ChemWiki - User contributions [en]

Rep:Mod:Zhou1c

2014-03-08T00:00:40Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly.<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891.{{DOI|10.1021/ja00398a00}}3</ref> This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)<ref name="zhenxinfan">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. RogersJ. Am. Chem. Soc. , 1990, 112, 277-283. {{DOI|10.1021/ja00157a043}}</ref>
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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<ref name="zhenxinfan" />
|}

{| class="wikitable" border="1"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|Shi catalyst epoxidation<ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338.{{DOI|10.1021/jo900739q}}</ref>]] || [[Image:jacobsencat.jpg|thumb|400px|Jacobsen catalyst epoxidation<ref>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng J. Am. Chem. Soc., 1991, 113, 7063–7064. {{DOI|10.1021/ja00018a068}}</ref><ref>M. Palucki , N. S. Finney , P. J. Pospisil , M. L. Güler , T. Ishida , and E. N. Jacobsen, J. Am. Chem. Soc., 1998, 120, 948–954. {{DOI|10.1021/ja973468j}}</ref>]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}<ref>https://www.reaxys.com/reaxys/secured/paging.do?performed=true&action=restore</ref>

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

===Suggesting new candidates for investigation===
Cis R-(+)-pulegone oxide were found to have a optical rotatory power of 853.9o in ethanol at 324 nm.

<jmol><jmolApplet><title>Cis R-(+)-pulegone oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>newinvestigation.cml</uploadedFileContents>
</jmolApplet></jmol>

==References==
<references />

Rep:Mod:Zhou1c

2014-03-07T23:57:43Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly.<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891.{{DOI|10.1021/ja00398a00}}3</ref> This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)<ref name="zhenxinfan">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. RogersJ. Am. Chem. Soc. , 1990, 112, 277-283. {{DOI|10.1021/ja00157a043}}</ref>
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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<ref name="zhenxinfan" />
|}

{| class="wikitable" border="1"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|Shi catalyst epoxidation<ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338.{{DOI|10.1021/jo900739q}}</ref>]] || [[Image:jacobsencat.jpg|thumb|400px|Jacobsen catalyst epoxidation<ref>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng J. Am. Chem. Soc., 1991, 113, 7063–7064. {{DOI|10.1021/ja00018a068}}</ref><ref>M. Palucki , N. S. Finney , P. J. Pospisil , M. L. Güler , T. Ishida , and E. N. Jacobsen, J. Am. Chem. Soc., 1998, 120, 948–954. {{DOI|10.1021/ja973468j}}</ref>]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}<ref>https://www.reaxys.com/reaxys/secured/paging.do?performed=true&action=restore</ref>

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

===Suggesting new candidates for investigation===
Cis R-(+)-pulegone oxide were found to have a optical rotatory power of 853.9o in ethanol at 324 nm.<ref>Reusch; Johnson Journal of Organic Chemistry 1963, 28, 2557.</ref>

<jmol><jmolApplet><title>Cis R-(+)-pulegone oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>newinvestigation.cml</uploadedFileContents>
</jmolApplet></jmol>

==References==
<references />

File:Newinvestigation.cml

2014-03-07T23:56:23Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T23:44:45Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T23:43:53Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly.<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891.{{DOI|10.1021/ja00398a00}}3</ref> This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)<ref name="zhenxinfan">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. RogersJ. Am. Chem. Soc. , 1990, 112, 277-283. {{DOI|10.1021/ja00157a043}}</ref>
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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<ref name="zhenxinfan" />
|}

{| class="wikitable" border="1"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|Shi catalyst epoxidation<ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338.{{DOI|10.1021/jo900739q}}</ref>]] || [[Image:jacobsencat.jpg|thumb|400px|Jacobsen catalyst epoxidation<ref>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng J. Am. Chem. Soc., 1991, 113, 7063–7064. {{DOI|10.1021/ja00018a068}}</ref><ref>M. Palucki , N. S. Finney , P. J. Pospisil , M. L. Güler , T. Ishida , and E. N. Jacobsen, J. Am. Chem. Soc., 1998, 120, 948–954. {{DOI|10.1021/ja973468j}}</ref>]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

==References==
<references />

Rep:Mod:Zhou1c

2014-03-07T23:42:52Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly.<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891.{{DOI|10.1021/ja00398a00}}3</ref> This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)<ref name="zhenxinfan">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. RogersJ. Am. Chem. Soc. , 1990, 112, 277-283. {{DOI|10.1021/ja00157a043}}</ref>
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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<ref name="zhenxinfan" />

{| class="wikitable" border="1"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|Shi catalyst epoxidation<ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338.{{DOI|10.1021/jo900739q}}</ref>]] || [[Image:jacobsencat.jpg|thumb|400px|Jacobsen catalyst epoxidation<ref>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng J. Am. Chem. Soc., 1991, 113, 7063–7064. {{DOI|10.1021/ja00018a068}}</ref><ref>M. Palucki , N. S. Finney , P. J. Pospisil , M. L. Güler , T. Ishida , and E. N. Jacobsen, J. Am. Chem. Soc., 1998, 120, 948–954. {{DOI|10.1021/ja973468j}}</ref>]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

==References==
<references />

Rep:Mod:Zhou1c

2014-03-07T23:40:01Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly.<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891.{{DOI|10.1021/ja00398a00}}3</ref> This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)<ref>L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. RogersJ. Am. Chem. Soc. , 1990, 112, 277-283. {{DOI|10.1021/ja00157a043}}</ref>
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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<ref>L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. RogersJ. Am. Chem. Soc. , 1990, 112, 277-283. {{DOI|10.1021/ja00157a043}}</ref>
|}

{| class="wikitable" border="1"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|Shi catalyst epoxidation<ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338.{{DOI|10.1021/jo900739q}}</ref>]] || [[Image:jacobsencat.jpg|thumb|400px|Jacobsen catalyst epoxidation<ref>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng J. Am. Chem. Soc., 1991, 113, 7063–7064. {{DOI|10.1021/ja00018a068}}</ref><ref>M. Palucki , N. S. Finney , P. J. Pospisil , M. L. Güler , T. Ishida , and E. N. Jacobsen, J. Am. Chem. Soc., 1998, 120, 948–954. {{DOI|10.1021/ja973468j}}</ref>]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

==References==
<references />

Rep:Mod:Zhou1c

2014-03-07T23:38:30Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly.<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891.{{DOI|10.1021/ja00398a00}}3</ref> This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|Shi catalyst epoxidation<ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338.{{DOI|10.1021/jo900739q}}</ref>]] || [[Image:jacobsencat.jpg|thumb|400px|Jacobsen catalyst epoxidation<ref>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng J. Am. Chem. Soc., 1991, 113, 7063–7064. {{DOI|10.1021/ja00018a068}}</ref><ref>M. Palucki , N. S. Finney , P. J. Pospisil , M. L. Güler , T. Ishida , and E. N. Jacobsen, J. Am. Chem. Soc., 1998, 120, 948–954. {{DOI|10.1021/ja973468j}}</ref>]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

==References==
<references />

Rep:Mod:Zhou1c

2014-03-07T23:35:15Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|Shi catalyst epoxidation<ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338.{{DOI|10.1021/jo900739q}}</ref>]] || [[Image:jacobsencat.jpg|thumb|400px|Jacobsen catalyst epoxidation<ref>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng J. Am. Chem. Soc., 1991, 113, 7063–7064. {{DOI|10.1021/ja00018a068}}</ref><ref>M. Palucki , N. S. Finney , P. J. Pospisil , M. L. Güler , T. Ishida , and E. N. Jacobsen, J. Am. Chem. Soc., 1998, 120, 948–954. {{DOI|10.1021/ja973468j}}</ref>]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

==References==
<references />

Rep:Mod:Zhou1c

2014-03-07T23:33:14Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|Shi catalyst epoxidation<ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338.{{DOI|10.1021/jo900739q}}</ref>]] || [[Image:jacobsencat.jpg|thumb|400px|Jacobsen catalyst epoxidation]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

==References==
<references />

Rep:Mod:Zhou1c

2014-03-07T23:31:49Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|Shi catalyst epoxidation<ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338;DOI:10.1021/jo900739q</ref>]] || [[Image:jacobsencat.jpg|thumb|400px|Jacobsen catalyst epoxidation]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}
<references />

Rep:Mod:Zhou1c

2014-03-07T23:22:42Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -982.14783927 || -982.14789044
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -982.14859930 || -982.14864902
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -982.17393930 || -982.17393893
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -982.17584930 || -982.17459954
|-
| Average ΔG(Hartrees) (kcal/mol)|| 982.15947383 || 982.15442342
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.0049483993020384833 ||
|-
| K || 76.4 ||
|-
| Relative population (%)|| 99.7 || 0.3
|-
| Enantiomeric excess (%)|| 99.4 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -2067.89483203 || -2067.89543828
|-
| Free Energies of 2 (Hartrees) (kcal/mol)|| -2067.89054392 || -2067.89954235
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00204872595047354353 ||
|-
| K || 1.2 ||
|-
| Relative Population (%) || 56.3 || 43.7
|-
| Enantiomeric Excess (%) || 12.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

Rep:Mod:Zhou1c

2014-03-07T23:13:18Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of styrene
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Jacobsen epoxidation of styrene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transition states of Shi epoxidation of trans-stilbene
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

Rep:Mod:Zhou1c

2014-03-07T23:08:04Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrenre.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Styrene promoted by Shi's catalyst
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Styrene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide promoted by Shi's catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transstilbene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

Rep:Mod:Zhou1c

2014-03-07T23:06:56Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===

{| class="wikitable" border="1"
|+
! R-styrene oxide !! S-styrene oxide !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| <jmol><jmolApplet><title>R-styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S- styrene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstyrene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>R,R-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>rrtransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>S,S-trans-stilbene oxide</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>sstransstilbene.cml</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Styrene promoted by Shi's catalyst
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Styrene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide promoted by Shi's catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transstilbene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

File:Sstyrene.cml

2014-03-07T23:02:35Z

Xz4811:

File:Rstyrenre.cml

2014-03-07T23:02:35Z

Xz4811:

File:Rrtransstilbene.cml

2014-03-07T23:02:34Z

Xz4811:

File:Sstransstilbene.cml

2014-03-07T23:02:33Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T22:53:20Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===
{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Styrene promoted by Shi's catalyst
! !! R-series !! S-series
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Styrene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide promoted by Shi's catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transstilbene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===
===Investigating the Electronic topology (QTAIM) in the active-site of the reaction transition state===

Rep:Mod:Zhou1c

2014-03-07T22:50:43Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===
{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===

{| class="wikitable" border="1"
|+ Trans-stilbene oxide promoted by Shi's catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transstilbene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===
===Investigating the Electronic topology (QTAIM) in the active-site of the reaction transition state===

Rep:Mod:Zhou1c

2014-03-07T22:37:37Z

Xz4811:

==Part 1==
===The Hydrogenation of Cyclopentadiene Dimer===

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

===Astroisomerism in an Intermediate related to the Synthesis of Taxol===
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

===Spectroscopic Simulation using Quantum Mechanics===
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Part 2==
===Analysis of the properties of the synthesised alkene epoxides===
{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

===The calculated NMR properties of styrene oxide and trans-stilbene oxide===
{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

===Using the (calculated ) properties of transition state for the reaction===

{| class="wikitable" border="1"
|+ Trans-stilbene oxide promoted by Shi's catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transstilbene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

Rep:Mod:Zhou1c

2014-03-07T22:33:51Z

Xz4811:

==The Hydrogenation of Cyclopentadiene Dimer==

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

==Astroisomerism in an Intermediate related to the Synthesis of Taxol==
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

==Spectroscopic Simulation using Quantum Mechanics==
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Analysis of the properties of the synthesised alkene epoxides==

{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

==The calculated NMR properties of styrene oxide and trans-stilbene oxide==
{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

==Using the (calculated ) properties of transition state for the reaction==

{| class="wikitable" border="1"
|+ Trans-stilbene oxide promoted by Shi's catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044
|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511
|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112
|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725
|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||
|-
| K || 235.7 ||
|-
| Relative population (%)|| 99.5 || 0.5
|-
| Enantiomeric excess (%)|| 99.0 ||
|}

{| class="wikitable" border="1"
|+ Transstilbene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free Energies of 1 (Hartrees) (kcal/mol)|| -3575.66547138 || -3575.66429705
|-
| Free Energy Difference (RR-SS) (Hartrees) (kcal/mol)|| -0.00117432999968514 ||
|-
| K || 3.5 ||
|-
| Relative Population (%) || 77.8 || 22.2
|-
| Enantiomeric Excess (%) || 55.6 ||
|}

Rep:Mod:Zhou1c

2014-03-07T22:31:26Z

Xz4811:

==The Hydrogenation of Cyclopentadiene Dimer==

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

==Astroisomerism in an Intermediate related to the Synthesis of Taxol==
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

==Spectroscopic Simulation using Quantum Mechanics==
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Analysis of the properties of the synthesised alkene epoxides==

{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

==The calculated NMR properties of styrene oxide and trans-stilbene oxide==
{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

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

{| class="wikitable" border="1"
|+ Literature values for optical properties of styrene oxide and tran-stilbene oxide
! !! S-styrene oxide !! R-styrene oxide !! S，S-trans-stilbene oxides !! R,R-trans-stilbene oxides
|-
| Concentrantion (g/100ml) || 0.48 || 0.73 || 0.56 || 0.73
|-
| Enantiometric excess (%) || 99 || 99 || 89 || 97
|-
| Solvent || CHCl3 || C6H6 || CHCl3 || CHCl3
|-
| Optical rotation (degree) || 26.1 || 5.05 || -205.2 || 334.6
|-
| Wavelength (nm) || 589 || 589 || 589 || 589
|-
| Tamperature (Celcius) || 23 || 21 || 20 || 25
|}

==Using the (calculated ) properties of transition state for the reaction==

{| class="wikitable" border="1"
|+ Trans-stilbene oxide promoted by Shi's catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| Free energies of 1 (Hartrees) (kcal/mol)|| -1535.14760552 || -1535.14668122
|-
| Free energies of 2 (Hartrees) (kcal/mol)|| -1535.14902029 || -1535.14601044

|-
| Free energies of 3 (Hartrees) (kcal/mol)|| -1535.16270178 || -1535.15629511

|-
| Free energies of 4 (Hartrees) (kcal/mol)|| -1535.16270154 || -1535.15243112

|-
| Average ΔG(Hartrees) (kcal/mol)|| -1535.1555072825 || -1535.1503544725

|-
| Free energy difference (RR-SS)(Hartrees) (kcal/mol)|| -0.00515281000002688 ||

|-
| K || 235.7 ||

|-
| Relative population (%)|| 99.5 || 0.5

|-
| Enantiomeric excess (%)|| 99.0 ||

|}

{| class="wikitable" border="1"
|+ Transstilbene oxides promoted by Jacobsen catalyst
! !! R,R-trans-stilbene oxide !! S,S-trans-stilbene oxide
|-
| cell || cell
|-
| cell || cell
|-
| cell || cell
|-
| cell || cell
|-
| cell || cell
|}

Rep:Mod:Zhou1c

2014-03-07T22:20:57Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T21:58:57Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T21:57:16Z

Xz4811:

==The Hydrogenation of Cyclopentadiene Dimer==

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

==Astroisomerism in an Intermediate related to the Synthesis of Taxol==
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

==Spectroscopic Simulation using Quantum Mechanics==
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Analysis of the properties of the synthesised alkene epoxides==

{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ Trans-stilbene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol2hnmr.svg|thumb|400px|]] || [[Image:mol2cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol2hnmr.JPG|thumb|400px|]] || [[Image:mol2cnmr.JPG|thumb|400px|]]
|}

Rep:Mod:Zhou1c

2014-03-07T21:55:14Z

Xz4811:

==The Hydrogenation of Cyclopentadiene Dimer==

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

==Astroisomerism in an Intermediate related to the Synthesis of Taxol==
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

==Spectroscopic Simulation using Quantum Mechanics==
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Analysis of the properties of the synthesised alkene epoxides==

{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ styrene oxide
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

Rep:Mod:Zhou1c

2014-03-07T21:54:02Z

Xz4811:

==The Hydrogenation of Cyclopentadiene Dimer==

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

==Astroisomerism in an Intermediate related to the Synthesis of Taxol==
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

==Spectroscopic Simulation using Quantum Mechanics==
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However,
it should be noted that in the literature, several multiplets are reported
as ranges. The plot of literature values is actually even distributed among
those ranges, which is an auumption that I made. This assumption cannot
reflect the true picture of multiplets, so more appropriate analysis should
be done here. Also the hydrogen with the highest chemical shift seems to be
different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

==Analysis of the properties of the synthesised alkene epoxides==

{| class="wikitable" border="1"
|+
! Shi catalyst epoxidation !! Jacobsen catalyst epoxidation
|-
| [[Image:shicat.jpg|thumb|400px|]] || [[Image:jacobsencat.jpg|thumb|400px|]]
|}

{| class="wikitable" border="1"
|+ caption
! !! 1H NMR !! 13C NMR
|-
| NMR || [[Image:mol1hnmr.svg|thumb|400px|]] || [[Image:mol1cnmr.svg|thumb|400px|]]
|-
| Calculated value || [[Image:mol1hnmr.JPG|thumb|400px|]] || [[Image:mol1cnmr.JPG|thumb|400px|]]
|}

File:Mol2hnmr.svg

2014-03-07T21:50:20Z

Xz4811:

File:Mol2hnmr.JPG

2014-03-07T21:50:19Z

Xz4811: uploaded a new version of "File:Mol2hnmr.JPG"

File:Mol2hnmr.JPG

2014-03-07T21:50:19Z

Xz4811:

File:Mol2cnmr.svg

2014-03-07T21:50:19Z

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File:Mol1hnmr.svg

2014-03-07T21:50:18Z

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File:Mol2cnmr.JPG

2014-03-07T21:50:18Z

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File:Mol1hnmr.JPG

2014-03-07T21:50:17Z

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File:Mol1cnmr.svg

2014-03-07T21:50:17Z

Xz4811:

File:Mol1cnmr.JPG

2014-03-07T21:48:34Z

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Rep:Mod:Zhou1c

2014-03-07T21:45:34Z

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Rep:Mod:Zhou1c

2014-03-07T21:44:20Z

Xz4811:

File:Jacobsencat.jpg

2014-03-07T21:43:22Z

Xz4811:

File:Shicat.jpg

2014-03-07T21:43:04Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T21:28:54Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T21:15:32Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T21:14:33Z

Xz4811:

==The Hydrogenation of Cyclopentadiene Dimer==

[[Image:dimerdimer.jpg|thumb|500px|Dimerisation of cyclopentadiene]]

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! [[Image:cp1c.jpg|thumb|200px|Exo dimer]] !! [[Image:cp2c.jpg|thumb|200px|Endo dimer]] !! [[Image:cp3c.jpg|thumb|200px|Hydrogenation 1]] !! [[Image:cp4c.jpg|thumb|200px|Hydrogenation 2]]
|-
| Calculation of geometries || <jmolFile text="Exo dimer">cp1a.cml</jmolFile> || <jmolFile text="Endo dimer">cp2a.cml</jmolFile> || <jmolFile text="Hydrogenation 1">cp3a.cml</jmolFile> || <jmolFile text="Hydrogenation 2">cp4a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 3.55458 || 3.46867 || 3.29230 || 2.81802
|-
| Total angle bending energy (kcal/mol)|| 30.88543 || 33.18206 || 31.34021 || 24.71764
|-
| Total stretch bending energy (kcal/mol)|| -2.04552 || -2.08263 || -2.03250 || -1.65474
|-
| Total torsional energy (kcal/mol)|| -2.87356 || -2.95359 || -0.50042 || -0.35570
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.01619 || 0.02198 || 0.01622 || 0.00036
|-
| Total van der Waals enery (kcal/mol)|| 12.92500 || 12.36446 || 13.73285 || 10.59251
|-
| Total electrostatic energy (kcal/mol)|| 13.01489 || 14.19038 || 5.11908 || 5.14732
|-
| Total energy (kcal/mol)|| 55.47701 || 58.19134 || 50.96772 || 41.26541
|}

According to the data calculated from Avogadro, the endo dimer is slightly higher in total energy than the exo dimer, which means the exo dimer is more thermodynamically stable. Thus the endo dimer is kinetic product while the exo dimer is the thermodynamic product. While the dimerisation of cyclopentadiene specifically produce the endo dimer, this reaction is kinetically controlled. The main contribution of energy difference comes from the angle bending term. While the endo dimer is more "twisted" in the structure, this result should be expected.

While the endo dimer can be hydrogenated on double bonds either in the five-membered ring or in the six-membered ring, the product of the second type hydrogenation is lower in total energy than the first type hydrogenation, which is true because the hydrogenation in the norbornene is five times faster than the hydrogenation in the cyclopentane ring. The main energy difference comes from total angle bending energy and total Van der Waals energy, which means the type 2 hydrogenation has less ring strain and less readily to react.

==Astroisomerism in an Intermediate related to the Synthesis of Taxol==
{| class="wikitable" border="1"
|+ Intermediates related to the synthesis of Taxol
! !! [[Image:im9c.jpg|thumb|300px|Intermediate 1]] !! [[Image:im10c.jpg|thumb|300px|Intermediate 2]]
|-
| Calculation of geometries || <jmolFile text="Intermediate 1">mol9a.cml</jmolFile> || <jmolFile text="Intermediate 2">mol10a.cml</jmolFile>
|-
| Total bond stretching energy (kcal/mol)|| 7.63860 || 7.92531
|-
| Total angle bending energy (kcal/mol)|| 28.26560 || 17.19358
|-
| Total stretch bending energy (kcal/mol)|| -0.088862 || -0.17182
|-
| Total torsional energy (kcal/mol)|| 0.42140 || 2.09931
|-
| Total out-of-plane bending energy (kcal/mol)|| 0.97902 || 0.79894
|-
| Total van der Waals enery (kcal/mol)|| 33.04442 || 34.41399
|-
| Total electrostatic energy (kcal/mol)|| 0.30846 || -0.08004
|-
| Total energy (kcal/mol)|| 70.56889 || 62.17927
|}

The optimisation of the 2 possible intermediates realted to the synthesis of Taxol is examed here. As the stereochemistry of carbonyl addition depends on which isomer is most stable, we can see clearly that the molecule with oxygen "pointing down" is lower in energy. The energy difference mainly comes from the angle bending energy. As we can see from the optimised molecule, intermediate 1 is more "twisted" in shape while intermediate 2 tends to be more "relaxed".

As for the reactivity of the double bond in both intermediates, both molecules tend to react slowly. This might be accounted by "hyperstability". The bridgehead double bond is part of a largy polycyclic system and makes the molecule less in torsinal strain than the parent hydrocarbon, which makes the intermediate more stable and unusually unreactive.

==Spectroscopic Simulation using Quantum Mechanics==
[[Image:mol17c.jpg|thumb|4500px|Molecule 17, optimized structure on the left]]
<jmol><jmolApplet><title>Optimized structure of molecule 17</title><color>white</color>
<size>400</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>mol17a.cml</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable" border="1"
|+ NMR of Molecule 17
! NMR !! Calculated NMR summary !! Literature value
|-
| [[Image:mol17hnmr.svg|thumb|500px|1H NMR]] || [[Image:Mol17hnmr.JPG|thumb|500px|]] || 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)
|-
| [[Image:mol17cnmr.svg|thumb|500px|13C NMR]] || [[Image:Mol17cnmr.JPG|thumb|500px|]] || 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"
|+ Literature value and calculated value comparison
! [[Image:mol17hnmrc.jpg|thumb|500px| ]] !! [[Image:mol17cnmrc.jpg|thumb|500px| ]]
|-
| In the 1H NMR data, the data matched quite well at most values. However, it should be noted that in the literature, several multiplets are reported as ranges. The plot of literature values is actually even distributed among those ranges, which is an auumption that I made. This assumption cannot reflect the true picture of multiplets, so more appropriate analysis should be done here. Also the hydrogen with the highest chemical shift seems to be different from the literature value. || In the 13C NMR data, the data also match quite well as all those carbons were separately reported.
|}

{| class="wikitable" border="1"
|+ Vibrational analysis of molecule 17
! !! Molecule 17
|-
| Zero-point correction (kcal/mol)|| 0.466600
|-
| Thermal correction to Energy (kcal/mol)|| 0.488551
|-
| Thermal correction to Enthalpy (kcal/mol)|| 0.489495
|-
| Thermal correction to Gibbs Free Energy (kcal/mol)|| 0.418950
|-
| Sum of electronic and zero-point Energies (kcal/mol)|| -1651.320095
|-
| Sum of electronic and thermal Energies (kcal/mol)|| -1651.298144
|-
| Sum of electronic and thermal Enthalpies (kcal/mol)|| -1651.297200
|-
| Sum of electronic and thermal Free Energies (kcal/mol)|| -1651.367745
|}

Rep:Mod:Zhou1c

2014-03-07T21:06:36Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T21:05:41Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T21:05:09Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T21:00:13Z

Xz4811:

Rep:Mod:Zhou1c

2014-03-07T20:59:09Z

Xz4811: