=Shiying Li's 1C Report=
==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[File:Cyclopentadiene-dimerisation.png|thumb|center|1000px|'''Scheme 1''':Reaction Scheme for the Dimerisation]]

In '''Scheme 1''', the cyclopentadiene undergoes dimerization then form two possible dimers which are ''endo'' and ''exo'' conformations in room temperature. However, experimental result shows that only one of the dimers could exist, just the ''endo'' form. To figure why the ''endo'' dimer is preferred, two dimers (Molecule 1 and 2 in the scheme) were drawn using ChemDraw and their molecular geometries were optimized by Avogadro.

{| class="wikitable" border="1"
|+ Table 1: Energy minima after optimizations
!Molecules !! 1 (kcal/mol)!! 2 (kcal/mol) !! 3 (kcal/mol) !! 4 (kcal/mol)
|-
|Geometries||<jmol><jmolApplet><title>Cp-dimer1.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 5 4 3;measure 3 9 8;measure 8 7 6;measure 9 10 6;measure 4 3 9</script>
<uploadedFileContents>Cp-dimer1.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Cp-dimer2.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 5 4 3;measure 9 3 4;measure 9 10 6;measure 8 9 3;measure 7 8 9</script>
<uploadedFileContents>Cp-dimer2.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Hydrogenated-3.mol</title><color>white</color>
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<uploadedFileContents>Hydrogenated-3.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Hydrogenated-4.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 5 4 3;measure 3 9 8;measure 8 7 6;measure 9 10 6;measure 4 3 9</script>
<uploadedFileContents>Hydrogenated-4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Total Bond Stretching Energy || 3.54301 || 3.46745|| 3.31176 || 2.82306
|-
|Total Angle Bending Energy|| 30.77268 ||33.19079 || 31.96288 || 24.68543
|-
|Total Stretch-Bending Energy || -2.04138||-2.08217 ||-2.10361 || -1.65717
|-
|Total Torsional Energy || -2.73105 || -2.94971 || -1.49561 || -0.37830
|-
|Total Out-of-Plane Bending Energy ||0.01485|| 0.02193 || 0.01298 || 0.00028
|-
|Total VAN DER WAALS Energy || 12.80166 || 12.353773 || 13.63776 ||10.63717
|-
|Total Electrostatic Energy || 13.01367 || 14.18466 || 5.11952 || 5.14702
|-
|Total Energy|| 55.37344 || 58.19070 || 50.44568 || 41.25749
|}

The energy of the conformer’s maximum was calculated using MMF94s force field and conjugate gradients algorithm. The hydrogenation of the ''endo'' form produces two different hydrogenated product that are Molecule 3 and 4. Same optimisations process was applied to molecule 3 and 4 to investigate which hydrogenation is preferred. The results were showed in '''Table 1'''. From the table shows above, molecule 4 has a lower energy than the molecule 3. If the hygenation of the dimer is under thermodynamic controlled, the double bond in the norbornene is hydrogenated faster than the double bond in the cylcopentane ring. Besides, the molecules 3 and 4 can be accounted in different energy terms. Besides the total electrostatic energy and total stretch bending energy, the molecule 4 generally has a lower value than molecule 3 in the remained energy contributions. In conclusion, the total angle bending energy and total van der Waals energy are the most contribution towards the lower stability of the molecule 4.

== Part 1: Atropisomerism in an Intermediate related to the Synthesis of Taxol ==

=== Introduction ===
[[File:Int9.PNG|left||thumb|400x400px|'''Scheme 2''':Molecules '''9''']] [[File:Int10.PNG|center||thumb|400x400px|'''Scheme 3''':Molecules '''10''']]

Molecule 9 or 10 are the most important structure of taxol (used in chemotherapy for ovarian cancers) synthesis. They are atropisomers to each other and the main difference is the C=O bond pointing direction, one point up another point down. The energy barrier of bond rotation for these 9 and 10 intermediates enables them to be isolated separately. They both are synthesised from an oxy-Cope rearrangement and their stability was investigated by using Avogadro with the MMFF94(s) force field.

{| class="wikitable" border="1"
|+ Table 2: Energy minima of Molecule '''9''' and '''10''' and their hydrogenated products '''9*''' and '''10*'''
!Molecules !! 9 (kcal/mol)!! 10 (kcal/mol) !! 9* (kcal/mol) !! 10* (kcal/mol)
|-
|Geometries||<jmol><jmolApplet><title>Molecule_9.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_9.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_10.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_10.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_9-hydrogenated.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_9-hydrogenated.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_10-hydrogenated.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Molecule_10-hydrogenated.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Total Bond Stretching Energy || 7.6447 || 7.58965 || 7.29234 || 6.40661
|-
|Total Angle Bending Energy|| 28.24946 ||18.77878 ||23.29595 ||
22.30294
|-
|Total Stretch-Bending Energy || -0.08815||-0.14633||0.15268 || 0.29349
|-
|Total Torsional Energy ||0.33774 || 0.19473 || 10.71749 || 9.27344
|-
|Total Out-of-Plane Bending Energy ||0.97957|| 0.84700 || 0.13196 || 0.03641
|-
|Total VAN DER WAALS Energy || 33.12333 || 33.25936 || 34.24838 ||
31.23140
|-
|Total Electrostatic Energy || 0.30327 || -0.04868 || 0.00000 ||
0.00000
|-
|Total Energy|| 70.54924 || 60.55231 || 75.83879 ||
69.54428
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table 3:Possible structures of molecule 9 and 10 but with higher energy than optimised one
! !! molecule 9 !! molecule 9 !! molecule 9 !! molecule 10 !! molecule 10 !! molecule 10
|-
| Structure || <jmolFile text="Another Chair form">Intermediate taxol 9 chair 1.cml</jmolFile> || <jmolFile text="Slightly twisted boat form">Intermediate taxol 9 twisted boat shape.cml</jmolFile>|| <jmolFile text=" Optimised form but with trans H pointing down">Intermediate taxol 9 chair 2 with H pointing down.cml</jmolFile>|| <jmolFile text="Another Chair form">Intermediate taxol 10 chair form 1.cml</jmolFile>|| <jmolFile text=" Slightly twisted boat form">Intermediate taxol 10 twisted boat.cml</jmolFile>|| <jmolFile text=" Optimised form but with trans H pointing down">Intermediate taxol 10 chair form 2 with H point down.cml</jmolFile>
|-
| Total Energy (kcal/mol) || 82.66844 || 88.45541 || 77.64221 || 75.02369 ||66.36975 || 61.05214
|}

=== Results and Discussions ===

For 9 and 10 molecules, the position of the H in trans alkene and the cyclohexane ring are main factor affect the minimising the energy of the structure. Chair form is he most stable conformation of the cyclohexane ring is and the boat form is the second stable conformation. For the molecule 9 and 10, the cyclohexane ring owns three different conformations two in chair forms and 1 slightly twisted boat form. The result shows the lowest energy structure of the intermediate contains chair conformation in the cyclohexane ring .The Hydrogen in trans alkene form can either pointing up or down in the plane of the 11-member ring. However, it need to point up to get lowest energy for both molecules. After the optimisation, results shows molecule 10 is more stable (9.98 kcal / mol lower in energy). In conclusion, the stereochemistry of the product is more dependent on the structure of molecule 10 rather than molecule 9.

Different from most of the bridgehead olefin being unstable due to large olefin strain, the double bond for both intermediate would react slowly, for example. in hydrogenation. This inertness is due to the fact that the bridgehead double bond is part of a large polycyclic system<ref name="hyper stable olefin ">W. F. Maier, P. Von Rague Schleyer, ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891. {{DOI|10.1021/ja00398a003}}</ref>. From calculation shows above, the intermediate molecule have a lower total energy than their corresponding parent hydrocarbons, so a lower strain is related to their structures so they become more stable. This stability causes the molecules become unusually less reactive.

== Part 1:Spectroscopic Simulation using Quantum Mechanics ==

=== Introduction ===
[[Image: Mo_17_18.jpg|center|]]

The molecules 17 and 18 are the derivative of molecules 9 and 10 , besides they are atropisomers due to formation from the oxyanionic Cope process. Refer to the method used before , MMFF94s mechanics forces field in the Avogadro program was calculated in the first step of the optimisation of molecules 17 and 18.

=== Results and Discussions ===
It’s 1H and 13C NMR spectra were created by using the Gaussian and HPC calculations (using Theory: B3LYP, Basis: 6-31G(d,p), Solvation model: SCRF(CPCM, Solvent = chloroform), Frequency and NMR as key word and Empirical Dispersion : GD3 ). The resulted NMR data was presented in the table below; which compared to the literature values by plotting them in the same graph in excel.For both 1H and 13C NMR spectra, the graphs showed that the literature value and the calculated values were quiet similar apart from small deviations. In the 13 C NMR, presented a better match and this is due to all 20 carbon signals were clearly showed in the literature, no assumption use in the 1H data. So the literature values are correctly interpreted and assigned. Those small deviations might from the sensitivity and precision of NMR instrument that used in the literature and the one accounted in the calculation, heavy atom effect of the two sulfur atom, besides the environment effect during the measurement. In the 1H NMR data, the peaks were quite similar in the chemical shift from 3.5 - 5ppm, besides it observed deviation at lower chemical shift value below 3.5 ppm region. The literature showed a multiplet of 14H in the chemical shift range of 1.35-2.80, it was meant that the 14H are equally distributed in the chemical shift range in the graph plotted by excel. However, it is known that this assumption cannot reflect the exact picture of the multiplet, and then results the deviation.Molecule 17 was chosen to discuss later.

{| class="wikitable" border="1"
|+ Table 4: Comparison of NMR data of Molecule 17 between HPC calaculation and Literature value {{DOI|10042/28018}}
! Calculated Data for 1H !! Calculated Data for 13C
|-
| Shift (ppm) Degeneracy Atoms
5.4439822349 1.0000 25
3.2892695297 2.0000 50,39
3.1496592391 3.0000 51,53,52
2.7409210163 1.0000 28
2.5683745590 1.0000 31
2.4851652536 1.0000 19
2.3705014206 2.0000 26,30
2.2695721945 4.0000 41,32,29,36
1.9557286479 2.0000 40,42
1.8107191580 2.0000 44,45
1.6044369622 3.0000 43,27,33
1.2636806013 1.0000 47
1.1967315790 1.0000 48
1.1097025805 2.0000 49,46
0.8380095085 4.0000 35,34,38,37
|| Shift (ppm) Degeneracy Atoms
216.8932607019 1.0000 10
151.7542056168 1.0000 6
117.1461064746 1.0000 3
88.7324043974 1.0000 15
57.0696825355 1.0000 14
56.4946034132 1.0000 13
54.7593650872 1.0000 5
52.0535966940 1.0000 7
48.4854448109 1.0000 4
45.1643921682 1.0000 22
43.6549221877 1.0000 23
40.4318873597 1.0000 16
34.4801060018 1.0000 12
34.1462414903 1.0000 18
33.8871317620 1.0000 1
27.2445457944 1.0000 2
27.0908804922 1.0000 8
21.9122917539 1.0000 20
21.7727797741 1.0000 17
19.0713888197 1.0000 9
|}

{| class="wikitable" border="1"
|+ Table 5: Comparison of NMR data of Molecule 17 between HPC calaculation and Literature value {{DOI|10042/28018}}
! Calculated Data for 1H !! Calculated Data for 13C
|-
| 1H NMR (300 MHz, CDCl3) ppm
4.84 (dd, J = 7.2,4.7 Hz, 1 H) ,3.40-3.10 (m ,4H), 2.99 ( dd, J = 6.8, 5.2 Hz, 1 H), 2.80-1.35 (series of m, 14 H), 1.38 (s, 3 H), 1.25 (s, 3 H), 1.10 (s, 3 H), 1.00-0.80 (m, 1 H)
|| 13C NMR (75 MHz, CDCL3) ppm
218.79, 144.63, 125.33, 72.88, 56.19, 52.52,48.50, 46.80, 45.76, 39.80,38.81, 35.85, 32.66, 28.79, 28.29, 26.88, 25.66, 23.86, 20.96, 18.71
|}

{| class="wikitable" border="1"
|+ Table 6: Comparison of NMR data of Molecule 17 {{DOI|10042/28018}}
! Compare Data for 1H !! Compare Data for 13C
|-
| [[File:COMPARE_17.PNG|500px|right|SVG]]
|| [[File:COMPARE_17C.PNG|500px|right|SVG]]
|}

Besides, the HPC calculation enabled vibrational analysis of the molecule 17 and 18 to be reported. The Gibbs free energy (∆G) were came from the entropy and zero-point-energy correction, presents in the table 9. Molecule 18 has a more negative value of the free energy than molecule 17, so it indicates that molecule 18 is the prefer conformation to be formed upon synthesis. Combining the fact that molecule 18 was found out to be the lower energy conformation, molecule 18 is the most thermodynamically stable conformation and transformation from molecule 17 to molecule 18 would work. In order for the transformation to happen, energy input (e.g. reflux) is required for the rearrangement of structure, would observe the sigma-bond rotations and changing the carbonyl oxygen to point down<ref name="molecule 17 and 18">Spectroscopic data: L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>. Despite of a lower energy is attained in this conformation, the methyl which alpha position to the carbonyl was need to be closer to the methyl group in the bridgehead from 0.571nm to 0.385 nm.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table 7: Vibrational Analysis of Molecule 17 and 18
! Hartree/Particle!! Molecule 17 {{DOI|10042/28018}} !! Molecule 18 {{DOI|10042/28021}}
|-
| Zero-point correction|| 0.467240 || 0.467562
|-
| Thermal correction to Energy|| 0.489298 || 0.489349
|-
| Thermal correction to Enthalpy || 0.490242 || 0.490293
|-
| Thermal correction to Gibbs Free Energy || 0.418299 || 0.420041
|-
| Sum of electronic and zero-point Energies(E0 = Elec + ZPE)|| -1651.400866 || 1651.407622
|-
| Sum of electronic and thermal Energies (E=E0+Evib+Erot+Etrans)|| -1651.378808 || -1651.385835
|-
| Sum of electronic and thermal Enthalpies(H=E+RT) || -1651.377864 || -1651.384891
|-
| Sum of electronic and thermal Free Energies (free energies) (G=H-TS)|| -1651.449807|| -1651.455144
|}

==Part 2: Analysis of the properties of the synthesised alkene epoxides==
[[File:Shi_and_jac.PNG|400px|thumb|'''Scheme 4. '''21''' Jacobsen and '''24''' Shi's catalyst]]

===the Jacobsen and shi's Catalyst===

Jacobsen and shi's catalysts (Scheme '''4''') were used to accelerate asymmetric epoxidation of alkenes. The conformation was used to search for the crystal structure of these catalysts in Cambridge Crystal Database (CCDC). Besides, Mercury program was used to obtain those crystal structures. Two crystal structures presents below<ref name="Shi">Zhi-Xian Wang, S.M.Miller, O.P.Anderson, Yian Shi, ''J.Org.Chem. '', '''2001''', ''66'', 521. {{DOI|10.1021/jo001343i}}</ref> <ref name="Jacobsen">J.W.Yoon, T.-S.Yoon, S.W.Lee, W.Shin, ''Acta Crystallogr.,Sect.C:Cryst.Struct.Commun. '', '''1999''', ''55'', 1766. {{DOI|10.1107/S0108270199009397}}</ref> .

{| class="wikitable" border="1"
|+ '''Crystal structure of Shi and Jacobsen catalyst'''
! '''21'''Jacobsen catalyst!! '''23'''Shi's catalyst
|-
|<jmol><jmolApplet>
<title>Jacobsen structure</title>
<color>black</color>
<size>400</size>
<script>measure 140 186;measure 143 183;measure 94 46;measure 88 51;cpk -20;zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Jacobsen's_one_molecule.mol</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<title>Shi's structure</title>
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<size>400</size>
<script>measure 4 3;measure 3 12;measure 8 16;measure 16 10;measure 8 7;measure 9 10;measure 1 2;measure 2 15;measure 15 4;measure 11 12;; cpk -20;zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Shi catalyst_one_molecule.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:Analyse.PNG]]

There have four anomeric centres within the structure of pre catalyst 21. However just a few C-O bonds are shorter than the normal C-O bond, 0.142 nm (sum of the covalent radii of oxygen and carbon). Due to the anomeric effect, the lone pair of the oxygen atom is donated to the sigma * C-O orbital adjacent then in get shorten the C-O bond. Will the C-O bond get shorten or not is dependent on the direction of the inductive effect of the carbonyl group. In the crystallised structure and the diagram shows below, which owns four shorter C-O bonds in the pre catalyst 21.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
! Atom
! C-O bond length/nm
|-
| O5-C28
| 0.1409
|-
| O4-C28
| 0.1439
|-
| O6-C10
| 0.1403
|-
| O7-C10
| 0.1403
|-
| O7-C1
| 0.1441
|-
| O19-C1
| 0.1413
|}

For Jacobsen catalyst, four distances between two closely distributed hydrogen atoms on two tertiary butyl groups were measured then shown on '''Crystal structure of Shi and Jacobsen catalyst'''. Compared to interaction values to van de Waals distance for hydrogen (2.40 Å), <ref name="vdw">{{DOI|10.1021/jp8111556}}</ref>, which found the attractive interactions between all four pairs of hydrogen atoms. So,during alkene epoxidation, these interactions stop alkene from approaching to the Mg center from tertiary butyl side causes the alkenes be fully stereoselectively epoxidized.

Noticed that the presence of anomeric centres (carbon centres connecting to two oxygen) in Shi's catalyst. For each anomeric centre, one of the C-O bond is shorter than the average C-O bond length (142 pm) however the other one is longer.(see Figure '''4'''). Due to the lone pair electrons donation from one of the oxygen to the C-O σ <sup>*</sup> orbital, that shortens the carbon oxygen bond between the oxygen which has donated the lone pair electrons and the carbon, lengthening another carbon oxygen bond which electron density in the σ <sup>*</sup> anti-bonding orbital increases.

===The Calculated NMR Properties of the Epoxides===
[[File:Shi_and_jac.PNG|500px|thumb|'''Scheme 5. Epoxidations of trans-stilbene and 1,2-dihydronaphthalene]]

Two alkenes (trans-stilbene and 1,2-dihydronaphthalene) were been epoxidized, each of them coming out two alkene oxides enantiomers (see Scheme '''5'''). Both products were optimized by Avogadro with energy minimized ('''Optimized Alkene Oxides'''). The structures of R,S-trans-stilbene oxide and R,R-dihydronaphthalene oxide were calculated using Gaussian. 1H and 13C NMR spectra were simulated under B3LYP theory and 6-31G(d,p) basis, with chloroform as the solvent(Figure '''4''' to '''7''') ({{DOI|10042/28024}}and {{DOI|10042/28025}}). The chemical shifts of four spectra were shown in Table '''5''' to '''8'''.

{| class="wikitable" border="1"
|+ '''Optimized Alkene Oxides'''
! R,R-trans-stilbene oxide!! S,S-trans-stilbene oxide !! R,S-Dihydronaphthalene oxide !! S,R-Dihydronaphthalene oxide
|-
|<jmol><jmolApplet>
<title>R,R-Stilbene_Oxide.mol</title>
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<script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>S,S-trans-stilbene.mol</uploadedFileContents>
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<script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>R,S-1,2-dihydronaphthalene_oxide.mol</uploadedFileContents>
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<uploadedFileContents>S,R-1,2-dihydronaphthalene_oxide.mol</uploadedFileContents>
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|}

[[File:RR_trans_stibene_nmr_13C.PNG|600px|thumb|right|'''Figure 4 Predicted <sup>13</sup>C NMR of R,R-trans-stilbene oxide''']]

{| class="wikitable" border="1"
|+ Table 5: 13C NMR shifts of R,R-trans-stilbene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 134.0870000000 || 2.0000|| 5,9
|-
| 124.2190000000 || 2.0000 || 3,13
|-
| 123.5175000000 || 2.0000 || 1,11
|-
| 123.2128500000 || 2.0000|| 12,2
|-
| 123.0770000000 || 2.0000 || 10,6
|-
| 118.2640000000 || 2.0000 || 14,4
|-
| 66.4240000000 || 2.0000|| 7,8
|}

[[File:RR_trans_stibene_nmr_1H.PNG|600px|thumb|right|'''Figure 5 Predicted <sup>1</sup>H NMR of R,R-trans-stilbene oxide''']]

{| class="wikitable" border="1"
|+ Table 6: 1H NMR shifts of R,R-trans-stilbene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.5704000000 || 2.0000|| 18,26
|-
| 7.4700000000 || 8.0000|| 20,23,16,24,17,25,19,27
|-
| 3.5380000000 || 2.0000 || 21,22
|}

[[File:RS_Dihydrona._13C.PNG|600px|thumb|right|'''Figure 6 Predicted <sup>13</sup>C NMR of R,S-dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 7: 13C NMR shifts of R,S-dihydronapthalene oxide oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 135.3877560205 || 1.0000 || 4
|-
| 130.3705995748 || 1.0000 || 5
|-
| 126.6664754359 || 1.0000 || 6
|-
| 123.7910886822 || 1.0000 || 2
|-
| 123.5334121254 || 1.0000 || 3
|-
| 121.7441913397 || 1.0000 || 1
|-
| 52.8211670356 || 1.0000 || 10
|-
| 52.1924643324 || 1.0000 || 7
|-
| 30.1802794498 || 1.0000 || 8
|-
| 29.0634872612 || 1.0000 || 9
|}

[[File:RS_Dihydrona._1H.PNG|600px|thumb|right|'''Figure 7 Predicted <sup>1</sup>H NMR of R,S-dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 8: 1H NMR shifts of R,S-dihydronapthalene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.6151181280 || 1.0000 || 15
|-
| 7.3900000000 || 2.0000 || 13,12
|-
| 7.2514926773 || 1.0000 || 14
|-
| 3.5595613767 || 1.0000 || 16
|-
| 3.4831000000 || 1.0000 || 21
|-
| 2.9466313163 || 1.0000 || 17
|-
| 2.2672859897 || 1.0000 || 18
|-
| 2.2090255293 || 1.0000 || 19
|-
| 1.8734432001 || 1.0000 || 20
|}

[[File:13_CHydro.PNG|600px|thumb|right|'''Figure 8 Predicted <sup>13</sup>C NMR of R,R-dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 5: 13C NMR shifts of R,R-dihydronapthalene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 159.0583525316 || 1.0000|| 4
|-
| 158.8103855320 || 1.0000|| 5
|-
| 143.0888073617 || 1.0000 || 6
|-
| 142.1069708605 || 1.0000 || 1
|-
| 140.4097181276 || 1.0000 || 2
|-
| 136.1738515816 || 1.0000|| 3
|-
| 76.5157945443 || 1.0000 || 11
|-
| 69.1405631356 || 1.0000 || 14
|-
| 45.6264520368 || 1.0000|| 7
|-
| 43.0944021631 || 1.0000 || 8
|}

[[File:1_HHydro.PNG|600px|thumb|right|'''Figure 9 Predicted <sup>1</sup>H NMR of R,R-dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 6: 1H NMR shifts of R,R-dihydronapthalene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.3174463253 || 3.0000|| 16,18,15
|-
| 7.2361771974 || 1.0000|| 17
|-
| 3.3982744035 || 1.0000 || 9
|-
| 3.0766366869 || 1.0000|| 10
|-
| 2.9151339569 || 1.0000|| 20
|-
| 2.5271290601 || 1.0000|| 13
|-
| 2.2423640897 || 3.0000|| 21
|-
| 2.0341021979 || 3.0000|| 12
|-
|}

In conclusion, from the table shows above that the epoxide has a very similar calculated 1H and 13C NMR spectrums within a same pair of enantiomer. Therefore, NMR still not a good tool in determining the absolute configuration of the epoxide.

===The Assignment of the Absolute Configurations for products===

Alkene epoxidation is stereospecific to the nature of alkenes that would not alter the trans/cis configuration of the alkene. The alkenes proceeds through a concerted syn-addition mechanism, cause the trans-stilbene gives R,R- or S,S-trans-stilbene oxides while a cis- alkene: 1,2-dihydronapthalene gives 1R,2S- or 1S,2R-dihydronapthalene oxide as shown on Scheme '''5'''. Finally, the stereochemistry of final products after epoxidation should be characterized using analytical techniques.

====Optical rotatory power====
The optical rotatory power is one of the measurements that distinguish the absolute configurations of the enantiomes. Initially, literature values of optial rotatory powers of four epoxides were searched from Reaxys (Table '''9'''). Computational analyses were carried out to predict the optical rotatory powers of four optimized epoxides in chloroform at 589 nm and 365 nm using Gaussian with CAM-B3LYP method, 6-311++g(2df,p) basis. The outcomes were summarized in Table '''10'''.

{|class="wikitable" border="1"
|+ Table 9: Literature Values for Optical Properties of dihydronaphthalene oxides and trans-stilbene oxides
! Epoxides !! R,S-dihydronaphthalene oxides<ref name="R,S-dihydronaphthalene oxides"> Pedragosa-Moreau, S.; Archelas, A.; Furstoss, R. ''Tetrahedron'' '''1996''', 52, 4593 </ref>!! S,R-dihydronaphthalene oxides<ref name="S,R-dihydronaphthalene oxides"> Lin, H.; Qiao, J.; Liu, Y.; Wu, Z.-L. ''Journal of Molecular Catalysis B: Enzymatic '' '''2010''', 67, 236 </ref> !! S，S-trans-stilbene oxides<ref name="S,S-trans-stilbene oxides"> Niwa, T.; Nakada, M. ''Journal of the American Chemical Society'' '''2012''', 134, 13538</ref> !! R,R-trans-stilbene oxides<ref name="R,R-trans-stilbene oxides"> Wong, O. A.; Wang, B.; Zhao, M.-X.; Shi, Y. ''Journal of Organic Chemistry'' '''2009''', 74, 6335 </ref>
|-
| Concentration (g/100ml) || 0.81 || 0.21|| 0.56 || 0.73
|-
|Enantiometric Excess (%) || 99 ||99 || 89 || 97
|-
|Solvent || CHCl<sub>3</sub>||CHCl<sub>3</sub> ||CHCl<sub>3</sub> || CHCl<sub>3</sub>
|-
|Optical Rotation ||129<sup>o</sup>|| -39<sup>o</sup> || -205.2<sup>o</sup> || 334.6<sup>o</sup>
|-
|Wavelength (nm) || 589 || 589 || 589 || 589
|-
|Temperature ||20<sup>o</sup>C || 25<sup>o</sup>C || 20<sup>o</sup>C || 25<sup>o</sup>C
|-
|}

{|class="wikitable" border="1"
|+ Table 10: Computed Values for Optical and Thermodynamic Properties of dihydronaphthalene oxides and trans-stilbene oxides
! epoxides !!R,R-trans-stilbene oxides {{DOI|10042/28050}} !! S,S-trans-stilbene oxides{{DOI|10042/28051}} !! R,S-dihydronaphthalene oxides {{DOI|10042/28048}}!! S,R-dihydronaphthalene oxides {{DOI|10042/28049}}
|-
|α<sub>d</sub> at 589 nm|| 102.87<sup>o</sup> || -24.18<sup>o</sup>|| 177.43<sup>o</sup> || -52.74<sup>o</sup>
|-
|}

The predicted values calculated by the method mentioned above agrees with the literature values found with some extend of deviation tolerated. The sign of all predicted values perfectly match with the literature values. Therefore, the method introduced is reliable in calculating the optical rotatory power of those two epoxides.

====VCD and ECD====
Apart from optical rotatory power, the absolute configuration could be assigned by vibrational circular dichroism (VCD) and the electronic circular dichroism (ECD). VCD spectra of R,R- and S,S-trans-stilbene oxides were plotted to assign the configuration (Figure '''8''' and '''9'''). As for ECD, due to lacking of chromophore in epoxides, it fails to assign the configuration by using UV/Vis spectrum.

{{DOI|10042/28055}}
[[File:Rr_dihy_.PNG|thumb|600x400px|right|Figure 8:ECD spectrum of R,R-dihydronaphthalene oxide]]

{{DOI|10042/28060}}
[[File:Ss_dihy_.PNG|thumb|600x400px|right|Figure 9:ECD spectrum of S,S-dihydronaphthalene oxide]]

{{DOI|10042/28058}}
[[File:Rs_dihy_.PNG|thumb|600x400px|right|Figure 10:ECD spectrum of R,S-dihydronaphthalene oxide]]

{{DOI|10042/28059}}
[[File:Sr_dihy_.PNG|thumb|600x400px|right|Figure 11:ECD spectrum of S,R-dihydronaphthalene oxide]]

{{DOI|10042/28057}}
[[File:Rr_trans_.PNG|thumb|600x400px|right|Figure 10:ECD spectrum of R,R-trans-stilbene oxide]]

{{DOI|10042/28056}}
[[File:Ss_trans_.PNG|thumb|600x400px|right|Figure 11:ECD spectrum of S,S-trans-stilbene oxide]]

====Vibrational Circular Dichroism (VCD)====

Dislike ECD, as the table shows below, VCD can be used in assigning the absolute chemistry of the epoxides. As the same pair of enantiomer, the VCD spectrums are mirror images to each other. This is due to the two complete and opposite vibrational environments presented in the enantiomers pair. In conclusion, the instrument is not available in the department, hence it cannot be done.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table:18 VCD spectrum of the Trans-stilbene
! Tran-stilbene RR {{DOI|10042/28167}} !! Tran-stilbene SS {{DOI|10042/28166}}
|-
|[[File: TRANS-RR.PNG|600px|right]]||[[File:TRANS-SS.PNG|600px|right]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table:19 VCD spectrums of the 1,2 dihydronaphtalene oxide
! 1,2 dihydronaphtalene oxide RR {{DOI|10042/28165}}!! 1,2 dihydronaphtalene oxide SS{{DOI|10042/28164}}
|-
|[[File:1,2_Hydro_RR.PNG |600px|right]]||[[File:1,2_Hydro_RR.PNG|600px|right]]
|-
! 1,2 dihydronaphtalene oxide RS {{DOI|10042/28163}}!! 1,2 dihydronaphtalene oxide RS{{DOI|10042/28162}}
|-
|[[File:1,2_Hydro_RS.PNG|600px|right]]||[[File:1,2_Hydro_SR.PNG|600px|right]]
|}

====Using the (calculated) properties of transition state for the reaction====
By using The free energy different between the transition stats of two diastereomeric (ΔG) to calculate the enantiomeric excess of four product mixtures.
The ratio of concentrations of the two species (K) for each epoxide can be transferred from the each ΔG according to the equation "ΔG=-RTlnK". For the values of K,equilibrium constant each enantiomeric excess was distributed (Table '''11''' to '''14''').

In table '''11''' to '''14''', R,S transition states and R,R transition states are predominant for both Shi's catalyst and Jacobsen catalyst used for epoxidations because of having lower free energy comparing to S,R and S,S transition states separately. So the R,S-trans-stilbene oxide and R,R-dihydronaphthalene oxide are expected to be the major products in trans-stilbene and 1,2-dihydronaphthalene epoxidation used by both Shi's and Jacobsen catalyst.

{|class="wikitable" border="11"
|+ Table 11: Analysis for Computed Thermodynamic Properties of trans-stilbene oxides promoted by Shi's catalyst
|-
| Transition State||R,R-trans-stilbene oxide||S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees)||-1535.14760552||-1535.14668122
|-
| Free Energies of 2(Hartrees)||-1535.14902029||-1535.14601044
|-
| Free Energies of 3(Hartrees)||-1535.16270178||-1535.15629511
|-
| Free Energies of 4(Hartrees)||-1535.16270154||-1535.15243112
|-
| Average ΔG(Hartrees)||-1535.1555072825||-1535.1503544725
|-
| Free Energy Difference (RR-SS)(Hartrees) ||-0.00515281000002688||
|-
| K||235.7||
|-
| Relative Population (%)||99.5||0.5
|-
| Enantiomeric Excess (%)||99.0||
|-
|}

{|class="wikitable" border="12"
|+ Table 12: Analysis for Computed Thermodynamic Properties of trans-stilbene oxides promoted by Jacobsen catalyst
|-
| Transition State||R,R-trans-stilbene oxide||S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees)||-3575.66547138||-3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) ||-0.00117432999968514||
|-
| K||3.5||
|-
| Relative Population (%)||77.8||22.2
|-
| Enantiomeric Excess (%)||55.6||
|-
|}

{|class="wikitable" border="13"
|+ Table 13: Analysis for Computed Thermodynamic Properties of dihydronaphthalene oxides promoted by Shi's catalyst
|-
| Transition State||R,S-dihydronaphthalene oxide||S,R-dihydronaphthalene oxide
|-
| Free Energies of 1 (Hartrees)||-1381.54381947||-1381.55280118
|-
| Free Energies of 2 (Hartrees)||-1381.5472601||-1381.53607543
|-
| Free Energies of 3 (Hartrees)||-1381.556204||-1381.54761301
|-
| Free Energies of 4 (Hartrees)||-1381.54990117||-1381.55813219
|-
| Average ΔG (Hartrees)||-1381.549296185||-1381.5486554525
|-
| Free Energy Difference (RR-SS) (Hartrees)||-0.000640732500414742||
|-
| K||1.9||
|-
| Relative Population (%)||65.5||34.5
|-
| Enantiomeric Excess (%)||31.0||
|}

{|class="wikitable" border="14"
|+ Table 14: Analysis for Computed Thermodynamic Properties of dihydronaphthalene oxides promoted by Jacobsen catalyst
|-
| Transition State||R,S-dihydronaphthalene oxide||S,R-dihydronaphthalene oxide
|-
| Free Energies of 1 (Hartrees)||-3422.06853796||-3422.06054777
|-
| Free Energies of 2 (Hartrees)||-3422.05830133||-3422.05965215
|-
| Average ΔG (Hartrees)||-3422.063419645||-3422.06009996
|-
| Free Energy Difference (RR-SS) (Hartrees)||-0.00331968499995128||
|-
| K||33.8||
|-
| Relative Population (%)||97.1||2.9
|-
| Enantiomeric Excess (%)||94.2||
|}

===NCI Analysis for the Transition State===

Gaussview(Figure '''10''')used for analysed the the non-covalent interactions for R,R- transition state of Shi's catalyst promoted epoxidation of trans-stilbene

[[File:123.PNG|thumb|600x600px|centre|Figure 10]]

'''Figure 10. The non-covalent interactions for R,R- transition state of Shi's catalyst promoted epoxidation of trans-stilbene'''

As the picture shows above, this transition state is stabilized by the attractive interactions to determine the stereoselectivity of the epoxidation,the green region demonstrates attractive interaction that active catalyst binds to the substrate via the oxygen atoms. The substrate should have oriented itself to maximize the attractive interaction before binding to minimize the energy of the transition state.

===QTAIM analysis for transition state of R,R-trans-stilbene oxide promoted by Shi's catalyst===
[[File:Pz.PNG|thumb|600x600px|centre|Figure 11:QTAIM for transition state of R,R-trans-stilbene oxide promoted by Shi's catalyst]]
The QTAIM analysis was conducted to calculate the orientation of R,R-trans-stilbene oxide in respect to Shi's catalyst. All the non-covalent bond critical points from weak interaction associated with weak interaction between oxygen and hydrogen were assigned (Figure '''11''').

===New Candidates for investigations===

From the data base from Reaxy, two possible new candidates of exoxide and their alkene presented below.Two epoxides are (4R,1R)-pulegone oxide and (1R,4S)-pulegone oxide with their structure are listed in diagram below. They both can be synthesised from the (+) Pulegone (with potassium hydroxide and dioxygen peroxide<ref name=" new candidates synthesis methods"> W. Treibs, " Berichte der deutschen chemischen Gesellschaft (A and B Series) ", '' Journal of Organic Chemistry '', '''1933''', ''66(10) '', 1483–1492{{DOI| 10.1002/cber.19330661008}}</ref>), which is commercial available in the catalogue of the Sigma Aldwich . In,conclusion, they are the suitable epoxides for the future investigation.

[[File:PZ.PNG|centre]]

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table:23 Possible Epoxide candidates
! !! (1R,4R)-pulegone oxide<ref name=" new candidates optical"> Reusch; Johnson, " The Pulegone Oxides ", '' Journal of Organic Chemistry '', '''1963''', ''28 '', 2557.{{DOI| 10.1021/jo01045a016 }}</ref> !! (1R,4S)-pulegone oxide<ref name=" new candidates optical"> Reusch; Johnson, " The Pulegone Oxides ", '' Journal of Organic Chemistry '', '''1963''', ''28 '', 2557.{{DOI| 10.1021/jo01045a016 }}</ref>
|-
|Condition || C=0.03 , ethanol, 324 nm, 25 degree celsius ||C=0.03 , ethanol, 327 nm, 25 degree celsius
|-
| Rotation [Aplha] ||853.9 deg ||-1177.9 deg
|}

<jmol><jmolApplet><title>untitled.mol</title><color>white</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>PZ.mol</uploadedFileContents>
</jmolApplet></jmol>
==Limitations of the software and further works==

===Limitations of the software===
*Gassview: It is less time consuming for running and it needs particular files : fchk, log. in order to get the required information on the epoxide molecules. Besides it is a good tool to the predicted ECD and VCD,UV,NMR,IR spectrums for the specific molecule.
*QTAIM: The coordinates of the molecules cannot be saved; therefore screenshots are needed. It will be good if the result diagram can be rotated in 3D after uploaded to the wiki page, as it is easier for understanding the analysis.
*Avagordro: For small molecule, it is easy to draw the structure within the program directly, but it is not easy for big molecule. The big molecule can be drawn instead with ChemDraw first and import into the program. However, the stereochemistry of the molecules was lost in the import and there also had a minor change to the configuration of the structure.

===Further work===
*Investigate the suggested candidates of the epoxide with the similar approach above
*Repeat the optimisation of the molecules with ChemBIO3D and compare the results to the one obtained in this investigation. This is because all the molecule were optimised with Avogadro in this case.
*Although the calculation of the coupling constant of the epoxide were obtained in this investigation, time was not sufficient to combine them with the chemical shift value and stimulate the actual spectrum from gNMR. It will be good if more guideline on how to use gNMR is provided in the Toolbox section,so the actual NMR can be stimulated.
*Search for the ORP for epoxide 4 RR and SS in other chemical database and compare them with the calculated value above.

==Reference==
<references/>

File:Pz.PNG

2014-03-21T15:47:10Z

Sl5811:

2014-03-19T15:28:00Z

Sl5811:

2014-03-19T13:20:41Z

Sl5811:

Rep:Mod:shiyingli

2014-03-19T13:14:44Z

Sl5811:

=Shiying Li's 1C Report=
==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[File:Cyclopentadiene-dimerisation.png|thumb|center|1000px|'''Scheme 1''':Reaction Scheme for the Dimerisation]]

Referring to '''Scheme 1''', under room temperature, the cyclopentadiene undergoes dimerisation readily giving two possible dimers that are ''endo'' and ''exo''. However, experimental result shows that only one of the dimers could form, which is the ''endo'' form. To investigate the reason that the ''endo'' dimer is preferred, two dimers (Molecule 1 and 2 in the scheme) were drawn using ChemDraw and their geometries were optimized by Avogadro. The energy maximum were calculated using MMF94s force field and conjugate gradients algorithm. The hydrogenation of the ''endo'' dimer yields two different hydrogenated product that are Molecule 3 and 4. Same optimisations were applied to Molecule 3 and 4 to investigate which hydrogenation is preferred. The results were tabulated in '''Table 1'''.

{| class="wikitable" border="1"
|+ Table 1: Energy minima after optimizations
!Molecules !! 1 (kcal/mol)!! 2 (kcal/mol) !! 3 (kcal/mol) !! 4 (kcal/mol)
|-
|Geometries||<jmol><jmolApplet><title>Cp-dimer1.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Cp-dimer1.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Cp-dimer2.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Cp-dimer2.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Hydrogenated-3.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Hydrogenated-3.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Hydrogenated-4.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Hydrogenated-4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Total Bond Stretching Energy || 3.54301 || 3.46745|| 3.31176 || 2.82306
|-
|Total Angle Bending Energy|| 30.77268 ||33.19079 || 31.96288 || 24.68543
|-
|Total Stretch-Bending Energy || -2.04138||-2.08217 ||-2.10361 || -1.65717
|-
|Total Torsional Energy || -2.73105 || -2.94971 || -1.49561 || -0.37830
|-
|Total Out-of-Plane Bending Energy ||0.01485|| 0.02193 || 0.01298 || 0.00028
|-
|Total VAN DER WAALS Energy || 12.80166 || 12.353773 || 13.63776 ||10.63717
|-
|Total Electrostatic Energy || 13.01367 || 14.18466 || 5.11952 || 5.14702
|-
|Total Energy|| 55.37344 || 58.19070 || 50.44568 || 41.25749
|}

== Part 1: Atropisomerism in an Intermediate related to the Synthesis of Taxol ==

=== Introduction ===
[[File:Int9.PNG|left||thumb|400x400px|'''Scheme 2''':Molecules '''9''']] [[File:Int10.PNG|center||thumb|400x400px|'''Scheme 3''':Molecules '''10''']]

Intermediate 9 or 10 are the key part of taxol (used in chemotherapy for ovarian cancers) synthesis. They are atropisomers to each other and the main difference is the C=O bond pointing either up or down. The barrier of bond rotation within these two intermediates enables them to be isolated separately. They both are synthesised from an oxy-Cope rearrangement and their stability was investigated by using Avogadro with the MMFF94(s) force field.

{| class="wikitable" border="1"
|+ Table 2: Energy minima of Molecule '''9''' and '''10''' and their hydrogenated products '''9*''' and '''10*'''
!Molecules !! 9 (kcal/mol)!! 10 (kcal/mol) !! 9* (kcal/mol) !! 10* (kcal/mol)
|-
|Geometries||<jmol><jmolApplet><title>Molecule_9.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_9.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_10.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_10.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_9-hydrogenated.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_9-hydrogenated.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_10-hydrogenated.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Molecule_10-hydrogenated.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Total Bond Stretching Energy || 7.6447 || 7.58965 || 7.29234 || 6.40661
|-
|Total Angle Bending Energy|| 28.24946 ||18.77878 ||23.29595 ||
22.30294
|-
|Total Stretch-Bending Energy || -0.08815||-0.14633||0.15268 || 0.29349
|-
|Total Torsional Energy ||0.33774 || 0.19473 || 10.71749 || 9.27344
|-
|Total Out-of-Plane Bending Energy ||0.97957|| 0.84700 || 0.13196 || 0.03641
|-
|Total VAN DER WAALS Energy || 33.12333 || 33.25936 || 34.24838 ||
31.23140
|-
|Total Electrostatic Energy || 0.30327 || -0.04868 || 0.00000 ||
0.00000
|-
|Total Energy|| 70.54924 || 60.55231 || 75.83879 ||
69.54428
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table 3:Possible structures of Intermediates 9 and 10 but with higher energy than optimised one
! !! Intermediate 9 !! Intermediate 9 !! Intermediate 9 !! Intermediate 10 !! Intermediate 10 !! Intermediate 10
|-
| Structure || <jmolFile text="Another Chair form">Intermediate taxol 9 chair 1.cml</jmolFile> || <jmolFile text="Slightly twisted boat form">Intermediate taxol 9 twisted boat shape.cml</jmolFile>|| <jmolFile text=" Optimised form but with trans H pointing down">Intermediate taxol 9 chair 2 with H pointing down.cml</jmolFile>|| <jmolFile text="Another Chair form">Intermediate taxol 10 chair form 1.cml</jmolFile>|| <jmolFile text=" Slightly twisted boat form">Intermediate taxol 10 twisted boat.cml</jmolFile>|| <jmolFile text=" Optimised form but with trans H pointing down">Intermediate taxol 10 chair form 2 with H point down.cml</jmolFile>
|-
| Total Energy (kcal/mol) || 82.66844 || 88.45541 || 77.64221 || 75.02369 ||66.36975 || 61.05214
|}

=== Results and Discussions ===

For both intermediates, the position of the H in trans alkene and the fused cyclohexane ring are important factors in minimising the energy of the structure. The most stable conformation of the cyclohexane ring is known to be chair and the second stable conformation is boat. For the intermediates 9 and 10, the fused cyclohexane ring is able to adopt three different conformations (two chairs and 1 slightly twisted boat form, see below). As expected, the lowest energy structure of the intermediate contains chair conformation in the cyclohexane ring (see in the optimised structures). The H in trans alkene can either pointing up or down in the plane of the 11-member ring, but it needs to be pointing up for achieving lowest energy structure for both intermediates. After both intermediate get optimised, it was found out that intermediate 10 is more stable (9.98 kcal / mol lower in energy). It can be said that upon carbonyl addition, the stereochemistry of the product is dependent on the structure of intermediate 10 rather than intermediate 9.

Unlike most of the bridgehead olefin being unstable due to large olefin strain, the double bond within both intermediates was observed to be reacted slowly, i.e. in hydrogenation. This inertness can be accounted by the fact that the bridgehead double bond is part of a large polycyclic system<ref name="hyper stable olefin ">W. F. Maier, P. Von Rague Schleyer, ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891. {{DOI|10.1021/ja00398a003}}</ref>
. From calculation (see table below), the intermediates have a lower total energy than their corresponding parent hydrocarbons, so a lower strain is associated within their structures, hence they are much more stable. This stability makes the intermediates become unusually unreactive.

== Part 1:Spectroscopic Simulation using Quantum Mechanics ==

=== Introduction ===
[[Image: Mo_17_18.jpg|center|]]

The molecules 17 and 18 are derivative of 9 and 10 above, they are also atropisomers due to formation from the oxyanionic Cope process. Same as before, MMFF94s mechanics forces field in the Avogadro program was used in the first stage of the optimisation of molecules 17 and 18.

=== Results and Discussions ===
Molecule 17 was chosen to investigate further. It’s 1H and 13C NMR spectra were stimulated by using the Gaussian and HPC calculations (using Theory: B3LYP, Basis: 6-31G(d,p), Solvation model: SCRF(CPCM, Solvent = chloroform), Freq and NMR as key word and Empirical Dispersion : GD3 ). The obtained NMR data was indicated in the table below, it was compared directly to the literature values by plotting them in the same graph. In the 1H NMR data, the data matched quite well in the chemical shift from 3.5 - 5ppm, but with an observable deviation at lower chemical shift value (< 3.5 ppm). This is mainly arise from the assumption that used in the plotting the literature data. The literature reported a multiplet of 14H in the chemical shift range of 1.35-2.80, it was assumed that the 14H are equally distributed in the chemical shift range in the plotting of the graph. However, it is known that this assumption cannot reflect the true picture of the multiplet, so deviations were resulted. In the 13 C data, a better match was observed and this is because all 20 carbon signals were explicitly reported in the literature, no assumption need to make as in the 1H data. For both 1H and 13C NMR spectra, the graphs reflected that the literature value and the calculated values were in a good match although with small deviations. Therefore, it can be said that the literature values are correctly interpreted and assigned. The other possible origin of the small deviations can come from the sensitivity and precision of NMR instrument that used in the literature and the one accounted in the calculation,heavy atom effect of the two sulfur atom, as well as the temperature and pressure during the measurement.

{| class="wikitable" border="1"
|+ Table 4: Comparison of NMR data of Molecule 17 between HPC calaculation and Literature value {{DOI|10042/28018}}
! Calculated Data for 1H !! Calculated Data for 13C
|-
| Shift (ppm) Degeneracy Atoms
5.4439822349 1.0000 25
3.2892695297 2.0000 50,39
3.1496592391 3.0000 51,53,52
2.7409210163 1.0000 28
2.5683745590 1.0000 31
2.4851652536 1.0000 19
2.3705014206 2.0000 26,30
2.2695721945 4.0000 41,32,29,36
1.9557286479 2.0000 40,42
1.8107191580 2.0000 44,45
1.6044369622 3.0000 43,27,33
1.2636806013 1.0000 47
1.1967315790 1.0000 48
1.1097025805 2.0000 49,46
0.8380095085 4.0000 35,34,38,37
|| Shift (ppm) Degeneracy Atoms
216.8932607019 1.0000 10
151.7542056168 1.0000 6
117.1461064746 1.0000 3
88.7324043974 1.0000 15
57.0696825355 1.0000 14
56.4946034132 1.0000 13
54.7593650872 1.0000 5
52.0535966940 1.0000 7
48.4854448109 1.0000 4
45.1643921682 1.0000 22
43.6549221877 1.0000 23
40.4318873597 1.0000 16
34.4801060018 1.0000 12
34.1462414903 1.0000 18
33.8871317620 1.0000 1
27.2445457944 1.0000 2
27.0908804922 1.0000 8
21.9122917539 1.0000 20
21.7727797741 1.0000 17
19.0713888197 1.0000 9
|}

{| class="wikitable" border="1"
|+ Table 5: Comparison of NMR data of Molecule 17 between HPC calaculation and Literature value {{DOI|10042/28018}}
! Calculated Data for 1H !! Calculated Data for 13C
|-
| 1H NMR (300 MHz, CDCl3) ppm
4.84 (dd, J = 7.2,4.7 Hz, 1 H) ,3.40-3.10 (m ,4H), 2.99 ( dd, J = 6.8, 5.2 Hz, 1 H), 2.80-1.35 (series of m, 14 H), 1.38 (s, 3 H), 1.25 (s, 3 H), 1.10 (s, 3 H), 1.00-0.80 (m, 1 H)
|| 13C NMR (75 MHz, CDCL3) ppm
218.79, 144.63, 125.33, 72.88, 56.19, 52.52,48.50, 46.80, 45.76, 39.80,38.81, 35.85, 32.66, 28.79, 28.29, 26.88, 25.66, 23.86, 20.96, 18.71
|}

{| class="wikitable" border="1"
|+ Table 6: Comparison of NMR data of Molecule 17 {{DOI|10042/28018}}
! Compare Data for 1H !! Compare Data for 13C
|-
| [[File:COMPARE_17.PNG|500px|right|SVG]]
|| [[File:COMPARE_17C.PNG|500px|right|SVG]]
|}

In addition, the HPC calculation enabled vibrational analysis of the molecule 17 and 18 to be reported. The entropy and zero-point-energy correction were computed to give a Gibbs free energy (∆G), see in the table 9. Molecule 18 has a more negative value of the free energy than molecule 17, so it indicates that molecule 18 is the prefer conformation to be formed upon synthesis. Combining the fact that molecule 18 was found out to be the lower energy conformation, molecule 18 is the most thermodynamically stable conformation and transformation from molecule 17 to molecule 18 is feasible. In order for the transformation to happen, energy input (e.g. reflux) is required for the rearrangement of structure, which involves several sigma-bond rotations and turning the carbonyl oxygen to point down<ref name="molecule 17 and 18">Spectroscopic data: L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>. Despite of a lower energy is attained in this conformation, the methyl that is alpha to the carbonyl was required to be brought closer to the methyl group in the bridgehead ( from 0.571nm to 0.385 nm).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table 7: Vibrational Analysis of Molecule 17 and 18
! Hartree/Particle!! Molecule 17 {{DOI|10042/28018}} !! Molecule 18 {{DOI|10042/28021}}
|-
| Zero-point correction|| 0.467240 || 0.467562
|-
| Thermal correction to Energy|| 0.489298 || 0.489349
|-
| Thermal correction to Enthalpy || 0.490242 || 0.490293
|-
| Thermal correction to Gibbs Free Energy || 0.418299 || 0.420041
|-
| Sum of electronic and zero-point Energies(E0 = Elec + ZPE)|| -1651.400866 || 1651.407622
|-
| Sum of electronic and thermal Energies (E=E0+Evib+Erot+Etrans)|| -1651.378808 || -1651.385835
|-
| Sum of electronic and thermal Enthalpies(H=E+RT) || -1651.377864 || -1651.384891
|-
| Sum of electronic and thermal Free Energies (free energies) (G=H-TS)|| -1651.449807|| -1651.455144
|}

==Part 2: Analysis of the properties of the synthesised alkene epoxides==
[[File:Shi_and_jac.PNG|400px|thumb|'''Scheme 4. '''21''' Jacobsen and '''24''' Shi's catalyst]]

===the Jacobsen and shi's Catalyst===

Jacobsen and shi's catalysts (Scheme '''4''') were used to promote asymmetric epoxidation of alkenes. The Conquest was used to search for the crystal structure of these catalysts in Cambridge Crystal Database (CCDC). Also, Mercury program was introduced to analyze those crystal structures. Two crystal structures were shown as following<ref name="Shi">Zhi-Xian Wang, S.M.Miller, O.P.Anderson, Yian Shi, ''J.Org.Chem. '', '''2001''', ''66'', 521. {{DOI|10.1021/jo001343i}}</ref> <ref name="Jacobsen">J.W.Yoon, T.-S.Yoon, S.W.Lee, W.Shin, ''Acta Crystallogr.,Sect.C:Cryst.Struct.Commun. '', '''1999''', ''55'', 1766. {{DOI|10.1107/S0108270199009397}}</ref> .

{| class="wikitable" border="1"
|+ '''Crystal structure of Shi and Jacobsen catalyst'''
! '''21'''Jacobsen catalyst!! '''23'''Shi's catalyst
|-
|<jmol><jmolApplet>
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|| [[File:]]

{| class="wikitable" style="margin: 1em auto 1em auto;"
|-
! Atom
! C-O bond length/nm
|-
| O5-C28
| 0.1409
|-
| O4-C28
| 0.1439
|-
| O6-C10
| 0.1403
|-
| O7-C10
| 0.1403
|-
| O7-C1
| 0.1441
|-
| O19-C1
| 0.1413
|}

|}
The presence of anomeric centres (carbon centres connecting to two oxygen) in Shi's catalyst should be noted. At each anomeric centre, one of the C-O bond is shorter than the average C-O bond length (142 pm),whilst the other one is longer.(see Figure '''4'''). This is due to the lone pair electrons donation from one of the oxygen to the C-O σ <sup>*</sup> orbital, which shortens the carbon oxygen bond between the oxygen that has donated the lone pair electrons and the carbon, lengthening the other carbon oxygen bond whose electron density in the σ <sup>*</sup> anti-bonding orbital increases.

As for Jacobsen catalyst, four distances between two closely distributed hydrogen atoms on two tertiary butyl groups were measured as shown on '''Crystal structure of Shi and Jacobsen catalyst'''. All the values of those interaction were compared to the van der Waals distance for hydrogen (2.40 Å), <ref name="vdw">{{DOI|10.1021/jp8111556}}</ref>. It could be found the interactions between all four pairs of hydrogen atoms are attractive. Therefore, during alkene epoxidation, these interactions prevents alkene from approaching to the manganese centre from tertiary butyl side, ensuring that alkenes could be stereoselectively epoxidized.

===The Calculated NMR Properties of the Epoxides===
[[File:Shi_and_jac.PNG|500px|thumb|'''Scheme 5. Epoxidations of trans-stilbene and 1,2-dihydronaphthalene]]

Two alkenes (trans-stilbene and 1,2-dihydronaphthalene) were chosen to be epoxidized, each giving two alkene oxides enantiomers (see Scheme '''5'''). Each products were optimized by Avogadro with energy minimized ('''Optimized Alkene Oxides'''). The geometries of R,R-trans-stilbene oxide and R,S-dihydronaphthalene oxide at the denisty functional level were calculated using Gaussian. 13C and 1H NMR spectra were simulated under B3LYP theory and 6-31G(d,p) basis, with chloroform as the solvent(Figure '''4''' to '''7''') ({{DOI|10042/28024}}and {{DOI|10042/28025}}). The chemical shifts of four spectra were summarized in Table '''5''' to '''8'''.

{| class="wikitable" border="1"
|+ '''Optimized Alkene Oxides'''
! R,R-trans-stilbene oxide!! S,S-trans-stilbene oxide !! R,S-Dihydronaphthalene oxide !! S,R-Dihydronaphthalene oxide
|-
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[[File:RR_trans_stibene_nmr_13C.PNG|600px|thumb|right|'''Figure 4 Predicted <sup>13</sup>C NMR of trans-stilbene oxide''']]

{| class="wikitable" border="1"
|+ Table 5: 13C NMR shifts of trans-stilbene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 134.0870000000 || 2.0000|| 5,9
|-
| 124.2190000000 || 2.0000 || 3,13
|-
| 123.5175000000 || 2.0000 || 1,11
|-
| 123.2128500000 || 2.0000|| 12,2
|-
| 123.0770000000 || 2.0000 || 10,6
|-
| 118.2640000000 || 2.0000 || 14,4
|-
| 66.4240000000 || 2.0000|| 7,8
|}

[[File:RR_trans_stibene_nmr_1H.PNG|600px|thumb|right|'''Figure 5 Predicted <sup>1</sup>H NMR of trans-stilbene oxide''']]

{| class="wikitable" border="1"
|+ Table 6: 1H NMR shifts of trans-stilbene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.5704000000 || 2.0000|| 18,26
|-
| 7.4700000000 || 8.0000|| 20,23,16,24,17,25,19,27
|-
| 3.5380000000 || 2.0000 || 21,22
|}

[[File:RS_Dihydrona._13C.PNG|600px|thumb|right|'''Figure 6 Predicted <sup>13</sup>C NMR of dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 7: 13C NMR shifts of dihydronapthalene oxide oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 135.3877560205 || 1.0000 || 4
|-
| 130.3705995748 || 1.0000 || 5
|-
| 126.6664754359 || 1.0000 || 6
|-
| 123.7910886822 || 1.0000 || 2
|-
| 123.5334121254 || 1.0000 || 3
|-
| 121.7441913397 || 1.0000 || 1
|-
| 52.8211670356 || 1.0000 || 10
|-
| 52.1924643324 || 1.0000 || 7
|-
| 30.1802794498 || 1.0000 || 8
|-
| 29.0634872612 || 1.0000 || 9
|}

[[File:RS_Dihydrona._1H.PNG|600px|thumb|right|'''Figure 7 Predicted <sup>1</sup>H NMR of dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 8: 1H NMR shifts of dihydronapthalene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.6151181280 || 1.0000 || 15
|-
| 7.3900000000 || 2.0000 || 13,12
|-
| 7.2514926773 || 1.0000 || 14
|-
| 3.5595613767 || 1.0000 || 16
|-
| 3.4831000000 || 1.0000 || 21
|-
| 2.9466313163 || 1.0000 || 17
|-
| 2.2672859897 || 1.0000 || 18
|-
| 2.2090255293 || 1.0000 || 19
|-
| 1.8734432001 || 1.0000 || 20
|}

[[File:13_CHydro.PNG|600px|thumb|right|'''Figure 8 Predicted <sup>13</sup>C NMR of R,R-dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 5: 13C NMR shifts of R,R-dihydronapthalene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 159.0583525316 || 1.0000|| 4
|-
| 158.8103855320 || 1.0000|| 5
|-
| 143.0888073617 || 1.0000 || 6
|-
| 142.1069708605 || 1.0000 || 1
|-
| 140.4097181276 || 1.0000 || 2
|-
| 136.1738515816 || 1.0000|| 3
|-
| 76.5157945443 || 1.0000 || 11
|-
| 69.1405631356 || 1.0000 || 14
|-
| 45.6264520368 || 1.0000|| 7
|-
| 43.0944021631 || 1.0000 || 8
|}

[[File:1_HHydro.PNG|600px|thumb|right|'''Figure 9 Predicted <sup>1</sup>H NMR of R,R-dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 6: 1H NMR shifts of R,R-dihydronapthalene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.3174463253 || 3.0000|| 16,18,15
|-
| 7.2361771974 || 1.0000|| 17
|-
| 3.3982744035 || 1.0000 || 9
|-
| 3.0766366869 || 1.0000|| 10
|-
| 2.9151339569 || 1.0000|| 20
|-
| 2.5271290601 || 1.0000|| 13
|-
| 2.2423640897 || 3.0000|| 21
|-
| 2.0341021979 || 3.0000|| 12
|-
|}

===The Assignment of the Absolute Configurations for products===

Alkenen epoxidation is stereospecfic with respect to alkenes that would not alter the trans/cis configuration of the alkene. It proceeds via a concerted syn-addition mechanism, therefore the trans-stilbene gives R,R- or S,S-trans-stilbene oxides whereas 1,2-dihydronapthalene (a cis- alkene) gives 1R,2S- or 1S,2R-dihydronapthalene oxide as shown on Scheme '''5'''. Consequently, the stereochemistry of final products after epoxidation should be characterized using analytical techniques.

====Optical rotatory power====
The optical rotatory power is one of the measurements that distinguish the absolute configurations of the enantiomes. Initially, literature values of optial rotatory powers of four epoxides were searched from Reaxys (Table '''9'''). Computational analyses were carried out to predict the optical rotatory powers of four optimized epoxides in chloroform at 589 nm and 365 nm using Gaussian with CAM-B3LYP method, 6-311++g(2df,p) basis. The outcomes were summarized in Table '''10'''.

{|class="wikitable" border="1"
|+ Table 9: Literature Values for Optical Properties of dihydronaphthalene oxides and trans-stilbene oxides
! Epoxides !! R,S-dihydronaphthalene oxides<ref name="R,S-dihydronaphthalene oxides"> Pedragosa-Moreau, S.; Archelas, A.; Furstoss, R. ''Tetrahedron'' '''1996''', 52, 4593 </ref>!! S,R-dihydronaphthalene oxides<ref name="S,R-dihydronaphthalene oxides"> Lin, H.; Qiao, J.; Liu, Y.; Wu, Z.-L. ''Journal of Molecular Catalysis B: Enzymatic '' '''2010''', 67, 236 </ref> !! S，S-trans-stilbene oxides<ref name="S,S-trans-stilbene oxides"> Niwa, T.; Nakada, M. ''Journal of the American Chemical Society'' '''2012''', 134, 13538</ref> !! R,R-trans-stilbene oxides<ref name="R,R-trans-stilbene oxides"> Wong, O. A.; Wang, B.; Zhao, M.-X.; Shi, Y. ''Journal of Organic Chemistry'' '''2009''', 74, 6335 </ref>
|-
| Concentration (g/100ml) || 0.81 || 0.21|| 0.56 || 0.73
|-
|Enantiometric Excess (%) || 99 ||99 || 89 || 97
|-
|Solvent || CHCl<sub>3</sub>||CHCl<sub>3</sub> ||CHCl<sub>3</sub> || CHCl<sub>3</sub>
|-
|Optical Rotation ||129<sup>o</sup>|| -39<sup>o</sup> || -205.2<sup>o</sup> || 334.6<sup>o</sup>
|-
|Wavelength (nm) || 589 || 589 || 589 || 589
|-
|Temperature ||20<sup>o</sup>C || 25<sup>o</sup>C || 20<sup>o</sup>C || 25<sup>o</sup>C
|-
|}

{|class="wikitable" border="1"
|+ Table 10: Computed Values for Optical and Thermodynamic Properties of dihydronaphthalene oxides and trans-stilbene oxides
! epoxides !!R,R-trans-stilbene oxides {{DOI|10042/28050}} !! S,S-trans-stilbene oxides{{DOI|10042/28051}} !! R,S-dihydronaphthalene oxides {{DOI|10042/28048}}!! S,R-dihydronaphthalene oxides {{DOI|10042/28049}}
|-
|α<sub>d</sub> at 589 nm|| 102.87<sup>o</sup> || -24.18<sup>o</sup>|| 177.43<sup>o</sup> || -52.74<sup>o</sup>
|-
|}

The predicted values calculated by the method mentioned above agrees with the literature values found with some extend of deviation tolerated. The sign of all predicted values perfectly match with the literature values. Therefore, the method introduced is reliable in calculating the optical rotatory power of those two epoxides.

====VCD and ECD====
Apart from optical rotatory power, the absolute configuration could be assigned by vibrational circular dichroism (VCD) and the electronic circular dichroism (ECD). VCD spectra of R,R- and S,S-trans-stilbene oxides were plotted to assign the configuration (Figure '''8''' and '''9'''). As for ECD, due to lacking of chromophore in epoxides, it fails to assign the configuration by using UV/Vis spectrum.

{{DOI|10042/28055}}
[[File:Rr_dihy_.PNG|thumb|600x400px|right|Figure 8:ECD spectrum of R,R-dihydronaphthalene oxide]]

{{DOI|10042/28060}}
[[File:Ss_dihy_.PNG|thumb|600x400px|right|Figure 9:ECD spectrum of S,S-dihydronaphthalene oxide]]

{{DOI|10042/28058}}
[[File:Rs_dihy_.PNG|thumb|600x400px|right|Figure 10:ECD spectrum of R,S-dihydronaphthalene oxide]]

{{DOI|10042/28059}}
[[File:Sr_dihy_.PNG|thumb|600x400px|right|Figure 11:ECD spectrum of S,R-dihydronaphthalene oxide]]

{{DOI|10042/28057}}
[[File:Rr_trans_.PNG|thumb|600x400px|right|Figure 10:ECD spectrum of R,R-trans-stilbene oxide]]

{{DOI|10042/28056}}
[[File:Ss_trans_.PNG|thumb|600x400px|right|Figure 11:ECD spectrum of S,S-trans-stilbene oxide]]

====Vibrational Circular Dichroism (VCD)====

Unlike ECD, VCD can be used in assigning the absolute chemistry of the epoxides, see that in table below. For a same pair of enantiomer, the VCD spectrums are mirror images to each other. This is because of the two complete and opposite vibrational environments presented in the enantiomers pair. Unfortunately, the instrument is not available in the department, hence it cannot be done.

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table:18 VCD spectrum of the Trans-stilbene
! Tran-stilbene RR {{DOI|10042/28167}} !! Tran-stilbene SS {{DOI|10042/28166}}
|-
|[[File: |400px|right]]||[[File:|400px|right]]
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table:19 VCD spectrums of the 1,2 dihydronaphtalene oxide
! 1,2 dihydronaphtalene oxide RR {{DOI|10042/28165}}!! 1,2 dihydronaphtalene oxide SS{{DOI|10042/28164}}
|-
|[[File:1,2_Hydro_RR.PNG |400px|right]]||[[File:1,2_Hydro_RR.PNG|400px|right]]
|-
! 1,2 dihydronaphtalene oxide RS {{DOI|10042/28163}}!! 1,2 dihydronaphtalene oxide RS{{DOI|10042/28162}}
|-
|[[File:1,2_Hydro_RS.PNG|400px|right]]||[[File:1,2_Hydro_SR.PNG|400px|right]]
|}

====Using the (calculated) properties of transition state for the reaction====
The enantiomeric excess of four product mixtures(two epoxidation promoted by each catalyst) could be calculated using free energy difference between two diastereomeric transition states (ΔG). The ratio of concentrations of the two species (K) for each product mixture could be converted from the each ΔG according to the equation "ΔG=-RTlnK". Knowing the values of K, each enantiomeric excess was calculated (Table '''11''' to '''14''').

{|class="wikitable" border="1"
|+ Table 11: Analysis for Computed Thermodynamic Properties of trans-stilbene oxides promoted by Shi's catalyst
|-
| Transition State||R,R-trans-stilbene oxide||S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees)||-1535.14760552||-1535.14668122
|-
| Free Energies of 2(Hartrees)||-1535.14902029||-1535.14601044
|-
| Free Energies of 3(Hartrees)||-1535.16270178||-1535.15629511
|-
| Free Energies of 4(Hartrees)||-1535.16270154||-1535.15243112
|-
| Average ΔG(Hartrees)||-1535.1555072825||-1535.1503544725
|-
| Free Energy Difference (RR-SS)(Hartrees) ||-0.00515281000002688||
|-
| K||235.7||
|-
| Relative Population (%)||99.5||0.5
|-
| Enantiomeric Excess (%)||99.0||
|-
|}

{|class="wikitable" border="1"
|+ Table 12: Analysis for Computed Thermodynamic Properties of trans-stilbene oxides promoted by Jacobsen catalyst
|-
| Transition State||R,R-trans-stilbene oxide||S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees)||-3575.66547138||-3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) ||-0.00117432999968514||
|-
| K||3.5||
|-
| Relative Population (%)||77.8||22.2
|-
| Enantiomeric Excess (%)||55.6||
|-
|}

{|class="wikitable" border="1"
|+ Table 13: Analysis for Computed Thermodynamic Properties of dihydronaphthalene oxides promoted by Shi's catalyst
|-
| Transition State||R,S-dihydronaphthalene oxide||S,R-dihydronaphthalene oxide
|-
| Free Energies of 1 (Hartrees)||-1381.54381947||-1381.55280118
|-
| Free Energies of 2 (Hartrees)||-1381.5472601||-1381.53607543
|-
| Free Energies of 3 (Hartrees)||-1381.556204||-1381.54761301
|-
| Free Energies of 4 (Hartrees)||-1381.54990117||-1381.55813219
|-
| Average ΔG (Hartrees)||-1381.549296185||-1381.5486554525
|-
| Free Energy Difference (RR-SS) (Hartrees)||-0.000640732500414742||
|-
| K||1.9||
|-
| Relative Population (%)||65.5||34.5
|-
| Enantiomeric Excess (%)||31.0||
|}

{|class="wikitable" border="1"
|+ Table 14: Analysis for Computed Thermodynamic Properties of dihydronaphthalene oxides promoted by Jacobsen catalyst
|-
| Transition State||R,S-dihydronaphthalene oxide||S,R-dihydronaphthalene oxide
|-
| Free Energies of 1 (Hartrees)||-3422.06853796||-3422.06054777
|-
| Free Energies of 2 (Hartrees)||-3422.05830133||-3422.05965215
|-
| Average ΔG (Hartrees)||-3422.063419645||-3422.06009996
|-
| Free Energy Difference (RR-SS) (Hartrees)||-0.00331968499995128||
|-
| K||33.8||
|-
| Relative Population (%)||97.1||2.9
|-
| Enantiomeric Excess (%)||94.2||
|}

As can be seen on Table '''11''' to '''14''', R,R transition states and R,S transition states are predominant for both Shi's catalyst and Jacobsen catalyst promoted epoxidations due to having lower free energy comparing to S,S and S,R transition states respectively. Therefore, the R,R-trans-stilbene oxide and R,S-dihydronaphthalene oxide are supposed to be the major products in trans-stilbene and 1,2-dihydronaphthalene epoxidation promoted by both Shi's and Jacobsen catalyst.

===NCI Analysis for the Transition State===

The non-covalent interactions for R,R- transition state of Shi's catalyst promoted epoxidation of trans-stilbene was analyzed by Gaussview(Figure '''10''').

<jmol>
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<title>Orbital</title><color>white</color><size>600</size>
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'''Figure 10. The non-covalent interactions for R,R- transition state of Shi's catalyst promoted epoxidation of trans-stilbene'''

Referring to the figure shown above, the green region indicates attractive interaction that active catalyst binds to the substrate via the oxygen atoms. The substrate should have oriented itself to maximize the attractive interaction before binding to minimize the energy of the transition state. This transition state is stabilized by the attractive interactions which therefore determine the stereoselectivity of the epoxidation.

===QTAIM analysis for transition state of R,R-trans-stilbene oxide promoted by Shi's catalyst===
[[File:QTAIM_R,R.png|thumb|600x600px|centre|Figure 11:QTAIM for transition state of R,R-trans-stilbene oxide promoted by Shi's catalyst]]
The QTAIM analysis was conducted to calculate the orientation of R,R-trans-stilbene oxide in respect to Shi's catalyst. All the non-covalent bond critical points from weak interaction associated with weak interaction between oxygen and hydrogen were assigned (Figure '''11''').

===New Candidates for investigations===

By searching on Reaxys with the required range of molecular weight and ORP, two possible new candidates of epoxide and their corresponding alkene were found. The epoxides are (1R,4R)-pulegone oxide and (1R,4S)-pulegone oxide with their structure are listed in diagram below. They both can be synthesised from the (+) Pulegone (with potassium hydroxide and dioxygen peroxide<ref name=" new candidates synthesis methods"> W. Treibs, " Berichte der deutschen chemischen Gesellschaft (A and B Series) ", '' Journal of Organic Chemistry '', '''1933''', ''66(10) '', 1483–1492{{DOI| 10.1002/cber.19330661008}}</ref>), which is available in the catalogue of the Sigma Aldwich and costs around £63.60 for 100G. Therefore, they are the suitable epoxides for the future investigation.

[[File:PZ.PNG|centre]]

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table:23 Possible Epoxide candidates
! !! (1R,4R)-pulegone oxide<ref name=" new candidates optical"> Reusch; Johnson, " The Pulegone Oxides ", '' Journal of Organic Chemistry '', '''1963''', ''28 '', 2557.{{DOI| 10.1021/jo01045a016 }}</ref> !! (1R,4S)-pulegone oxide<ref name=" new candidates optical"> Reusch; Johnson, " The Pulegone Oxides ", '' Journal of Organic Chemistry '', '''1963''', ''28 '', 2557.{{DOI| 10.1021/jo01045a016 }}</ref>
|-
|Condition || C=0.03 , ethanol, 324 nm, 25 degree celsius ||C=0.03 , ethanol, 327 nm, 25 degree celsius
|-
| Rotation [Aplha] ||853.9 deg ||-1177.9 deg
|}

<jmol><jmolApplet><title>untitled.mol</title><color>white</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>PZ.mol</uploadedFileContents>
</jmolApplet></jmol>
==Limitations of the software and further works==

===Limitations of the software===
*Avagordro: For small molecule, it is easy to draw the structure within the program directly, but it is not easy for big molecule. The big molecule can be drawn instead with ChemDraw first and import into the program. However, the stereochemistry of the molecules was lost in the import and there also had a minor change to the configuration of the structure.
*QTAIM: The coordinates of the molecules cannot be saved; therefore screenshots are needed. It will be good if the result diagram can be rotated in 3D after uploaded to the wiki page, as it is easier for understanding the analysis.
*Gassview: It takes a sufficient time for running and it needs specific files (e.g fchk, log etc) in order to get the required information on the molecule. However, it is able to generate the predicted UV, IR, NMR, ECD and VCD spectrums for the specific molecule.
===Further work===
*Investigate the suggested candidates of the epoxide with the similar approach above
*Repeat the optimisation of the molecules with ChemBIO3D and compare the results to the one obtained in this investigation. This is because all the molecule were optimised with Avogadro in this case.
*Although the calculation of the coupling constant of the epoxide were obtained in this investigation, time was not sufficient to combine them with the chemical shift value and stimulate the actual spectrum from gNMR. It will be good if more guideline on how to use gNMR is provided in the Toolbox section,so the actual NMR can be stimulated.
*Search for the ORP for epoxide 4 RR and SS in other chemical database and compare them with the calculated value above.

==Reference==
<references/>

Rep:Mod:shiyingli

2014-03-19T10:52:31Z

2014-03-17T15:37:55Z

Sl5811:

2014-03-16T21:46:50Z

Sl5811:

File:1 HHydro.PNG

2014-03-16T21:46:50Z

Sl5811:

Rep:Mod:shiyingli

2014-03-16T21:21:26Z

Sl5811: /* The Calculated NMR Properties of the Epoxides */

=Shiying Li's 1C Report=
==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[File:Cyclopentadiene-dimerisation.png|thumb|center|1000px|'''Scheme 1''':Reaction Scheme for the Dimerisation]]

Referring to '''Scheme 1''', under room temperature, the cyclopentadiene undergoes dimerisation readily giving two possible dimers that are ''endo'' and ''exo''. However, experimental result shows that only one of the dimers could form, which is the ''endo'' form. To investigate the reason that the ''endo'' dimer is preferred, two dimers (Molecule 1 and 2 in the scheme) were drawn using ChemDraw and their geometries were optimized by Avogadro. The energy maximum were calculated using MMF94s force field and conjugate gradients algorithm. The hydrogenation of the ''endo'' dimer yields two different hydrogenated product that are Molecule 3 and 4. Same optimisations were applied to Molecule 3 and 4 to investigate which hydrogenation is preferred. The results were tabulated in '''Table 1'''.

{| class="wikitable" border="1"
|+ Table 1: Energy minima after optimizations
!Molecules !! 1 (kcal/mol)!! 2 (kcal/mol) !! 3 (kcal/mol) !! 4 (kcal/mol)
|-
|Geometries||<jmol><jmolApplet><title>Cp-dimer1.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Cp-dimer1.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Cp-dimer2.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Cp-dimer2.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Hydrogenated-3.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Hydrogenated-3.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Hydrogenated-4.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Hydrogenated-4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Total Bond Stretching Energy || 3.54301 || 3.46745|| 3.31176 || 2.82306
|-
|Total Angle Bending Energy|| 30.77268 ||33.19079 || 31.96288 || 24.68543
|-
|Total Stretch-Bending Energy || -2.04138||-2.08217 ||-2.10361 || -1.65717
|-
|Total Torsional Energy || -2.73105 || -2.94971 || -1.49561 || -0.37830
|-
|Total Out-of-Plane Bending Energy ||0.01485|| 0.02193 || 0.01298 || 0.00028
|-
|Total VAN DER WAALS Energy || 12.80166 || 12.353773 || 13.63776 ||10.63717
|-
|Total Electrostatic Energy || 13.01367 || 14.18466 || 5.11952 || 5.14702
|-
|Total Energy|| 55.37344 || 58.19070 || 50.44568 || 41.25749
|}

== Part 1: Atropisomerism in an Intermediate related to the Synthesis of Taxol ==

=== Introduction ===
[[File:Int9.PNG|left||thumb|400x400px|'''Scheme 2''':Molecules '''9''']] [[File:Int10.PNG|center||thumb|400x400px|'''Scheme 3''':Molecules '''10''']]

Intermediate 9 or 10 are the key part of taxol (used in chemotherapy for ovarian cancers) synthesis. They are atropisomers to each other and the main difference is the C=O bond pointing either up or down. The barrier of bond rotation within these two intermediates enables them to be isolated separately. They both are synthesised from an oxy-Cope rearrangement and their stability was investigated by using Avogadro with the MMFF94(s) force field.

{| class="wikitable" border="1"
|+ Table 2: Energy minima of Molecule '''9''' and '''10''' and their hydrogenated products '''9*''' and '''10*'''
!Molecules !! 9 (kcal/mol)!! 10 (kcal/mol) !! 9* (kcal/mol) !! 10* (kcal/mol)
|-
|Geometries||<jmol><jmolApplet><title>Molecule_9.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_9.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_10.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_10.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_9-hydrogenated.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_9-hydrogenated.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_10-hydrogenated.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Molecule_10-hydrogenated.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Total Bond Stretching Energy || 7.6447 || 7.58965 || 7.29234 || 6.40661
|-
|Total Angle Bending Energy|| 28.24946 ||18.77878 ||23.29595 ||
22.30294
|-
|Total Stretch-Bending Energy || -0.08815||-0.14633||0.15268 || 0.29349
|-
|Total Torsional Energy ||0.33774 || 0.19473 || 10.71749 || 9.27344
|-
|Total Out-of-Plane Bending Energy ||0.97957|| 0.84700 || 0.13196 || 0.03641
|-
|Total VAN DER WAALS Energy || 33.12333 || 33.25936 || 34.24838 ||
31.23140
|-
|Total Electrostatic Energy || 0.30327 || -0.04868 || 0.00000 ||
0.00000
|-
|Total Energy|| 70.54924 || 60.55231 || 75.83879 ||
69.54428
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table 3:Possible structures of Intermediates 9 and 10 but with higher energy than optimised one
! !! Intermediate 9 !! Intermediate 9 !! Intermediate 9 !! Intermediate 10 !! Intermediate 10 !! Intermediate 10
|-
| Structure || <jmolFile text="Another Chair form">Intermediate taxol 9 chair 1.cml</jmolFile> || <jmolFile text="Slightly twisted boat form">Intermediate taxol 9 twisted boat shape.cml</jmolFile>|| <jmolFile text=" Optimised form but with trans H pointing down">Intermediate taxol 9 chair 2 with H pointing down.cml</jmolFile>|| <jmolFile text="Another Chair form">Intermediate taxol 10 chair form 1.cml</jmolFile>|| <jmolFile text=" Slightly twisted boat form">Intermediate taxol 10 twisted boat.cml</jmolFile>|| <jmolFile text=" Optimised form but with trans H pointing down">Intermediate taxol 10 chair form 2 with H point down.cml</jmolFile>
|-
| Total Energy (kcal/mol) || 82.66844 || 88.45541 || 77.64221 || 75.02369 ||66.36975 || 61.05214
|}

=== Results and Discussions ===

For both intermediates, the position of the H in trans alkene and the fused cyclohexane ring are important factors in minimising the energy of the structure. The most stable conformation of the cyclohexane ring is known to be chair and the second stable conformation is boat. For the intermediates 9 and 10, the fused cyclohexane ring is able to adopt three different conformations (two chairs and 1 slightly twisted boat form, see below). As expected, the lowest energy structure of the intermediate contains chair conformation in the cyclohexane ring (see in the optimised structures). The H in trans alkene can either pointing up or down in the plane of the 11-member ring, but it needs to be pointing up for achieving lowest energy structure for both intermediates. After both intermediate get optimised, it was found out that intermediate 10 is more stable (9.98 kcal / mol lower in energy). It can be said that upon carbonyl addition, the stereochemistry of the product is dependent on the structure of intermediate 10 rather than intermediate 9.

Unlike most of the bridgehead olefin being unstable due to large olefin strain, the double bond within both intermediates was observed to be reacted slowly, i.e. in hydrogenation. This inertness can be accounted by the fact that the bridgehead double bond is part of a large polycyclic system<ref name="hyper stable olefin ">W. F. Maier, P. Von Rague Schleyer, ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891. {{DOI|10.1021/ja00398a003}}</ref>
. From calculation (see table below), the intermediates have a lower total energy than their corresponding parent hydrocarbons, so a lower strain is associated within their structures, hence they are much more stable. This stability makes the intermediates become unusually unreactive.

== Part 1:Spectroscopic Simulation using Quantum Mechanics ==

=== Introduction ===
[[Image: Mo_17_18.jpg|center|]]

The molecules 17 and 18 are derivative of 9 and 10 above, they are also atropisomers due to formation from the oxyanionic Cope process. Same as before, MMFF94s mechanics forces field in the Avogadro program was used in the first stage of the optimisation of molecules 17 and 18.

=== Results and Discussions ===
Molecule 17 was chosen to investigate further. It’s 1H and 13C NMR spectra were stimulated by using the Gaussian and HPC calculations (using Theory: B3LYP, Basis: 6-31G(d,p), Solvation model: SCRF(CPCM, Solvent = chloroform), Freq and NMR as key word and Empirical Dispersion : GD3 ). The obtained NMR data was indicated in the table below, it was compared directly to the literature values by plotting them in the same graph. In the 1H NMR data, the data matched quite well in the chemical shift from 3.5 - 5ppm, but with an observable deviation at lower chemical shift value (< 3.5 ppm). This is mainly arise from the assumption that used in the plotting the literature data. The literature reported a multiplet of 14H in the chemical shift range of 1.35-2.80, it was assumed that the 14H are equally distributed in the chemical shift range in the plotting of the graph. However, it is known that this assumption cannot reflect the true picture of the multiplet, so deviations were resulted. In the 13 C data, a better match was observed and this is because all 20 carbon signals were explicitly reported in the literature, no assumption need to make as in the 1H data. For both 1H and 13C NMR spectra, the graphs reflected that the literature value and the calculated values were in a good match although with small deviations. Therefore, it can be said that the literature values are correctly interpreted and assigned. The other possible origin of the small deviations can come from the sensitivity and precision of NMR instrument that used in the literature and the one accounted in the calculation,heavy atom effect of the two sulfur atom, as well as the temperature and pressure during the measurement.

{| class="wikitable" border="1"
|+ Table 4: Comparison of NMR data of Molecule 17 between HPC calaculation and Literature value {{DOI|10042/28018}}
! Calculated Data for 1H !! Calculated Data for 13C
|-
| Shift (ppm) Degeneracy Atoms
5.4439822349 1.0000 25
3.2892695297 2.0000 50,39
3.1496592391 3.0000 51,53,52
2.7409210163 1.0000 28
2.5683745590 1.0000 31
2.4851652536 1.0000 19
2.3705014206 2.0000 26,30
2.2695721945 4.0000 41,32,29,36
1.9557286479 2.0000 40,42
1.8107191580 2.0000 44,45
1.6044369622 3.0000 43,27,33
1.2636806013 1.0000 47
1.1967315790 1.0000 48
1.1097025805 2.0000 49,46
0.8380095085 4.0000 35,34,38,37
|| Shift (ppm) Degeneracy Atoms
216.8932607019 1.0000 10
151.7542056168 1.0000 6
117.1461064746 1.0000 3
88.7324043974 1.0000 15
57.0696825355 1.0000 14
56.4946034132 1.0000 13
54.7593650872 1.0000 5
52.0535966940 1.0000 7
48.4854448109 1.0000 4
45.1643921682 1.0000 22
43.6549221877 1.0000 23
40.4318873597 1.0000 16
34.4801060018 1.0000 12
34.1462414903 1.0000 18
33.8871317620 1.0000 1
27.2445457944 1.0000 2
27.0908804922 1.0000 8
21.9122917539 1.0000 20
21.7727797741 1.0000 17
19.0713888197 1.0000 9
|}

{| class="wikitable" border="1"
|+ Table 5: Comparison of NMR data of Molecule 17 between HPC calaculation and Literature value {{DOI|10042/28018}}
! Calculated Data for 1H !! Calculated Data for 13C
|-
| 1H NMR (300 MHz, CDCl3) ppm
4.84 (dd, J = 7.2,4.7 Hz, 1 H) ,3.40-3.10 (m ,4H), 2.99 ( dd, J = 6.8, 5.2 Hz, 1 H), 2.80-1.35 (series of m, 14 H), 1.38 (s, 3 H), 1.25 (s, 3 H), 1.10 (s, 3 H), 1.00-0.80 (m, 1 H)
|| 13C NMR (75 MHz, CDCL3) ppm
218.79, 144.63, 125.33, 72.88, 56.19, 52.52,48.50, 46.80, 45.76, 39.80,38.81, 35.85, 32.66, 28.79, 28.29, 26.88, 25.66, 23.86, 20.96, 18.71
|}

{| class="wikitable" border="1"
|+ Table 6: Comparison of NMR data of Molecule 17 {{DOI|10042/28018}}
! Compare Data for 1H !! Compare Data for 13C
|-
| [[File:COMPARE_17.PNG|500px|right|SVG]]
|| [[File:COMPARE_17C.PNG|500px|right|SVG]]
|}

In addition, the HPC calculation enabled vibrational analysis of the molecule 17 and 18 to be reported. The entropy and zero-point-energy correction were computed to give a Gibbs free energy (∆G), see in the table 9. Molecule 18 has a more negative value of the free energy than molecule 17, so it indicates that molecule 18 is the prefer conformation to be formed upon synthesis. Combining the fact that molecule 18 was found out to be the lower energy conformation, molecule 18 is the most thermodynamically stable conformation and transformation from molecule 17 to molecule 18 is feasible. In order for the transformation to happen, energy input (e.g. reflux) is required for the rearrangement of structure, which involves several sigma-bond rotations and turning the carbonyl oxygen to point down<ref name="molecule 17 and 18">Spectroscopic data: L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>. Despite of a lower energy is attained in this conformation, the methyl that is alpha to the carbonyl was required to be brought closer to the methyl group in the bridgehead ( from 0.571nm to 0.385 nm).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table 7: Vibrational Analysis of Molecule 17 and 18
! Hartree/Particle!! Molecule 17 {{DOI|10042/28018}} !! Molecule 18 {{DOI|10042/28021}}
|-
| Zero-point correction|| 0.467240 || 0.467562
|-
| Thermal correction to Energy|| 0.489298 || 0.489349
|-
| Thermal correction to Enthalpy || 0.490242 || 0.490293
|-
| Thermal correction to Gibbs Free Energy || 0.418299 || 0.420041
|-
| Sum of electronic and zero-point Energies(E0 = Elec + ZPE)|| -1651.400866 || 1651.407622
|-
| Sum of electronic and thermal Energies (E=E0+Evib+Erot+Etrans)|| -1651.378808 || -1651.385835
|-
| Sum of electronic and thermal Enthalpies(H=E+RT) || -1651.377864 || -1651.384891
|-
| Sum of electronic and thermal Free Energies (free energies) (G=H-TS)|| -1651.449807|| -1651.455144
|}

==Part 2: Analysis of the properties of the synthesised alkene epoxides==
[[File:Shi_and_jac.PNG|400px|thumb|'''Scheme 4. '''21''' Jacobsen and '''24''' Shi's catalyst]]

===the Jacobsen and shi's Catalyst===

Jacobsen and shi's catalysts (Scheme '''4''') were used to promote asymmetric epoxidation of alkenes. The Conquest was used to search for the crystal structure of these catalysts in Cambridge Crystal Database (CCDC). Also, Mercury program was introduced to analyze those crystal structures. Two crystal structures were shown as following<ref name="Shi">Zhi-Xian Wang, S.M.Miller, O.P.Anderson, Yian Shi, ''J.Org.Chem. '', '''2001''', ''66'', 521. {{DOI|10.1021/jo001343i}}</ref> <ref name="Jacobsen">J.W.Yoon, T.-S.Yoon, S.W.Lee, W.Shin, ''Acta Crystallogr.,Sect.C:Cryst.Struct.Commun. '', '''1999''', ''55'', 1766. {{DOI|10.1107/S0108270199009397}}</ref> .

{| class="wikitable" border="1"
|+ '''Crystal structure of Shi and Jacobsen catalyst'''
! '''21'''Jacobsen catalyst!! '''23'''Shi's catalyst
|-
|<jmol><jmolApplet>
<title>Jacobsen structure</title>
<color>black</color>
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<uploadedFileContents>Jacobsen's_one_molecule.mol</uploadedFileContents>
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|<jmol><jmolApplet>
<title>Shi's structure</title>
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<uploadedFileContents>Shi catalyst_one_molecule.mol</uploadedFileContents>
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|}
The presence of anomeric centres (carbon centres connecting to two oxygen) in Shi's catalyst should be noted. At each anomeric centre, one of the C-O bond is shorter than the average C-O bond length (142 pm),whilst the other one is longer.(see Figure '''4'''). This is due to the lone pair electrons donation from one of the oxygen to the C-O σ <sup>*</sup> orbital, which shortens the carbon oxygen bond between the oxygen that has donated the lone pair electrons and the carbon, lengthening the other carbon oxygen bond whose electron density in the σ <sup>*</sup> anti-bonding orbital increases.

As for Jacobsen catalyst, four distances between two closely distributed hydrogen atoms on two tertiary butyl groups were measured as shown on '''Crystal structure of Shi and Jacobsen catalyst'''. All the values of those interaction were compared to the van der Waals distance for hydrogen (2.40 Å), <ref name="vdw">{{DOI|10.1021/jp8111556}}</ref>. It could be found the interactions between all four pairs of hydrogen atoms are attractive. Therefore, during alkene epoxidation, these interactions prevents alkene from approaching to the manganese centre from tertiary butyl side, ensuring that alkenes could be stereoselectively epoxidized.

===The Calculated NMR Properties of the Epoxides===
[[File:Shi_and_jac.PNG|500px|thumb|'''Scheme 5. Epoxidations of trans-stilbene and 1,2-dihydronaphthalene]]

Two alkenes (trans-stilbene and 1,2-dihydronaphthalene) were chosen to be epoxidized, each giving two alkene oxides enantiomers (see Scheme '''5'''). Each products were optimized by Avogadro with energy minimized ('''Optimized Alkene Oxides'''). The geometries of R,R-trans-stilbene oxide and R,S-dihydronaphthalene oxide at the denisty functional level were calculated using Gaussian. 13C and 1H NMR spectra were simulated under B3LYP theory and 6-31G(d,p) basis, with chloroform as the solvent(Figure '''4''' to '''7''') ({{DOI|10042/28024}}and {{DOI|10042/28025}}). The chemical shifts of four spectra were summarized in Table '''5''' to '''8'''.

{| class="wikitable" border="1"
|+ '''Optimized Alkene Oxides'''
! R,R-trans-stilbene oxide!! S,S-trans-stilbene oxide !! R,S-Dihydronaphthalene oxide !! S,R-Dihydronaphthalene oxide
|-
|<jmol><jmolApplet>
<title>R,R-Stilbene_Oxide.mol</title>
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<uploadedFileContents>R,R-trans-stilbene.mol</uploadedFileContents>
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|<jmol><jmolApplet>
<title>S,S-Stilbene_Oxide.mol</title>
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<script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>S,S-trans-stilbene.mol</uploadedFileContents>
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|<jmol><jmolApplet>
<title>R,S-Dihydronaphthalene_oxide.mol</title>
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<script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>R,S-1,2-dihydronaphthalene_oxide.mol</uploadedFileContents>
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|<jmol><jmolApplet>
<title>S,R-Dihydronaphthalene_oxide.mol</title>
<color>white</color>
<size></size>240
<script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>S,R-1,2-dihydronaphthalene_oxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:RR_trans_stibene_nmr_13C.PNG|600px|thumb|right|'''Figure 4 Predicted <sup>13</sup>C NMR of trans-stilbene oxide''']]

{| class="wikitable" border="1"
|+ Table 5: 13C NMR shifts of trans-stilbene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 134.0870000000 || 2.0000|| 5,9
|-
| 124.2190000000 || 2.0000 || 3,13
|-
| 123.5175000000 || 2.0000 || 1,11
|-
| 123.2128500000 || 2.0000|| 12,2
|-
| 123.0770000000 || 2.0000 || 10,6
|-
| 118.2640000000 || 2.0000 || 14,4
|-
| 66.4240000000 || 2.0000|| 7,8
|}

[[File:RR_trans_stibene_nmr_1H.PNG|600px|thumb|right|'''Figure 5 Predicted <sup>1</sup>H NMR of trans-stilbene oxide''']]

{| class="wikitable" border="1"
|+ Table 6: 1H NMR shifts of trans-stilbene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.5704000000 || 2.0000|| 18,26
|-
| 7.4700000000 || 8.0000|| 20,23,16,24,17,25,19,27
|-
| 3.5380000000 || 2.0000 || 21,22
|}

[[File:RS_Dihydrona._13C.PNG|600px|thumb|right|'''Figure 6 Predicted <sup>13</sup>C NMR of dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 7: 13C NMR shifts of dihydronapthalene oxide oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 135.3877560205 || 1.0000 || 4
|-
| 130.3705995748 || 1.0000 || 5
|-
| 126.6664754359 || 1.0000 || 6
|-
| 123.7910886822 || 1.0000 || 2
|-
| 123.5334121254 || 1.0000 || 3
|-
| 121.7441913397 || 1.0000 || 1
|-
| 52.8211670356 || 1.0000 || 10
|-
| 52.1924643324 || 1.0000 || 7
|-
| 30.1802794498 || 1.0000 || 8
|-
| 29.0634872612 || 1.0000 || 9
|}

[[File:RS_Dihydrona._1H.PNG|600px|thumb|right|'''Figure 7 Predicted <sup>1</sup>H NMR of dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 8: 13C NMR shifts of dihydronapthalene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.6151181280 || 1.0000 || 15
|-
| 7.3900000000 || 2.0000 || 13,12
|-
| 7.2514926773 || 1.0000 || 14
|-
| 3.5595613767 || 1.0000 || 16
|-
| 3.4831000000 || 1.0000 || 21
|-
| 2.9466313163 || 1.0000 || 17
|-
| 2.2672859897 || 1.0000 || 18
|-
| 2.2090255293 || 1.0000 || 19
|-
| 1.8734432001 || 1.0000 || 20
|}

[[File:|600px|thumb|right|'''Figure 4 Predicted <sup>13</sup>C NMR of R,R-dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 5: 13C NMR shifts of R,R-dihydronapthalene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 134.0871000000 || 2.0000|| 5,9
|-
| 124.2190000000 || 2.0000 || 3,13
|-
| 123.5175000000 || 2.0000 || 1,11
|-
| 123.2128500000 || 2.0000|| 12,2
|-
| 123.0773500000 || 2.0000 || 10,6
|-
| 118.2643500000 || 2.0000 || 14,4
|-
| 66.4246500000 || 2.0000|| 7,8
|}

[[File:|600px|thumb|right|'''Figure 5 Predicted <sup>1</sup>H NMR of R,R-dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 6: 1H NMR shifts of R,R-dihydronapthalene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.5704000000 || 2.0000|| 18,26
|-
| 7.4791750000 || 8.0000|| 20,23,16,24,17,25,19,27
|-
| 3.5380500000 || 2.0000 || 21,22
|}

===The Assignment of the Absolute Configurations for products===

Alkenen epoxidation is stereospecfic with respect to alkenes that would not alter the trans/cis configuration of the alkene. It proceeds via a concerted syn-addition mechanism, therefore the trans-stilbene gives R,R- or S,S-trans-stilbene oxides whereas 1,2-dihydronapthalene (a cis- alkene) gives 1R,2S- or 1S,2R-dihydronapthalene oxide as shown on Scheme '''5'''. Consequently, the stereochemistry of final products after epoxidation should be characterized using analytical techniques.

====Optical rotatory power====
The optical rotatory power is one of the measurements that distinguish the absolute configurations of the enantiomes. Initially, literature values of optial rotatory powers of four epoxides were searched from Reaxys (Table '''9'''). Computational analyses were carried out to predict the optical rotatory powers of four optimized epoxides in chloroform at 589 nm and 365 nm using Gaussian with CAM-B3LYP method, 6-311++g(2df,p) basis. The outcomes were summarized in Table '''10'''.

{|class="wikitable" border="1"
|+ Table 9: Literature Values for Optical Properties of dihydronaphthalene oxides and trans-stilbene oxides
! Epoxides !! R,S-dihydronaphthalene oxides<ref name="R,S-dihydronaphthalene oxides"> Pedragosa-Moreau, S.; Archelas, A.; Furstoss, R. ''Tetrahedron'' '''1996''', 52, 4593 </ref>!! S,R-dihydronaphthalene oxides<ref name="S,R-dihydronaphthalene oxides"> Lin, H.; Qiao, J.; Liu, Y.; Wu, Z.-L. ''Journal of Molecular Catalysis B: Enzymatic '' '''2010''', 67, 236 </ref> !! S，S-trans-stilbene oxides<ref name="S,S-trans-stilbene oxides"> Niwa, T.; Nakada, M. ''Journal of the American Chemical Society'' '''2012''', 134, 13538</ref> !! R,R-trans-stilbene oxides<ref name="R,R-trans-stilbene oxides"> Wong, O. A.; Wang, B.; Zhao, M.-X.; Shi, Y. ''Journal of Organic Chemistry'' '''2009''', 74, 6335 </ref>
|-
| Concentration (g/100ml) || 0.81 || 0.21|| 0.56 || 0.73
|-
|Enantiometric Excess (%) || 99 ||99 || 89 || 97
|-
|Solvent || CHCl<sub>3</sub>||CHCl<sub>3</sub> ||CHCl<sub>3</sub> || CHCl<sub>3</sub>
|-
|Optical Rotation ||129<sup>o</sup>|| -39<sup>o</sup> || -205.2<sup>o</sup> || 334.6<sup>o</sup>
|-
|Wavelength (nm) || 589 || 589 || 589 || 589
|-
|Temperature ||20<sup>o</sup>C || 25<sup>o</sup>C || 20<sup>o</sup>C || 25<sup>o</sup>C
|-
|}

{|class="wikitable" border="1"
|+ Table 10: Computed Values for Optical and Thermodynamic Properties of dihydronaphthalene oxides and trans-stilbene oxides
! epoxides !!R,R-trans-stilbene oxides {{DOI|10042/28050}} !! S,S-trans-stilbene oxides{{DOI|10042/28051}} !! R,S-dihydronaphthalene oxides {{DOI|10042/28048}}!! S,R-dihydronaphthalene oxides {{DOI|10042/28049}}
|-
|α<sub>d</sub> at 589 nm|| 102.87<sup>o</sup> || -24.18<sup>o</sup>|| 177.43<sup>o</sup> || -52.74<sup>o</sup>
|-
|}

The predicted values calculated by the method mentioned above agrees with the literature values found with some extend of deviation tolerated. The sign of all predicted values perfectly match with the literature values. Therefore, the method introduced is reliable in calculating the optical rotatory power of those two epoxides.

====VCD and ECD====
Apart from optical rotatory power, the absolute configuration could be assigned by vibrational circular dichroism (VCD) and the electronic circular dichroism (ECD). VCD spectra of R,R- and S,S-trans-stilbene oxides were plotted to assign the configuration (Figure '''8''' and '''9'''). As for ECD, due to lacking of chromophore in epoxides, it fails to assign the configuration by using UV/Vis spectrum.

{{DOI|10042/28055}}
[[File:Rr_dihy_.PNG|thumb|600x400px|right|Figure 8:ECD spectrum of R,R-dihydronaphthalene oxide]]

{{DOI|10042/28060}}
[[File:Ss_dihy_.PNG|thumb|600x400px|right|Figure 9:ECD spectrum of S,S-dihydronaphthalene oxide]]

{{DOI|10042/28058}}
[[File:Rs_dihy_.PNG|thumb|600x400px|right|Figure 10:ECD spectrum of R,S-dihydronaphthalene oxide]]

{{DOI|10042/28059}}
[[File:Sr_dihy_.PNG|thumb|600x400px|right|Figure 11:ECD spectrum of S,R-dihydronaphthalene oxide]]

{{DOI|10042/28057}}
[[File:Rr_trans_.PNG|thumb|600x400px|right|Figure 10:ECD spectrum of R,R-trans-stilbene oxide]]

{{DOI|10042/28056}}
[[File:Ss_trans_.PNG|thumb|600x400px|right|Figure 11:ECD spectrum of S,S-trans-stilbene oxide]]

====Using the (calculated) properties of transition state for the reaction====
The enantiomeric excess of four product mixtures(two epoxidation promoted by each catalyst) could be calculated using free energy difference between two diastereomeric transition states (ΔG). The ratio of concentrations of the two species (K) for each product mixture could be converted from the each ΔG according to the equation "ΔG=-RTlnK". Knowing the values of K, each enantiomeric excess was calculated (Table '''11''' to '''14''').

{|class="wikitable" border="1"
|+ Table 11: Analysis for Computed Thermodynamic Properties of trans-stilbene oxides promoted by Shi's catalyst
|-
| Transition State||R,R-trans-stilbene oxide||S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees)||-1535.14760552||-1535.14668122
|-
| Free Energies of 2(Hartrees)||-1535.14902029||-1535.14601044
|-
| Free Energies of 3(Hartrees)||-1535.16270178||-1535.15629511
|-
| Free Energies of 4(Hartrees)||-1535.16270154||-1535.15243112
|-
| Average ΔG(Hartrees)||-1535.1555072825||-1535.1503544725
|-
| Free Energy Difference (RR-SS)(Hartrees) ||-0.00515281000002688||
|-
| K||235.7||
|-
| Relative Population (%)||99.5||0.5
|-
| Enantiomeric Excess (%)||99.0||
|-
|}

{|class="wikitable" border="1"
|+ Table 12: Analysis for Computed Thermodynamic Properties of trans-stilbene oxides promoted by Jacobsen catalyst
|-
| Transition State||R,R-trans-stilbene oxide||S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees)||-3575.66547138||-3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) ||-0.00117432999968514||
|-
| K||3.5||
|-
| Relative Population (%)||77.8||22.2
|-
| Enantiomeric Excess (%)||55.6||
|-
|}

{|class="wikitable" border="1"
|+ Table 13: Analysis for Computed Thermodynamic Properties of dihydronaphthalene oxides promoted by Shi's catalyst
|-
| Transition State||R,S-dihydronaphthalene oxide||S,R-dihydronaphthalene oxide
|-
| Free Energies of 1 (Hartrees)||-1381.54381947||-1381.55280118
|-
| Free Energies of 2 (Hartrees)||-1381.5472601||-1381.53607543
|-
| Free Energies of 3 (Hartrees)||-1381.556204||-1381.54761301
|-
| Free Energies of 4 (Hartrees)||-1381.54990117||-1381.55813219
|-
| Average ΔG (Hartrees)||-1381.549296185||-1381.5486554525
|-
| Free Energy Difference (RR-SS) (Hartrees)||-0.000640732500414742||
|-
| K||1.9||
|-
| Relative Population (%)||65.5||34.5
|-
| Enantiomeric Excess (%)||31.0||
|}

{|class="wikitable" border="1"
|+ Table 14: Analysis for Computed Thermodynamic Properties of dihydronaphthalene oxides promoted by Jacobsen catalyst
|-
| Transition State||R,S-dihydronaphthalene oxide||S,R-dihydronaphthalene oxide
|-
| Free Energies of 1 (Hartrees)||-3422.06853796||-3422.06054777
|-
| Free Energies of 2 (Hartrees)||-3422.05830133||-3422.05965215
|-
| Average ΔG (Hartrees)||-3422.063419645||-3422.06009996
|-
| Free Energy Difference (RR-SS) (Hartrees)||-0.00331968499995128||
|-
| K||33.8||
|-
| Relative Population (%)||97.1||2.9
|-
| Enantiomeric Excess (%)||94.2||
|}

As can be seen on Table '''11''' to '''14''', R,R transition states and R,S transition states are predominant for both Shi's catalyst and Jacobsen catalyst promoted epoxidations due to having lower free energy comparing to S,S and S,R transition states respectively. Therefore, the R,R-trans-stilbene oxide and R,S-dihydronaphthalene oxide are supposed to be the major products in trans-stilbene and 1,2-dihydronaphthalene epoxidation promoted by both Shi's and Jacobsen catalyst.

===NCI Analysis for the Transition State===

The non-covalent interactions for R,R- transition state of Shi's catalyst promoted epoxidation of trans-stilbene was analyzed by Gaussview(Figure '''10''').

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>600</size>
<script>isosurface color orange purple "images/3/3c/R%2CR-TS_Shi_NCI.cub.jvxl" translucent;</script>
<uploadedFileContents>R,R-trans-stilbene_epoxidation.jvxl</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>600</size>
<script>isosurface color orange purple "images/3/3c/R%2CR-TS_Shi_NCI.cub.jvxl" translucent;</script>
<uploadedFileContents>R,R-TS_Shi_NCI.cub.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

'''Figure 10. The non-covalent interactions for R,R- transition state of Shi's catalyst promoted epoxidation of trans-stilbene'''

Referring to the figure shown above, the green region indicates attractive interaction that active catalyst binds to the substrate via the oxygen atoms. The substrate should have oriented itself to maximize the attractive interaction before binding to minimize the energy of the transition state. This transition state is stabilized by the attractive interactions which therefore determine the stereoselectivity of the epoxidation.

===QTAIM analysis for transition state of R,R-trans-stilbene oxide promoted by Shi's catalyst===
[[File:QTAIM_R,R.png|thumb|600x600px|centre|Figure 11:QTAIM for transition state of R,R-trans-stilbene oxide promoted by Shi's catalyst]]
The QTAIM analysis was conducted to calculate the orientation of R,R-trans-stilbene oxide in respect to Shi's catalyst. All the non-covalent bond critical points from weak interaction associated with weak interaction between oxygen and hydrogen were assigned (Figure '''11''').

==Limitations of the software and further works==

===Limitations of the software===
*Avagordro: For small molecule, it is easy to draw the structure within the program directly, but it is not easy for big molecule. The big molecule can be drawn instead with ChemDraw first and import into the program. However, the stereochemistry of the molecules was lost in the import and there also had a minor change to the configuration of the structure.
*QTAIM: The coordinates of the molecules cannot be saved; therefore screenshots are needed. It will be good if the result diagram can be rotated in 3D after uploaded to the wiki page, as it is easier for understanding the analysis.
*Gassview: It takes a sufficient time for running and it needs specific files (e.g fchk, log etc) in order to get the required information on the molecule. However, it is able to generate the predicted UV, IR, NMR, ECD and VCD spectrums for the specific molecule.
===Further work===
*Investigate the suggested candidates of the epoxide with the similar approach above
*Repeat the optimisation of the molecules with ChemBIO3D and compare the results to the one obtained in this investigation. This is because all the molecule were optimised with Avogadro in this case.
*Although the calculation of the coupling constant of the epoxide were obtained in this investigation, time was not sufficient to combine them with the chemical shift value and stimulate the actual spectrum from gNMR. It will be good if more guideline on how to use gNMR is provided in the Toolbox section,so the actual NMR can be stimulated.
*Search for the ORP for epoxide 4 RR and SS in other chemical database and compare them with the calculated value above.

==Reference==
<references/>

Rep:Mod:shiyingli

2014-03-16T21:18:26Z

Sl5811:

=Shiying Li's 1C Report=
==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[File:Cyclopentadiene-dimerisation.png|thumb|center|1000px|'''Scheme 1''':Reaction Scheme for the Dimerisation]]

Referring to '''Scheme 1''', under room temperature, the cyclopentadiene undergoes dimerisation readily giving two possible dimers that are ''endo'' and ''exo''. However, experimental result shows that only one of the dimers could form, which is the ''endo'' form. To investigate the reason that the ''endo'' dimer is preferred, two dimers (Molecule 1 and 2 in the scheme) were drawn using ChemDraw and their geometries were optimized by Avogadro. The energy maximum were calculated using MMF94s force field and conjugate gradients algorithm. The hydrogenation of the ''endo'' dimer yields two different hydrogenated product that are Molecule 3 and 4. Same optimisations were applied to Molecule 3 and 4 to investigate which hydrogenation is preferred. The results were tabulated in '''Table 1'''.

{| class="wikitable" border="1"
|+ Table 1: Energy minima after optimizations
!Molecules !! 1 (kcal/mol)!! 2 (kcal/mol) !! 3 (kcal/mol) !! 4 (kcal/mol)
|-
|Geometries||<jmol><jmolApplet><title>Cp-dimer1.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Cp-dimer1.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Cp-dimer2.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Cp-dimer2.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Hydrogenated-3.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Hydrogenated-3.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Hydrogenated-4.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;measure 4 3 2;measure 3 2 7;measure 2 7 8;measure 7 8 9;measure 7 10 6</script>
<uploadedFileContents>Hydrogenated-4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Total Bond Stretching Energy || 3.54301 || 3.46745|| 3.31176 || 2.82306
|-
|Total Angle Bending Energy|| 30.77268 ||33.19079 || 31.96288 || 24.68543
|-
|Total Stretch-Bending Energy || -2.04138||-2.08217 ||-2.10361 || -1.65717
|-
|Total Torsional Energy || -2.73105 || -2.94971 || -1.49561 || -0.37830
|-
|Total Out-of-Plane Bending Energy ||0.01485|| 0.02193 || 0.01298 || 0.00028
|-
|Total VAN DER WAALS Energy || 12.80166 || 12.353773 || 13.63776 ||10.63717
|-
|Total Electrostatic Energy || 13.01367 || 14.18466 || 5.11952 || 5.14702
|-
|Total Energy|| 55.37344 || 58.19070 || 50.44568 || 41.25749
|}

== Part 1: Atropisomerism in an Intermediate related to the Synthesis of Taxol ==

=== Introduction ===
[[File:Int9.PNG|left||thumb|400x400px|'''Scheme 2''':Molecules '''9''']] [[File:Int10.PNG|center||thumb|400x400px|'''Scheme 3''':Molecules '''10''']]

Intermediate 9 or 10 are the key part of taxol (used in chemotherapy for ovarian cancers) synthesis. They are atropisomers to each other and the main difference is the C=O bond pointing either up or down. The barrier of bond rotation within these two intermediates enables them to be isolated separately. They both are synthesised from an oxy-Cope rearrangement and their stability was investigated by using Avogadro with the MMFF94(s) force field.

{| class="wikitable" border="1"
|+ Table 2: Energy minima of Molecule '''9''' and '''10''' and their hydrogenated products '''9*''' and '''10*'''
!Molecules !! 9 (kcal/mol)!! 10 (kcal/mol) !! 9* (kcal/mol) !! 10* (kcal/mol)
|-
|Geometries||<jmol><jmolApplet><title>Molecule_9.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_9.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_10.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_10.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_9-hydrogenated.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Molecule_9-hydrogenated.mol</uploadedFileContents>||
</jmolApplet></jmol>||<jmol><jmolApplet><title>Molecule_10-hydrogenated.mol</title><color>white</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Molecule_10-hydrogenated.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
|Total Bond Stretching Energy || 7.6447 || 7.58965 || 7.29234 || 6.40661
|-
|Total Angle Bending Energy|| 28.24946 ||18.77878 ||23.29595 ||
22.30294
|-
|Total Stretch-Bending Energy || -0.08815||-0.14633||0.15268 || 0.29349
|-
|Total Torsional Energy ||0.33774 || 0.19473 || 10.71749 || 9.27344
|-
|Total Out-of-Plane Bending Energy ||0.97957|| 0.84700 || 0.13196 || 0.03641
|-
|Total VAN DER WAALS Energy || 33.12333 || 33.25936 || 34.24838 ||
31.23140
|-
|Total Electrostatic Energy || 0.30327 || -0.04868 || 0.00000 ||
0.00000
|-
|Total Energy|| 70.54924 || 60.55231 || 75.83879 ||
69.54428
|}

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table 3:Possible structures of Intermediates 9 and 10 but with higher energy than optimised one
! !! Intermediate 9 !! Intermediate 9 !! Intermediate 9 !! Intermediate 10 !! Intermediate 10 !! Intermediate 10
|-
| Structure || <jmolFile text="Another Chair form">Intermediate taxol 9 chair 1.cml</jmolFile> || <jmolFile text="Slightly twisted boat form">Intermediate taxol 9 twisted boat shape.cml</jmolFile>|| <jmolFile text=" Optimised form but with trans H pointing down">Intermediate taxol 9 chair 2 with H pointing down.cml</jmolFile>|| <jmolFile text="Another Chair form">Intermediate taxol 10 chair form 1.cml</jmolFile>|| <jmolFile text=" Slightly twisted boat form">Intermediate taxol 10 twisted boat.cml</jmolFile>|| <jmolFile text=" Optimised form but with trans H pointing down">Intermediate taxol 10 chair form 2 with H point down.cml</jmolFile>
|-
| Total Energy (kcal/mol) || 82.66844 || 88.45541 || 77.64221 || 75.02369 ||66.36975 || 61.05214
|}

=== Results and Discussions ===

For both intermediates, the position of the H in trans alkene and the fused cyclohexane ring are important factors in minimising the energy of the structure. The most stable conformation of the cyclohexane ring is known to be chair and the second stable conformation is boat. For the intermediates 9 and 10, the fused cyclohexane ring is able to adopt three different conformations (two chairs and 1 slightly twisted boat form, see below). As expected, the lowest energy structure of the intermediate contains chair conformation in the cyclohexane ring (see in the optimised structures). The H in trans alkene can either pointing up or down in the plane of the 11-member ring, but it needs to be pointing up for achieving lowest energy structure for both intermediates. After both intermediate get optimised, it was found out that intermediate 10 is more stable (9.98 kcal / mol lower in energy). It can be said that upon carbonyl addition, the stereochemistry of the product is dependent on the structure of intermediate 10 rather than intermediate 9.

Unlike most of the bridgehead olefin being unstable due to large olefin strain, the double bond within both intermediates was observed to be reacted slowly, i.e. in hydrogenation. This inertness can be accounted by the fact that the bridgehead double bond is part of a large polycyclic system<ref name="hyper stable olefin ">W. F. Maier, P. Von Rague Schleyer, ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891. {{DOI|10.1021/ja00398a003}}</ref>
. From calculation (see table below), the intermediates have a lower total energy than their corresponding parent hydrocarbons, so a lower strain is associated within their structures, hence they are much more stable. This stability makes the intermediates become unusually unreactive.

== Part 1:Spectroscopic Simulation using Quantum Mechanics ==

=== Introduction ===
[[Image: Mo_17_18.jpg|center|]]

The molecules 17 and 18 are derivative of 9 and 10 above, they are also atropisomers due to formation from the oxyanionic Cope process. Same as before, MMFF94s mechanics forces field in the Avogadro program was used in the first stage of the optimisation of molecules 17 and 18.

=== Results and Discussions ===
Molecule 17 was chosen to investigate further. It’s 1H and 13C NMR spectra were stimulated by using the Gaussian and HPC calculations (using Theory: B3LYP, Basis: 6-31G(d,p), Solvation model: SCRF(CPCM, Solvent = chloroform), Freq and NMR as key word and Empirical Dispersion : GD3 ). The obtained NMR data was indicated in the table below, it was compared directly to the literature values by plotting them in the same graph. In the 1H NMR data, the data matched quite well in the chemical shift from 3.5 - 5ppm, but with an observable deviation at lower chemical shift value (< 3.5 ppm). This is mainly arise from the assumption that used in the plotting the literature data. The literature reported a multiplet of 14H in the chemical shift range of 1.35-2.80, it was assumed that the 14H are equally distributed in the chemical shift range in the plotting of the graph. However, it is known that this assumption cannot reflect the true picture of the multiplet, so deviations were resulted. In the 13 C data, a better match was observed and this is because all 20 carbon signals were explicitly reported in the literature, no assumption need to make as in the 1H data. For both 1H and 13C NMR spectra, the graphs reflected that the literature value and the calculated values were in a good match although with small deviations. Therefore, it can be said that the literature values are correctly interpreted and assigned. The other possible origin of the small deviations can come from the sensitivity and precision of NMR instrument that used in the literature and the one accounted in the calculation,heavy atom effect of the two sulfur atom, as well as the temperature and pressure during the measurement.

{| class="wikitable" border="1"
|+ Table 4: Comparison of NMR data of Molecule 17 between HPC calaculation and Literature value {{DOI|10042/28018}}
! Calculated Data for 1H !! Calculated Data for 13C
|-
| Shift (ppm) Degeneracy Atoms
5.4439822349 1.0000 25
3.2892695297 2.0000 50,39
3.1496592391 3.0000 51,53,52
2.7409210163 1.0000 28
2.5683745590 1.0000 31
2.4851652536 1.0000 19
2.3705014206 2.0000 26,30
2.2695721945 4.0000 41,32,29,36
1.9557286479 2.0000 40,42
1.8107191580 2.0000 44,45
1.6044369622 3.0000 43,27,33
1.2636806013 1.0000 47
1.1967315790 1.0000 48
1.1097025805 2.0000 49,46
0.8380095085 4.0000 35,34,38,37
|| Shift (ppm) Degeneracy Atoms
216.8932607019 1.0000 10
151.7542056168 1.0000 6
117.1461064746 1.0000 3
88.7324043974 1.0000 15
57.0696825355 1.0000 14
56.4946034132 1.0000 13
54.7593650872 1.0000 5
52.0535966940 1.0000 7
48.4854448109 1.0000 4
45.1643921682 1.0000 22
43.6549221877 1.0000 23
40.4318873597 1.0000 16
34.4801060018 1.0000 12
34.1462414903 1.0000 18
33.8871317620 1.0000 1
27.2445457944 1.0000 2
27.0908804922 1.0000 8
21.9122917539 1.0000 20
21.7727797741 1.0000 17
19.0713888197 1.0000 9
|}

{| class="wikitable" border="1"
|+ Table 5: Comparison of NMR data of Molecule 17 between HPC calaculation and Literature value {{DOI|10042/28018}}
! Calculated Data for 1H !! Calculated Data for 13C
|-
| 1H NMR (300 MHz, CDCl3) ppm
4.84 (dd, J = 7.2,4.7 Hz, 1 H) ,3.40-3.10 (m ,4H), 2.99 ( dd, J = 6.8, 5.2 Hz, 1 H), 2.80-1.35 (series of m, 14 H), 1.38 (s, 3 H), 1.25 (s, 3 H), 1.10 (s, 3 H), 1.00-0.80 (m, 1 H)
|| 13C NMR (75 MHz, CDCL3) ppm
218.79, 144.63, 125.33, 72.88, 56.19, 52.52,48.50, 46.80, 45.76, 39.80,38.81, 35.85, 32.66, 28.79, 28.29, 26.88, 25.66, 23.86, 20.96, 18.71
|}

{| class="wikitable" border="1"
|+ Table 6: Comparison of NMR data of Molecule 17 {{DOI|10042/28018}}
! Compare Data for 1H !! Compare Data for 13C
|-
| [[File:COMPARE_17.PNG|500px|right|SVG]]
|| [[File:COMPARE_17C.PNG|500px|right|SVG]]
|}

In addition, the HPC calculation enabled vibrational analysis of the molecule 17 and 18 to be reported. The entropy and zero-point-energy correction were computed to give a Gibbs free energy (∆G), see in the table 9. Molecule 18 has a more negative value of the free energy than molecule 17, so it indicates that molecule 18 is the prefer conformation to be formed upon synthesis. Combining the fact that molecule 18 was found out to be the lower energy conformation, molecule 18 is the most thermodynamically stable conformation and transformation from molecule 17 to molecule 18 is feasible. In order for the transformation to happen, energy input (e.g. reflux) is required for the rearrangement of structure, which involves several sigma-bond rotations and turning the carbonyl oxygen to point down<ref name="molecule 17 and 18">Spectroscopic data: L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>. Despite of a lower energy is attained in this conformation, the methyl that is alpha to the carbonyl was required to be brought closer to the methyl group in the bridgehead ( from 0.571nm to 0.385 nm).

{| class="wikitable" style="margin: 1em auto 1em auto;"
|+ Table 7: Vibrational Analysis of Molecule 17 and 18
! Hartree/Particle!! Molecule 17 {{DOI|10042/28018}} !! Molecule 18 {{DOI|10042/28021}}
|-
| Zero-point correction|| 0.467240 || 0.467562
|-
| Thermal correction to Energy|| 0.489298 || 0.489349
|-
| Thermal correction to Enthalpy || 0.490242 || 0.490293
|-
| Thermal correction to Gibbs Free Energy || 0.418299 || 0.420041
|-
| Sum of electronic and zero-point Energies(E0 = Elec + ZPE)|| -1651.400866 || 1651.407622
|-
| Sum of electronic and thermal Energies (E=E0+Evib+Erot+Etrans)|| -1651.378808 || -1651.385835
|-
| Sum of electronic and thermal Enthalpies(H=E+RT) || -1651.377864 || -1651.384891
|-
| Sum of electronic and thermal Free Energies (free energies) (G=H-TS)|| -1651.449807|| -1651.455144
|}

==Part 2: Analysis of the properties of the synthesised alkene epoxides==
[[File:Shi_and_jac.PNG|400px|thumb|'''Scheme 4. '''21''' Jacobsen and '''24''' Shi's catalyst]]

===the Jacobsen and shi's Catalyst===

Jacobsen and shi's catalysts (Scheme '''4''') were used to promote asymmetric epoxidation of alkenes. The Conquest was used to search for the crystal structure of these catalysts in Cambridge Crystal Database (CCDC). Also, Mercury program was introduced to analyze those crystal structures. Two crystal structures were shown as following<ref name="Shi">Zhi-Xian Wang, S.M.Miller, O.P.Anderson, Yian Shi, ''J.Org.Chem. '', '''2001''', ''66'', 521. {{DOI|10.1021/jo001343i}}</ref> <ref name="Jacobsen">J.W.Yoon, T.-S.Yoon, S.W.Lee, W.Shin, ''Acta Crystallogr.,Sect.C:Cryst.Struct.Commun. '', '''1999''', ''55'', 1766. {{DOI|10.1107/S0108270199009397}}</ref> .

{| class="wikitable" border="1"
|+ '''Crystal structure of Shi and Jacobsen catalyst'''
! '''21'''Jacobsen catalyst!! '''23'''Shi's catalyst
|-
|<jmol><jmolApplet>
<title>Jacobsen structure</title>
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<uploadedFileContents>Jacobsen's_one_molecule.mol</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<title>Shi's structure</title>
<color>black</color>
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<script>measure 4 3;measure 3 12;measure 39 48;measure 39 40;; cpk -20;zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Shi catalyst_one_molecule.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
The presence of anomeric centres (carbon centres connecting to two oxygen) in Shi's catalyst should be noted. At each anomeric centre, one of the C-O bond is shorter than the average C-O bond length (142 pm),whilst the other one is longer.(see Figure '''4'''). This is due to the lone pair electrons donation from one of the oxygen to the C-O σ <sup>*</sup> orbital, which shortens the carbon oxygen bond between the oxygen that has donated the lone pair electrons and the carbon, lengthening the other carbon oxygen bond whose electron density in the σ <sup>*</sup> anti-bonding orbital increases.

As for Jacobsen catalyst, four distances between two closely distributed hydrogen atoms on two tertiary butyl groups were measured as shown on '''Crystal structure of Shi and Jacobsen catalyst'''. All the values of those interaction were compared to the van der Waals distance for hydrogen (2.40 Å), <ref name="vdw">{{DOI|10.1021/jp8111556}}</ref>. It could be found the interactions between all four pairs of hydrogen atoms are attractive. Therefore, during alkene epoxidation, these interactions prevents alkene from approaching to the manganese centre from tertiary butyl side, ensuring that alkenes could be stereoselectively epoxidized.

===The Calculated NMR Properties of the Epoxides===
[[File:Shi_and_jac.PNG|500px|thumb|'''Scheme 5. Epoxidations of trans-stilbene and 1,2-dihydronaphthalene]]

Two alkenes (trans-stilbene and 1,2-dihydronaphthalene) were chosen to be epoxidized, each giving two alkene oxides enantiomers (see Scheme '''5'''). Each products were optimized by Avogadro with energy minimized ('''Optimized Alkene Oxides'''). The geometries of R,R-trans-stilbene oxide and R,S-dihydronaphthalene oxide at the denisty functional level were calculated using Gaussian. 13C and 1H NMR spectra were simulated under B3LYP theory and 6-31G(d,p) basis, with chloroform as the solvent(Figure '''4''' to '''7''') ({{DOI|10042/28024}}and {{DOI|10042/28025}}). The chemical shifts of four spectra were summarized in Table '''5''' to '''8'''.

{| class="wikitable" border="1"
|+ '''Optimized Alkene Oxides'''
! R,R-trans-stilbene oxide!! S,S-trans-stilbene oxide !! R,S-Dihydronaphthalene oxide !! S,R-Dihydronaphthalene oxide
|-
|<jmol><jmolApplet>
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<title>S,S-Stilbene_Oxide.mol</title>
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<script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>S,S-trans-stilbene.mol</uploadedFileContents>
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|<jmol><jmolApplet>
<title>R,S-Dihydronaphthalene_oxide.mol</title>
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<script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>R,S-1,2-dihydronaphthalene_oxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|<jmol><jmolApplet>
<title>S,R-Dihydronaphthalene_oxide.mol</title>
<color>white</color>
<size></size>240
<script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>S,R-1,2-dihydronaphthalene_oxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

[[File:RR_trans_stibene_nmr_13C.PNG|600px|thumb|right|'''Figure 4 Predicted <sup>13</sup>C NMR of trans-stilbene oxide''']]

{| class="wikitable" border="1"
|+ Table 5: 13C NMR shifts of trans-stilbene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 134.0870000000 || 2.0000|| 5,9
|-
| 124.2190000000 || 2.0000 || 3,13
|-
| 123.5175000000 || 2.0000 || 1,11
|-
| 123.2128500000 || 2.0000|| 12,2
|-
| 123.0770000000 || 2.0000 || 10,6
|-
| 118.2640000000 || 2.0000 || 14,4
|-
| 66.4240000000 || 2.0000|| 7,8
|}

[[File:RR_trans_stibene_nmr_1H.PNG|600px|thumb|right|'''Figure 5 Predicted <sup>1</sup>H NMR of trans-stilbene oxide''']]

{| class="wikitable" border="1"
|+ Table 6: 1H NMR shifts of trans-stilbene oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.5704000000 || 2.0000|| 18,26
|-
| 7.4700000000 || 8.0000|| 20,23,16,24,17,25,19,27
|-
| 3.5380000000 || 2.0000 || 21,22
|}

[[File:RS_Dihydrona._13C.PNG|600px|thumb|right|'''Figure 6 Predicted <sup>13</sup>C NMR of dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 7: 13C NMR shifts of dihydronapthalene oxide oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 135.3877560205 || 1.0000 || 4
|-
| 130.3705995748 || 1.0000 || 5
|-
| 126.6664754359 || 1.0000 || 6
|-
| 123.7910886822 || 1.0000 || 2
|-
| 123.5334121254 || 1.0000 || 3
|-
| 121.7441913397 || 1.0000 || 1
|-
| 52.8211670356 || 1.0000 || 10
|-
| 52.1924643324 || 1.0000 || 7
|-
| 30.1802794498 || 1.0000 || 8
|-
| 29.0634872612 || 1.0000 || 9
|}

[[File:RS_Dihydrona._1H.PNG|600px|thumb|right|'''Figure 7 Predicted <sup>1</sup>H NMR of dihydronapthalene oxide''']]

{| class="wikitable" border="1"
|+ Table 8: 13C NMR shifts of dihydronapthalene oxide oxide
| Shift (ppm) || Degeneracy || Atoms
|-
| 7.6151181280 || 1.0000 || 15
|-
| 7.3900000000 || 2.0000 || 13,12
|-
| 7.2514926773 || 1.0000 || 14
|-
| 3.5595613767 || 1.0000 || 16
|-
| 3.4831000000 || 1.0000 || 21
|-
| 2.9466313163 || 1.0000 || 17
|-
| 2.2672859897 || 1.0000 || 18
|-
| 2.2090255293 || 1.0000 || 19
|-
| 1.8734432001 || 1.0000 || 20
|}

===The Assignment of the Absolute Configurations for products===

Alkenen epoxidation is stereospecfic with respect to alkenes that would not alter the trans/cis configuration of the alkene. It proceeds via a concerted syn-addition mechanism, therefore the trans-stilbene gives R,R- or S,S-trans-stilbene oxides whereas 1,2-dihydronapthalene (a cis- alkene) gives 1R,2S- or 1S,2R-dihydronapthalene oxide as shown on Scheme '''5'''. Consequently, the stereochemistry of final products after epoxidation should be characterized using analytical techniques.

====Optical rotatory power====
The optical rotatory power is one of the measurements that distinguish the absolute configurations of the enantiomes. Initially, literature values of optial rotatory powers of four epoxides were searched from Reaxys (Table '''9'''). Computational analyses were carried out to predict the optical rotatory powers of four optimized epoxides in chloroform at 589 nm and 365 nm using Gaussian with CAM-B3LYP method, 6-311++g(2df,p) basis. The outcomes were summarized in Table '''10'''.

{|class="wikitable" border="1"
|+ Table 9: Literature Values for Optical Properties of dihydronaphthalene oxides and trans-stilbene oxides
! Epoxides !! R,S-dihydronaphthalene oxides<ref name="R,S-dihydronaphthalene oxides"> Pedragosa-Moreau, S.; Archelas, A.; Furstoss, R. ''Tetrahedron'' '''1996''', 52, 4593 </ref>!! S,R-dihydronaphthalene oxides<ref name="S,R-dihydronaphthalene oxides"> Lin, H.; Qiao, J.; Liu, Y.; Wu, Z.-L. ''Journal of Molecular Catalysis B: Enzymatic '' '''2010''', 67, 236 </ref> !! S，S-trans-stilbene oxides<ref name="S,S-trans-stilbene oxides"> Niwa, T.; Nakada, M. ''Journal of the American Chemical Society'' '''2012''', 134, 13538</ref> !! R,R-trans-stilbene oxides<ref name="R,R-trans-stilbene oxides"> Wong, O. A.; Wang, B.; Zhao, M.-X.; Shi, Y. ''Journal of Organic Chemistry'' '''2009''', 74, 6335 </ref>
|-
| Concentration (g/100ml) || 0.81 || 0.21|| 0.56 || 0.73
|-
|Enantiometric Excess (%) || 99 ||99 || 89 || 97
|-
|Solvent || CHCl<sub>3</sub>||CHCl<sub>3</sub> ||CHCl<sub>3</sub> || CHCl<sub>3</sub>
|-
|Optical Rotation ||129<sup>o</sup>|| -39<sup>o</sup> || -205.2<sup>o</sup> || 334.6<sup>o</sup>
|-
|Wavelength (nm) || 589 || 589 || 589 || 589
|-
|Temperature ||20<sup>o</sup>C || 25<sup>o</sup>C || 20<sup>o</sup>C || 25<sup>o</sup>C
|-
|}

{|class="wikitable" border="1"
|+ Table 10: Computed Values for Optical and Thermodynamic Properties of dihydronaphthalene oxides and trans-stilbene oxides
! epoxides !!R,R-trans-stilbene oxides {{DOI|10042/28050}} !! S,S-trans-stilbene oxides{{DOI|10042/28051}} !! R,S-dihydronaphthalene oxides {{DOI|10042/28048}}!! S,R-dihydronaphthalene oxides {{DOI|10042/28049}}
|-
|α<sub>d</sub> at 589 nm|| 102.87<sup>o</sup> || -24.18<sup>o</sup>|| 177.43<sup>o</sup> || -52.74<sup>o</sup>
|-
|}

The predicted values calculated by the method mentioned above agrees with the literature values found with some extend of deviation tolerated. The sign of all predicted values perfectly match with the literature values. Therefore, the method introduced is reliable in calculating the optical rotatory power of those two epoxides.

====VCD and ECD====
Apart from optical rotatory power, the absolute configuration could be assigned by vibrational circular dichroism (VCD) and the electronic circular dichroism (ECD). VCD spectra of R,R- and S,S-trans-stilbene oxides were plotted to assign the configuration (Figure '''8''' and '''9'''). As for ECD, due to lacking of chromophore in epoxides, it fails to assign the configuration by using UV/Vis spectrum.

{{DOI|10042/28055}}
[[File:Rr_dihy_.PNG|thumb|600x400px|right|Figure 8:ECD spectrum of R,R-dihydronaphthalene oxide]]

{{DOI|10042/28060}}
[[File:Ss_dihy_.PNG|thumb|600x400px|right|Figure 9:ECD spectrum of S,S-dihydronaphthalene oxide]]

{{DOI|10042/28058}}
[[File:Rs_dihy_.PNG|thumb|600x400px|right|Figure 10:ECD spectrum of R,S-dihydronaphthalene oxide]]

{{DOI|10042/28059}}
[[File:Sr_dihy_.PNG|thumb|600x400px|right|Figure 11:ECD spectrum of S,R-dihydronaphthalene oxide]]

{{DOI|10042/28057}}
[[File:Rr_trans_.PNG|thumb|600x400px|right|Figure 10:ECD spectrum of R,R-trans-stilbene oxide]]

{{DOI|10042/28056}}
[[File:Ss_trans_.PNG|thumb|600x400px|right|Figure 11:ECD spectrum of S,S-trans-stilbene oxide]]

====Using the (calculated) properties of transition state for the reaction====
The enantiomeric excess of four product mixtures(two epoxidation promoted by each catalyst) could be calculated using free energy difference between two diastereomeric transition states (ΔG). The ratio of concentrations of the two species (K) for each product mixture could be converted from the each ΔG according to the equation "ΔG=-RTlnK". Knowing the values of K, each enantiomeric excess was calculated (Table '''11''' to '''14''').

{|class="wikitable" border="1"
|+ Table 11: Analysis for Computed Thermodynamic Properties of trans-stilbene oxides promoted by Shi's catalyst
|-
| Transition State||R,R-trans-stilbene oxide||S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees)||-1535.14760552||-1535.14668122
|-
| Free Energies of 2(Hartrees)||-1535.14902029||-1535.14601044
|-
| Free Energies of 3(Hartrees)||-1535.16270178||-1535.15629511
|-
| Free Energies of 4(Hartrees)||-1535.16270154||-1535.15243112
|-
| Average ΔG(Hartrees)||-1535.1555072825||-1535.1503544725
|-
| Free Energy Difference (RR-SS)(Hartrees) ||-0.00515281000002688||
|-
| K||235.7||
|-
| Relative Population (%)||99.5||0.5
|-
| Enantiomeric Excess (%)||99.0||
|-
|}

{|class="wikitable" border="1"
|+ Table 12: Analysis for Computed Thermodynamic Properties of trans-stilbene oxides promoted by Jacobsen catalyst
|-
| Transition State||R,R-trans-stilbene oxide||S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees)||-3575.66547138||-3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) ||-0.00117432999968514||
|-
| K||3.5||
|-
| Relative Population (%)||77.8||22.2
|-
| Enantiomeric Excess (%)||55.6||
|-
|}

{|class="wikitable" border="1"
|+ Table 13: Analysis for Computed Thermodynamic Properties of dihydronaphthalene oxides promoted by Shi's catalyst
|-
| Transition State||R,S-dihydronaphthalene oxide||S,R-dihydronaphthalene oxide
|-
| Free Energies of 1 (Hartrees)||-1381.54381947||-1381.55280118
|-
| Free Energies of 2 (Hartrees)||-1381.5472601||-1381.53607543
|-
| Free Energies of 3 (Hartrees)||-1381.556204||-1381.54761301
|-
| Free Energies of 4 (Hartrees)||-1381.54990117||-1381.55813219
|-
| Average ΔG (Hartrees)||-1381.549296185||-1381.5486554525
|-
| Free Energy Difference (RR-SS) (Hartrees)||-0.000640732500414742||
|-
| K||1.9||
|-
| Relative Population (%)||65.5||34.5
|-
| Enantiomeric Excess (%)||31.0||
|}

{|class="wikitable" border="1"
|+ Table 14: Analysis for Computed Thermodynamic Properties of dihydronaphthalene oxides promoted by Jacobsen catalyst
|-
| Transition State||R,S-dihydronaphthalene oxide||S,R-dihydronaphthalene oxide
|-
| Free Energies of 1 (Hartrees)||-3422.06853796||-3422.06054777
|-
| Free Energies of 2 (Hartrees)||-3422.05830133||-3422.05965215
|-
| Average ΔG (Hartrees)||-3422.063419645||-3422.06009996
|-
| Free Energy Difference (RR-SS) (Hartrees)||-0.00331968499995128||
|-
| K||33.8||
|-
| Relative Population (%)||97.1||2.9
|-
| Enantiomeric Excess (%)||94.2||
|}

As can be seen on Table '''11''' to '''14''', R,R transition states and R,S transition states are predominant for both Shi's catalyst and Jacobsen catalyst promoted epoxidations due to having lower free energy comparing to S,S and S,R transition states respectively. Therefore, the R,R-trans-stilbene oxide and R,S-dihydronaphthalene oxide are supposed to be the major products in trans-stilbene and 1,2-dihydronaphthalene epoxidation promoted by both Shi's and Jacobsen catalyst.

===NCI Analysis for the Transition State===

The non-covalent interactions for R,R- transition state of Shi's catalyst promoted epoxidation of trans-stilbene was analyzed by Gaussview(Figure '''10''').

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>600</size>
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<jmolApplet>
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'''Figure 10. The non-covalent interactions for R,R- transition state of Shi's catalyst promoted epoxidation of trans-stilbene'''

Referring to the figure shown above, the green region indicates attractive interaction that active catalyst binds to the substrate via the oxygen atoms. The substrate should have oriented itself to maximize the attractive interaction before binding to minimize the energy of the transition state. This transition state is stabilized by the attractive interactions which therefore determine the stereoselectivity of the epoxidation.

===QTAIM analysis for transition state of R,R-trans-stilbene oxide promoted by Shi's catalyst===
[[File:QTAIM_R,R.png|thumb|600x600px|centre|Figure 11:QTAIM for transition state of R,R-trans-stilbene oxide promoted by Shi's catalyst]]
The QTAIM analysis was conducted to calculate the orientation of R,R-trans-stilbene oxide in respect to Shi's catalyst. All the non-covalent bond critical points from weak interaction associated with weak interaction between oxygen and hydrogen were assigned (Figure '''11''').

==Limitations of the software and further works==

===Limitations of the software===
*Avagordro: For small molecule, it is easy to draw the structure within the program directly, but it is not easy for big molecule. The big molecule can be drawn instead with ChemDraw first and import into the program. However, the stereochemistry of the molecules was lost in the import and there also had a minor change to the configuration of the structure.
*QTAIM: The coordinates of the molecules cannot be saved; therefore screenshots are needed. It will be good if the result diagram can be rotated in 3D after uploaded to the wiki page, as it is easier for understanding the analysis.
*Gassview: It takes a sufficient time for running and it needs specific files (e.g fchk, log etc) in order to get the required information on the molecule. However, it is able to generate the predicted UV, IR, NMR, ECD and VCD spectrums for the specific molecule.
===Further work===
*Investigate the suggested candidates of the epoxide with the similar approach above
*Repeat the optimisation of the molecules with ChemBIO3D and compare the results to the one obtained in this investigation. This is because all the molecule were optimised with Avogadro in this case.
*Although the calculation of the coupling constant of the epoxide were obtained in this investigation, time was not sufficient to combine them with the chemical shift value and stimulate the actual spectrum from gNMR. It will be good if more guideline on how to use gNMR is provided in the Toolbox section,so the actual NMR can be stimulated.
*Search for the ORP for epoxide 4 RR and SS in other chemical database and compare them with the calculated value above.

==Reference==
<references/>