that can be envisaged for this reaction
=====Shi epoxidation of trans-stilbene=====
{| class="wikitable" border="1"
|+ structures of transiton state (R)
! RR1 !! RR2!! RR3!! RR4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR1.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ structures of transiton state (S)
! SS1 !! SS2!! SS3!! SS4
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS1.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS2.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS3.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS4.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for tans-stilbene transition state (R and S)(Shi epoxidation) 2625.5
! Type of transition !! SS1!! SS2!! SS3!! SS4
|-
| Sum of electronic and thermal Free Energies || -1534.683440||-1534.685089||-1534.693818|| -1534.691858
|-
!Type of transition!! RR1!! RR2!! RR3!! RR4
|-
| Sum of electronic and thermal Free Energies||-1534.687808|| -1534.687252||-1534.700037|| -1534.699901
|-
!''!!SS1-RR1!! SS2-RR2!! SS3-RR3!! SS4-RR4
|-
|Difference in Free energy(hartree) || 0.004368|| 0.002163|| 0.006219|| 0.008043
|-
|Difference in Free energy(kJ/mol) || 11.4681|| 5.6789|| 16.3279|| 21.1169
|-
|Equlibrium constant(K)|| 0.009784|| 0.1011|| 0.001377|| 0.0001994
|-
|Enantimeric excess of (RR or SS)|| 98.1%(RR)|| 81.6%(RR)|| 99.7%(RR)|| 99.9%(RR)
|}
Literature for this epoxidation has reported ee>95% favouring RR configuration which is in good agreement with transition states 1,3 and 4. This epoxidation is therefore likely to take any of the transition, 1,3 and 4, as the transiton state for this reaction.<ref>Yong Tu, Zhi-Xian Wang, and Yian Shi*,''J. Am. Chem. Soc.'' 1996, '''118''', 9806-9807</ref>
=====Jacobson epoxidation of trans-stilbene=====
{| class="wikitable" border="1"
|+ structures of transiton state
! RR5 !! SS5
|-
| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>RR1_J.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>''</title><color>white</color>
<size>150</size><uploadedFileContents>SS1_J.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{| class="wikitable" border="1"
|+ Summary of energies for trans-stilbene transition state (Jacobsen epoxidation)
! Type of transition !! SS5
|-
|Sum of electronic and thermal Free Energies ||-3574.923087
|-
!Type of transition !! RR5
|-
| Sum of electronic and thermal Free Energies || -3574.921174
|-
!''!!RR5-SS5
|-
|Difference in Free energy(hartree) || 0.001913
|-
|Difference in Free energy(kJ/mol) || 5.0225
|-
|Equlibrium constant|| 0.1318
|-
|Enantimeric excess(ee) of (RR or SS)|| 76.7%(SS)
|}
Literature for this epoxidation reported ee of 25% favouring the SS configuration.<ref>Bridget D. Brandes and Eric N. Jacobsen,''J. Org. Chem.'' 1994,'''59''', 4378-4380</ref> Although computed energies predicted the SS configuration to be favored, there is a big difference in the value of ee. This could be due to error in experimental data, or lack of accuracy in the computational data and therefore further analysis maybe needed to clarify this.

Overall it can be concluded that the predictions for the absolute configuration of these epoxide reactions using different catalyst via computational methods are relatively accurate, as can be seen by the good agreement with literature values.

====Investigating the non-covalent interactions in the active-site of the reaction transition state====
NCI ananlysis was done on both R2 and S2 transitions for comparison.

{| class="wikitable" border="1"
|+ Molecular model showing NCI
! R2 !! S2
|-
| [[File:Styrene_R2_2.jpg|thumb|center|'' ]] || [[File:Styrene_S2.jpg|thumb|center|'' ]]
|}

==reference==
<references/>

File:Styrene S2.jpg

2014-03-07T13:04:14Z

Ys4111:

2014-03-06T20:30:21Z

Ys4111:

2014-03-06T18:44:12Z

Ys4111:

2014-03-06T17:23:35Z

Ys4111:

2014-03-06T16:38:14Z

Ys4111: