File:NEWPRODUCT1JH.PNG

2013-11-21T16:43:03Z

Jh4611:

File:NEWJH.PNG

2013-11-21T16:34:12Z

Jh4611:

Rep:Mod:jh46111

2013-11-21T16:04:33Z

Jh4611: /* Investigating the Electronic topology (QTAIM) in the active-site of the reaction transition state */

==Part I==
===Hydrogenation of Cyclopentadiene Dimer===

The Diels-Alder Reaction of two Cyclopentadiene molecules can form two forms of dimers, one is Endo (Molecule 1) and the other is Exo (Molecule 2). Molecule 3 and 4 are the products after hydrogenation. The fact that Endo form is the major product of the reaction is concluded from experiments. The energy of Endo, Exo forms and their hydrogenated forms can be calculated by Avogadro programme using energy calculation method MMFF94s; the energies are listed in Table 2.

[[Image:1-4jhh.PNG]]
{| class="wikitable" border="1"
|+ Table 1 Structures of Molecules
! No. !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule1jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_2jh.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_3jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 22 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_4jh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 2 Energies of Molecules
! Property !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Total energy (kcal/mol) || 55.37342 || 58.19067|| 50.44566 || 41.34098
|-
| Total electronic energy (kcal/mol)|| 13.01368 ||14.18454 || 5.11949 || 5.14770
|-
|Total VdW's energy (kcal/mol)|| 12.80149|| 12.35877 || 13.63843 || 10.54000
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.01475 || 0.02183 || 0.01311 || 0.00053
|-
|Total torsional energy (kcal/mol)|| -2.73093 || -2.94949 || -1.46888 || -0.31691
|-
|Total stretch bending energy (kcal/mol)|| -2.04135 || -2.08221 || -2.10211 || -1.64420
|-
|Total angle bending energy (kcal/mol)|| 30.77274 || 33.18926 || 31.93395 || 24.80178
|-
|Total bond stretching energy (kcal/mol)|| 3.54304 || 3.46797 || 3.31167 || 2.81207
|}

After running the energy calculation of the 4 molecules listed above, 2 observations can be seen.
1. Total Energy of Molecule 1(Endo) is lower than the Total Energy of Molecule 2(Exo). Comparing different kinds of energies, it has been found that the main difference is due to the angle bending energy, 30.77274kcal/mol vs 33.18926kcal/mol.
2. Total Energy of Molecule 3 is higher than that of Molecule 4. The main difference is also due to angle bending energy, 31.93395kcal/mol vs 24.80178kcal/mol.

The rise of angle bending energy is because of the bond angles deviate from the natural occurring ones, such as 120° in sp<sup>2</sup> and 109.5° in sp<sup>3</sup>. By measuring the bond angles in the molecules, the deviations can be concluded in the Table 3. It is shown clearly that there is more Angle Deviation of Molecule 1 than that of Molecule 2; more Angle Deviation of Molecule 3 than Molecule 4.

{| class="wikitable" border="1"
|+ Table 3 Angles of Molecule 1 & 2
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 1)|| 114.9 (+5.4) ||110.5 (+1)|| 102.5 (-7)
|-
| Angle/Deviation (Molecule 2)|| 117.8 (+8.3)|| 113.0 (+3.5)|| 100.2 (-9.3)
|}

{| class="wikitable" border="1"
|+ Table 4 Angles of Molecule 3 & 4
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19/22,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 3)|| 118.8 (+9.3) ||111.7 (+2.2)|| 100.1 (-9.4)
|-
| Angle/Deviation (Molecule 4)|| 118.6 (+9.1)|| 110.5 (+1)|| 101.1 (-8.4)
|}

The reason that Endo form is the major product in experiment. The reason for this is due to the lower energy of Transition state of Endo form. Endo form has higher energy which mean it is more unstable. This Diels-Alder reaction is under kinetic control instead of thermodynamic control as the more unstable Endo form is the major product.

Molecule 3 & 4 are the production of hydrogenation from Molecule 2. The Total Energies of Molecule 3 & 4 are both lower than that of Molecule 2. It means the hydrogenation is favored.

=== Atropisomerism in an Intermediate related to the Synthesis of Taxol ===

[[Image:Molecule9-10jh.PNG]]

Molecule 9 and 10 <ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319;{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>are atropisomers and they give Molecule 9(saturated) and 10(saturated) after hydrogenation. Comparison can be done between the saturated form and unsaturated form of 9 and 10.

{| class="wikitable" border="1"
|+ Table 5 Structures of Molecules
! No. !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script> <uploadedFileContents>Molecule_9jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule_10jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule17_chair.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule10_saturatedjh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 6 Energies of Molecules
! Property !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Total energy (kcal/mol) || 70.54467 || 66.29108 || 81.75656 || 73.77833
|-
| Total electronic energy (kcal/mol)|| 0.30395 ||-0.06889 || 0.0000 || 0.0000
|-
|Total VdW's energy (kcal/mol)|| 33.11930|| 35.06832 || 32.71947 || 32.80239
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.97422 || 0.25399 || 70.54467 || 0.23332
|-
|Total torsional energy (kcal/mol)|| 0.31308 || 3.65335 || 9.47264 || 9.21881
|-
|Total stretch bending energy (kcal/mol)|| -0.08187 || 0.30222 || 0.30222 || 0.32484
|-
|Total angle bending energy (kcal/mol)|| 28.25720 || 32.05685 || 32.05685 || 24.29611
|-
|Total bond stretching energy (kcal/mol)|| 7.65878 || 6.95138 || 6.95138 || 6.90286
|}

{| class="wikitable" border="1"
|+ Table 7 Angles of Molecule 9 & 10
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C7,C3,C6 || H18,C11,C5|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 120
|-
| Angle/Deviation (Molecule 3)|| 118.5 (+9) ||107.9 (+1.6)|| 123.4 (-3.4)
|-
| Angle/Deviation (Molecule 4)|| 116.4 (+6.9)|| 108.8 (+0.7)|| 122.3 (-2.3)
|}

Same arguments here as of Molecule 1 to 4. Molecule 9 has higher energy than Molecule 10, among all types of energies, total angle bending energy contributes the most. It means the angles deviated more for Molecule 9, the details of deviations show in the table below.
Molecule 9 & 10(saturated) are the products of hydrogenation of Molecule 9 & 10 respectively. Olefin strain<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891{{DOI|10.1021/ja00398a003}}</ref> energy should be taken into account in this case. Olefin strain is the difference between the strain energy of olefin and its saturated product. The strain energies of saturated molecules are higher than the unsaturated molcules. This is because olefins are locating in the brigehead of the molecules and as a result, the rate of hydrogenation from Molecule 9 & 10 to their saturated forms is low.

=== Derivative Molecules from Taxol ===

{| class="wikitable" border="1"
|+ Table 8 Structures of Molecules
! No. !! Molecule 17 boat!! Molecule 17 chair!! Molecule 18 boat!! Molecule 18 chair
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17twist_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 9 Energies of Molecules
! Property !! Molecule 17 boat!! Molecule 17 chair !! Molecule 18 boat!! Molecule 18 chair
|-
| Total energy (kcal/mol) || 114.33657 || 104.98391 || 102.28716 || 100.46235
|-
| Total electronic energy (kcal/mol)|| -7.05008 ||-7.22117 || -6.24215 || -6.05131
|-
|Total VdW's energy (kcal/mol)|| 54.37213|| 52.21497 || 50.49934 || 49.45308
|-
|Total out-of-plane bending energy (kcal/mol)|| 1.18784 || 1.02419 || 96.99088 || 0.90018
|-
|Total torsional energy (kcal/mol)|| 14.28618 || 10.98776 || 13.58885 || 9.76322
|-
|Total stretch bending energy (kcal/mol)|| 0.76536 || 0.31639 || 0.48412 || 0.63651
|-
|Total angle bending energy (kcal/mol)|| 35.01470 || 31.52244 || 28.54054 || 30.70962
|-
|Total bond stretching energy (kcal/mol)|| 15.89062 || 15.97568 || 14.39227 || 15.05105
|}

It can be concluded from Table 8 that Molecule 17 has higher energy than Molecule 18 and the chair forms have lower energy than the boat forms.

Table 10 shows the energies of Molecule 17 & 18 chair forms.

{| class="wikitable" border="1"
|+ Table 10 Energies of Molecule 17 & 18
! Property !! Molecule 17 chair!! Molecule 18 chair
|-
| Sum of electronic and thermal Energies (kJ/mol) || -1615.412 || -1651.417
|-
| Sum of electronic and thermal Energies (kJ/mol)|| -1615.390 ||-1651.396
|-
|Sum of electronic and thermal Enthalpies (kJ/mol)|| -1615.389|| -1651.395
|-
|Sum of electronic and thermal Energies (kJ/mol)|| -1615.459 || -1651.464
|}

{| class="wikitable" border="1"
|+ Table 11 <sup>1</sup>H and <sup>13</sup>C NMR for Molecule 17 & 18
! No. !! Molecule 17 NMR!! Molecule 18 NMR
|-
| Structure || [[Image:MOLECULE_17_NMRjh.PNG|500px]] || [[Image:MOLECULE_18_NMRjh.PNG|500px]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 17
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m17_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m17_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 18
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m18_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m18_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

For Table 11, the NMR data are calculated by first optimising energy by Avogadro then introduced to Gaussian. B3LYP/6-31G (d,p)basis, chloroform solvent are used.

By comparing <sup>1</sup>H NMR spectra, the computed chemical shifts are generally larger than the chemical shifts in literature<ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>. The hydrogen atoms on the methyl group near carbonyl bond are more desheided. For <sup>13</sup>C NMR, the computed chemical shifts match the those in literature.

== Part 2 ==

=== Two Catalysts ===

Properties analysis of alkene epoxide

Two catalysts can be used to epoxide alkene: Shi <ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338;{{DOI|10.1021/jo900739q}}</ref>and Jacobsen catalyst<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>.

[[Image:Two_catalysts.PNG]]

For Shi catalyst, the C-O bond length in the anomeric centre is different.

{| class="wikitable" border="1"
|+ Table 12Shi Catalyst
|-
| Structure || [[Image:Ocojhh.PNG]] || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>350</size><script>measure 10 16; measure 8 16; measure 1 2; measure 2 15; measure 3 4; measure 4 15</script><uploadedFileContents>OCOjhh.mol</uploadedFileContents>
</jmolApplet></jmol>|| [[Image:Ejh.PNG]]
|}

The C-O bond length in the Shi catalyst varies and differs from the ideal C-O single bond length: 1.43Å.
There are three O-C-O centres and the bond lengths are shown in the graph above.

The lone pair on oxygen can overlap with the anti-bonding orbital of C-O bond when the orientation is anti-periplanar: LP<sub>O</sub>/σ<sup>*</sup><sub>C-O</sub>. There are six pairs of overlap in total which are shown on the graph above.
The C-O bond will compress when its its oxygen donates lone pair; the C-O bond will extend when other oxygen donates lone pair. This can answer the question why the C-O bond is different within the same anomeric centre.

For Jacobsen catalyst, the structure can be depicted as square pyramid.

[[Image:Jacojh.PNG]]

<jmol><jmolApplet><title>ah</title><color>white</color>
<size>350</size><uploadedFileContents>TOVNIB01jh.mol</uploadedFileContents></jmolApplet></jmol>

For a 5-coordinated Mn, trigonal bipyramidal should be the ideal stucture. Here for Jacobsen catalyst, square plane pyramid is preferred due to the steric effect. The H atoms in the tBu group close to each other, the distances are shown in the graph which are slightly larger than the two times of the van der Waals radius of hydrogen: 2 x 1.20Å =2.40Å. These are attraction interaction which can stabilize the molecule.

=== Two alkenes ===

The following 2 alkenes can be oxidized to epoxide when treated with catalyst.

[[Image:Reaction schemejh.PNG]]

The epoxides of methyl styrene and stilbene have two forms: R,R and S,S. Here are the structures in 3D.

{| class="wikitable" border="1"
|+ Table 13 Structures of Molecules
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S!! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> 2rr.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> 2_ss.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Rrr_3.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Ss_3.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

The <sup>1</sup>H and <sup>13</sup>C NMR of tran-methyl styrene oxide and Stilbene oxide are listed below.
[[Image:NMR_of_H_alkene_2.PNG]][[Image:Nmr_1jh.PNG]]
[[Image:NMR_of_C_alkene_2.PNG]][[Image:Nmr2jh.PNG]]
[[Image:NMR_of_H_alkene_3.PNG]][[Image:Nmr3jh.PNG]]
[[Image:NMR_of_C_alkene_3.PNG]][[Image:Nmr4jh.PNG]]

The alkene that under epoxiation can remain the E/Z stereochemistry. However, the epoxiation has enantimochemistry and the result product of the epoxide can be assigned as R,R or S,S (epoxidation is syn-reaction). As a result, techniques can be used to determine the stereochemistry of the final product. There are three ways can be used to show which enantiomer resulted: Reaxys used to know the optical rotation value in literature, calculated chiroptical properties of the product and properties of transition state for the reaction.

==== The reported literature for optical rotations====
Literature from Reaxys, the optical rotation:

{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! methyl-Styrene oxide !! R,R !! S,S
|-
| Optical rotation || 44.3 deg <ref>Wong,O.Andrea;Wang,Bin ;Zhao,Mei-Xin and Shi,Yian,''Journal of Organic Chemistry'', '''2009''', ''74'', 6335-6338. {{DOI|10.1021/jo900739q}}</ref>
||-41.8 deg <ref>Lin,Hui;Liu,Yan;Wu,Zhong-Liu,''Tetrahedron:Asymmetry'', '''2011''', ''22'', 134-137.{{DOI|10.1016/j.tetasy.2010.12.022}}</ref>
|-
| Concentration || 0.32 g/100ml
|| 1g/100mL
|-
| Temperature|| 25°C
|| 25°C
|-
| Solvent || chloroform
|| chloroform
|-
| Wavelength || 589nm
||589nm
|}
{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! Siltbene oxide !! R,R !! S,S
|-
| Optical rotation || 296 deg <ref>Solladie-Cavallo, Arlette; Diep-Vohuule, Anh; Sunjic, Vitomir; Vinkovic, Vladimir
Tetrahedron: Asymmetry, 1996 , vol. 7, # 6 p. 1783 - 1788{{DOI|10.1016/0957-4166(96)00213-3}}</ref>
||-291 deg <ref>Read; Campbell Journal of the Chemical Society, 1930 , p. 2377 Nature (London, United Kingdom), 1930 , vol. 125, p. 16{{DOI|10.1039/jr9300002377}}</ref>
|-
| Concentration || 1.01 g/100ml
|| 0.6g/100mL
|-
| Temperature|| 22°C
|| 15°C
|-
| Solvent || ethanol
|| acetone
|-
| Wavelength || 589nm
||589nm
|}

==== The calculated chiroptical properties of the product ====

By comparing the values of the computed chiroptical properties and the values gained from the experiment or literature, the specified enantiomer of epoxides can be predicted. The three chiroptical properties are:
1. The optical rotation at specified range of wavelength.
2. The electronic circular dichroism (ECD)
3. The vibrational circular dichroism(VCD)<ref>M. J. Fuchter, Ya-Pei Lo and H. S. Rzepa, J. Org. Chem., 2013,</ref>

1.The QM-Optimized geometry is used and input into Cambridge variation on B3LYP density functional method. Polar(optrot) calculated the [alpha]<sub>D</sub> optical rotation components of the epoxides.
[alpha]D optical rotation at wavelength range 589nm has the following vaules:

Methyl-styrene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 46.78 deg and [Alpha] ( 5890.0 A) = -46.78 deg repectively.
Silbene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 297.68 deg[Alpha], and(5890.0 A) = -298.24 deg respectively.
Both of the optical rotation data roughly match the literature data.
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! methyl-Styrene !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation ||46.78 deg ||-46.78 deg || 44.3 deg ||-41.8 deg
|}
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! Siltbene oxide !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation || 297.68 deg ||-298.24 deg || 296 deg ||-291 deg
|}

2.The ECD is useless for epoxides as there are no chromophore these epoxides

3.The VCD spectrum of methyl-styrene and siltbene and their oxides are attached here:

{| class="wikitable" border="1"
|+ VCD Spectrum of methyl styrene oxide
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S
|-
| Structure || [[File:Vcd_specturm_rr2.PNG|400px|left|thumb|The methyl-styrene oxide R,R]]
||[[File:Vcd_spectrum_ss2.PNG|400px|right|thumb|The methyl-styrene oxide S,S]]
|}

{| class="wikitable" border="1"
|+ VCD Spectrum of Stilbene oxide
! No. !! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || [[File:Vcd_spectrum_rr3.PNG|400px|left|thumb|The Siltbene oxide R,R]] ||
[[File:Vcd_spectrum_ss3.PNG|400px|right|thumb|The Siltbene oxide S,S]]
|}

As it can be seen from the VCD Spectrum above, the pair of enantimoers have similar but opposite spectrum. Since the R,R and S,S conformers are mirror images to each other, the vibrations in VCD Spectrum is opposite as well. This technique can be used to assign the stereochemistry of the molecule but it is not available in Imperial College.

==== Using the (calculated) properties of transition state for the reaction ====
The enantiomeric excess and relative population of the two two conformers of a molecule can be calculated by the following method.

The following is the transition state energies of the reaction Jacobsen catalyst and trans-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! R,R<ref>{{DOI|10.6084/m9.figshare.856651}}</ref>!! S,S<ref>{{DOI|10042/25945}}</ref>
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.183068 || -3383.188478
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.141188 ||-3383.145943
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.140244|| -3383.144999
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.254344 || -3383.262481
|-
|Free energy Difference (Hartee)|| -0.008137 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -21.36367 ||''' '''
|-
|Equilibrium Constant K|| 5533.018 ||''' '''
|-
|Enantiomeric excess|| 99.98% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. R is ideal gas constant= 8.314J/mol*K<ref>http://physics.nist.gov/cgi-bin/cuu/Value?r</ref>. T is the temperature, room temperature 298.15K is used here.
Equilibrium constant K can be calculated: 5533.018. The S,S conformation is a in large excess. The enantiomeric excess of S,S conformation is 99.98%.

The following is the transition state energies of the reaction Jacobsen catalyst and cis-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! S,R!! R,S
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.185100 || -3383.177857
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.142495 ||-3383.135845
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.141551|| -3383.134901
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.259559 || -3383.250270
|-
|Free energy Difference (Hartee)|| -0.009289 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -24.388 ||''' '''
|-
|Equilibrium Constant K|| 18744.52 ||''' '''
|-
|Enantiomeric excess|| 99.99% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. Equilibrium constant K can be calculated: 18744.52. The S,R conformation is a in large excess. The enantiomeric excess of S,R conformation is 99.99%.

=== Non covalent interaction analysis ===

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f0/Output-1jh_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Output-1_denjh.cub.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

[[Image:Jmol1jh.gif]]

This image is the Non covalent interaction electron cloud analysis of the transition state of tran-methyl styrene reacting with Jacobsen catalyst. Colour green in the graph means interaction and red means repulsion. As it is shown in the graph, the major colour is green. The alkene is reacting with the catalyst by maximizing the interaction. The red atom in the catalyst is bonding to the double bond of methyl styrene. From the orientation of the two reactants in the transition state, the product can be predicted to be S,S conformation.
The following is the reaction scheme that can predicted from the transition state graph above.
[[Image:Transition_statejh.PNG]]

=== QTAIM Analysis in the active-site of the S,S conformer from Jacobsen catalyst and tran-methyl sytrene reaction transition state ===

[[Image:Qqjh.PNG]]

BCP is known as bond critical point, which means the first derivatives of the electron cloud is zero at that point.
The first red line noted in the graph is the bond forming interaction of C and O. The second red line noted in the graph is the interaction of N and C. These two interaction can determine the stereochemistry of the product.

== Reference ==
<references />

File:Qqjh.PNG

2013-11-21T15:58:52Z

Jh4611:

Rep:Mod:jh46111

2013-11-21T15:21:56Z

Jh4611: /* Non covalent interaction analysis */

==Part I==
===Hydrogenation of Cyclopentadiene Dimer===

The Diels-Alder Reaction of two Cyclopentadiene molecules can form two forms of dimers, one is Endo (Molecule 1) and the other is Exo (Molecule 2). Molecule 3 and 4 are the products after hydrogenation. The fact that Endo form is the major product of the reaction is concluded from experiments. The energy of Endo, Exo forms and their hydrogenated forms can be calculated by Avogadro programme using energy calculation method MMFF94s; the energies are listed in Table 2.

[[Image:1-4jhh.PNG]]
{| class="wikitable" border="1"
|+ Table 1 Structures of Molecules
! No. !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule1jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_2jh.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_3jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 22 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_4jh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 2 Energies of Molecules
! Property !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Total energy (kcal/mol) || 55.37342 || 58.19067|| 50.44566 || 41.34098
|-
| Total electronic energy (kcal/mol)|| 13.01368 ||14.18454 || 5.11949 || 5.14770
|-
|Total VdW's energy (kcal/mol)|| 12.80149|| 12.35877 || 13.63843 || 10.54000
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.01475 || 0.02183 || 0.01311 || 0.00053
|-
|Total torsional energy (kcal/mol)|| -2.73093 || -2.94949 || -1.46888 || -0.31691
|-
|Total stretch bending energy (kcal/mol)|| -2.04135 || -2.08221 || -2.10211 || -1.64420
|-
|Total angle bending energy (kcal/mol)|| 30.77274 || 33.18926 || 31.93395 || 24.80178
|-
|Total bond stretching energy (kcal/mol)|| 3.54304 || 3.46797 || 3.31167 || 2.81207
|}

After running the energy calculation of the 4 molecules listed above, 2 observations can be seen.
1. Total Energy of Molecule 1(Endo) is lower than the Total Energy of Molecule 2(Exo). Comparing different kinds of energies, it has been found that the main difference is due to the angle bending energy, 30.77274kcal/mol vs 33.18926kcal/mol.
2. Total Energy of Molecule 3 is higher than that of Molecule 4. The main difference is also due to angle bending energy, 31.93395kcal/mol vs 24.80178kcal/mol.

The rise of angle bending energy is because of the bond angles deviate from the natural occurring ones, such as 120° in sp<sup>2</sup> and 109.5° in sp<sup>3</sup>. By measuring the bond angles in the molecules, the deviations can be concluded in the Table 3. It is shown clearly that there is more Angle Deviation of Molecule 1 than that of Molecule 2; more Angle Deviation of Molecule 3 than Molecule 4.

{| class="wikitable" border="1"
|+ Table 3 Angles of Molecule 1 & 2
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 1)|| 114.9 (+5.4) ||110.5 (+1)|| 102.5 (-7)
|-
| Angle/Deviation (Molecule 2)|| 117.8 (+8.3)|| 113.0 (+3.5)|| 100.2 (-9.3)
|}

{| class="wikitable" border="1"
|+ Table 4 Angles of Molecule 3 & 4
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19/22,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 3)|| 118.8 (+9.3) ||111.7 (+2.2)|| 100.1 (-9.4)
|-
| Angle/Deviation (Molecule 4)|| 118.6 (+9.1)|| 110.5 (+1)|| 101.1 (-8.4)
|}

The reason that Endo form is the major product in experiment. The reason for this is due to the lower energy of Transition state of Endo form. Endo form has higher energy which mean it is more unstable. This Diels-Alder reaction is under kinetic control instead of thermodynamic control as the more unstable Endo form is the major product.

Molecule 3 & 4 are the production of hydrogenation from Molecule 2. The Total Energies of Molecule 3 & 4 are both lower than that of Molecule 2. It means the hydrogenation is favored.

=== Atropisomerism in an Intermediate related to the Synthesis of Taxol ===

[[Image:Molecule9-10jh.PNG]]

Molecule 9 and 10 <ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319;{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>are atropisomers and they give Molecule 9(saturated) and 10(saturated) after hydrogenation. Comparison can be done between the saturated form and unsaturated form of 9 and 10.

{| class="wikitable" border="1"
|+ Table 5 Structures of Molecules
! No. !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script> <uploadedFileContents>Molecule_9jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule_10jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule17_chair.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule10_saturatedjh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 6 Energies of Molecules
! Property !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Total energy (kcal/mol) || 70.54467 || 66.29108 || 81.75656 || 73.77833
|-
| Total electronic energy (kcal/mol)|| 0.30395 ||-0.06889 || 0.0000 || 0.0000
|-
|Total VdW's energy (kcal/mol)|| 33.11930|| 35.06832 || 32.71947 || 32.80239
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.97422 || 0.25399 || 70.54467 || 0.23332
|-
|Total torsional energy (kcal/mol)|| 0.31308 || 3.65335 || 9.47264 || 9.21881
|-
|Total stretch bending energy (kcal/mol)|| -0.08187 || 0.30222 || 0.30222 || 0.32484
|-
|Total angle bending energy (kcal/mol)|| 28.25720 || 32.05685 || 32.05685 || 24.29611
|-
|Total bond stretching energy (kcal/mol)|| 7.65878 || 6.95138 || 6.95138 || 6.90286
|}

{| class="wikitable" border="1"
|+ Table 7 Angles of Molecule 9 & 10
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C7,C3,C6 || H18,C11,C5|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 120
|-
| Angle/Deviation (Molecule 3)|| 118.5 (+9) ||107.9 (+1.6)|| 123.4 (-3.4)
|-
| Angle/Deviation (Molecule 4)|| 116.4 (+6.9)|| 108.8 (+0.7)|| 122.3 (-2.3)
|}

Same arguments here as of Molecule 1 to 4. Molecule 9 has higher energy than Molecule 10, among all types of energies, total angle bending energy contributes the most. It means the angles deviated more for Molecule 9, the details of deviations show in the table below.
Molecule 9 & 10(saturated) are the products of hydrogenation of Molecule 9 & 10 respectively. Olefin strain<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891{{DOI|10.1021/ja00398a003}}</ref> energy should be taken into account in this case. Olefin strain is the difference between the strain energy of olefin and its saturated product. The strain energies of saturated molecules are higher than the unsaturated molcules. This is because olefins are locating in the brigehead of the molecules and as a result, the rate of hydrogenation from Molecule 9 & 10 to their saturated forms is low.

=== Derivative Molecules from Taxol ===

{| class="wikitable" border="1"
|+ Table 8 Structures of Molecules
! No. !! Molecule 17 boat!! Molecule 17 chair!! Molecule 18 boat!! Molecule 18 chair
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17twist_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 9 Energies of Molecules
! Property !! Molecule 17 boat!! Molecule 17 chair !! Molecule 18 boat!! Molecule 18 chair
|-
| Total energy (kcal/mol) || 114.33657 || 104.98391 || 102.28716 || 100.46235
|-
| Total electronic energy (kcal/mol)|| -7.05008 ||-7.22117 || -6.24215 || -6.05131
|-
|Total VdW's energy (kcal/mol)|| 54.37213|| 52.21497 || 50.49934 || 49.45308
|-
|Total out-of-plane bending energy (kcal/mol)|| 1.18784 || 1.02419 || 96.99088 || 0.90018
|-
|Total torsional energy (kcal/mol)|| 14.28618 || 10.98776 || 13.58885 || 9.76322
|-
|Total stretch bending energy (kcal/mol)|| 0.76536 || 0.31639 || 0.48412 || 0.63651
|-
|Total angle bending energy (kcal/mol)|| 35.01470 || 31.52244 || 28.54054 || 30.70962
|-
|Total bond stretching energy (kcal/mol)|| 15.89062 || 15.97568 || 14.39227 || 15.05105
|}

It can be concluded from Table 8 that Molecule 17 has higher energy than Molecule 18 and the chair forms have lower energy than the boat forms.

Table 10 shows the energies of Molecule 17 & 18 chair forms.

{| class="wikitable" border="1"
|+ Table 10 Energies of Molecule 17 & 18
! Property !! Molecule 17 chair!! Molecule 18 chair
|-
| Sum of electronic and thermal Energies (kJ/mol) || -1615.412 || -1651.417
|-
| Sum of electronic and thermal Energies (kJ/mol)|| -1615.390 ||-1651.396
|-
|Sum of electronic and thermal Enthalpies (kJ/mol)|| -1615.389|| -1651.395
|-
|Sum of electronic and thermal Energies (kJ/mol)|| -1615.459 || -1651.464
|}

{| class="wikitable" border="1"
|+ Table 11 <sup>1</sup>H and <sup>13</sup>C NMR for Molecule 17 & 18
! No. !! Molecule 17 NMR!! Molecule 18 NMR
|-
| Structure || [[Image:MOLECULE_17_NMRjh.PNG|500px]] || [[Image:MOLECULE_18_NMRjh.PNG|500px]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 17
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m17_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m17_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 18
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m18_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m18_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

For Table 11, the NMR data are calculated by first optimising energy by Avogadro then introduced to Gaussian. B3LYP/6-31G (d,p)basis, chloroform solvent are used.

By comparing <sup>1</sup>H NMR spectra, the computed chemical shifts are generally larger than the chemical shifts in literature<ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>. The hydrogen atoms on the methyl group near carbonyl bond are more desheided. For <sup>13</sup>C NMR, the computed chemical shifts match the those in literature.

== Part 2 ==

=== Two Catalysts ===

Properties analysis of alkene epoxide

Two catalysts can be used to epoxide alkene: Shi <ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338;{{DOI|10.1021/jo900739q}}</ref>and Jacobsen catalyst<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>.

[[Image:Two_catalysts.PNG]]

For Shi catalyst, the C-O bond length in the anomeric centre is different.

{| class="wikitable" border="1"
|+ Table 12Shi Catalyst
|-
| Structure || [[Image:Ocojhh.PNG]] || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>350</size><script>measure 10 16; measure 8 16; measure 1 2; measure 2 15; measure 3 4; measure 4 15</script><uploadedFileContents>OCOjhh.mol</uploadedFileContents>
</jmolApplet></jmol>|| [[Image:Ejh.PNG]]
|}

The C-O bond length in the Shi catalyst varies and differs from the ideal C-O single bond length: 1.43Å.
There are three O-C-O centres and the bond lengths are shown in the graph above.

The lone pair on oxygen can overlap with the anti-bonding orbital of C-O bond when the orientation is anti-periplanar: LP<sub>O</sub>/σ<sup>*</sup><sub>C-O</sub>. There are six pairs of overlap in total which are shown on the graph above.
The C-O bond will compress when its its oxygen donates lone pair; the C-O bond will extend when other oxygen donates lone pair. This can answer the question why the C-O bond is different within the same anomeric centre.

For Jacobsen catalyst, the structure can be depicted as square pyramid.

[[Image:Jacojh.PNG]]

<jmol><jmolApplet><title>ah</title><color>white</color>
<size>350</size><uploadedFileContents>TOVNIB01jh.mol</uploadedFileContents></jmolApplet></jmol>

For a 5-coordinated Mn, trigonal bipyramidal should be the ideal stucture. Here for Jacobsen catalyst, square plane pyramid is preferred due to the steric effect. The H atoms in the tBu group close to each other, the distances are shown in the graph which are slightly larger than the two times of the van der Waals radius of hydrogen: 2 x 1.20Å =2.40Å. These are attraction interaction which can stabilize the molecule.

=== Two alkenes ===

The following 2 alkenes can be oxidized to epoxide when treated with catalyst.

[[Image:Reaction schemejh.PNG]]

The epoxides of methyl styrene and stilbene have two forms: R,R and S,S. Here are the structures in 3D.

{| class="wikitable" border="1"
|+ Table 13 Structures of Molecules
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S!! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> 2rr.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> 2_ss.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Rrr_3.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Ss_3.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

The <sup>1</sup>H and <sup>13</sup>C NMR of tran-methyl styrene oxide and Stilbene oxide are listed below.
[[Image:NMR_of_H_alkene_2.PNG]][[Image:Nmr_1jh.PNG]]
[[Image:NMR_of_C_alkene_2.PNG]][[Image:Nmr2jh.PNG]]
[[Image:NMR_of_H_alkene_3.PNG]][[Image:Nmr3jh.PNG]]
[[Image:NMR_of_C_alkene_3.PNG]][[Image:Nmr4jh.PNG]]

The alkene that under epoxiation can remain the E/Z stereochemistry. However, the epoxiation has enantimochemistry and the result product of the epoxide can be assigned as R,R or S,S (epoxidation is syn-reaction). As a result, techniques can be used to determine the stereochemistry of the final product. There are three ways can be used to show which enantiomer resulted: Reaxys used to know the optical rotation value in literature, calculated chiroptical properties of the product and properties of transition state for the reaction.

==== The reported literature for optical rotations====
Literature from Reaxys, the optical rotation:

{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! methyl-Styrene oxide !! R,R !! S,S
|-
| Optical rotation || 44.3 deg <ref>Wong,O.Andrea;Wang,Bin ;Zhao,Mei-Xin and Shi,Yian,''Journal of Organic Chemistry'', '''2009''', ''74'', 6335-6338. {{DOI|10.1021/jo900739q}}</ref>
||-41.8 deg <ref>Lin,Hui;Liu,Yan;Wu,Zhong-Liu,''Tetrahedron:Asymmetry'', '''2011''', ''22'', 134-137.{{DOI|10.1016/j.tetasy.2010.12.022}}</ref>
|-
| Concentration || 0.32 g/100ml
|| 1g/100mL
|-
| Temperature|| 25°C
|| 25°C
|-
| Solvent || chloroform
|| chloroform
|-
| Wavelength || 589nm
||589nm
|}
{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! Siltbene oxide !! R,R !! S,S
|-
| Optical rotation || 296 deg <ref>Solladie-Cavallo, Arlette; Diep-Vohuule, Anh; Sunjic, Vitomir; Vinkovic, Vladimir
Tetrahedron: Asymmetry, 1996 , vol. 7, # 6 p. 1783 - 1788{{DOI|10.1016/0957-4166(96)00213-3}}</ref>
||-291 deg <ref>Read; Campbell Journal of the Chemical Society, 1930 , p. 2377 Nature (London, United Kingdom), 1930 , vol. 125, p. 16{{DOI|10.1039/jr9300002377}}</ref>
|-
| Concentration || 1.01 g/100ml
|| 0.6g/100mL
|-
| Temperature|| 22°C
|| 15°C
|-
| Solvent || ethanol
|| acetone
|-
| Wavelength || 589nm
||589nm
|}

==== The calculated chiroptical properties of the product ====

By comparing the values of the computed chiroptical properties and the values gained from the experiment or literature, the specified enantiomer of epoxides can be predicted. The three chiroptical properties are:
1. The optical rotation at specified range of wavelength.
2. The electronic circular dichroism (ECD)
3. The vibrational circular dichroism(VCD)<ref>M. J. Fuchter, Ya-Pei Lo and H. S. Rzepa, J. Org. Chem., 2013,</ref>

1.The QM-Optimized geometry is used and input into Cambridge variation on B3LYP density functional method. Polar(optrot) calculated the [alpha]<sub>D</sub> optical rotation components of the epoxides.
[alpha]D optical rotation at wavelength range 589nm has the following vaules:

Methyl-styrene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 46.78 deg and [Alpha] ( 5890.0 A) = -46.78 deg repectively.
Silbene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 297.68 deg[Alpha], and(5890.0 A) = -298.24 deg respectively.
Both of the optical rotation data roughly match the literature data.
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! methyl-Styrene !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation ||46.78 deg ||-46.78 deg || 44.3 deg ||-41.8 deg
|}
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! Siltbene oxide !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation || 297.68 deg ||-298.24 deg || 296 deg ||-291 deg
|}

2.The ECD is useless for epoxides as there are no chromophore these epoxides

3.The VCD spectrum of methyl-styrene and siltbene and their oxides are attached here:

{| class="wikitable" border="1"
|+ VCD Spectrum of methyl styrene oxide
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S
|-
| Structure || [[File:Vcd_specturm_rr2.PNG|400px|left|thumb|The methyl-styrene oxide R,R]]
||[[File:Vcd_spectrum_ss2.PNG|400px|right|thumb|The methyl-styrene oxide S,S]]
|}

{| class="wikitable" border="1"
|+ VCD Spectrum of Stilbene oxide
! No. !! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || [[File:Vcd_spectrum_rr3.PNG|400px|left|thumb|The Siltbene oxide R,R]] ||
[[File:Vcd_spectrum_ss3.PNG|400px|right|thumb|The Siltbene oxide S,S]]
|}

As it can be seen from the VCD Spectrum above, the pair of enantimoers have similar but opposite spectrum. Since the R,R and S,S conformers are mirror images to each other, the vibrations in VCD Spectrum is opposite as well. This technique can be used to assign the stereochemistry of the molecule but it is not available in Imperial College.

==== Using the (calculated) properties of transition state for the reaction ====
The enantiomeric excess and relative population of the two two conformers of a molecule can be calculated by the following method.

The following is the transition state energies of the reaction Jacobsen catalyst and trans-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! R,R<ref>{{DOI|10.6084/m9.figshare.856651}}</ref>!! S,S<ref>{{DOI|10042/25945}}</ref>
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.183068 || -3383.188478
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.141188 ||-3383.145943
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.140244|| -3383.144999
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.254344 || -3383.262481
|-
|Free energy Difference (Hartee)|| -0.008137 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -21.36367 ||''' '''
|-
|Equilibrium Constant K|| 5533.018 ||''' '''
|-
|Enantiomeric excess|| 99.98% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. R is ideal gas constant= 8.314J/mol*K<ref>http://physics.nist.gov/cgi-bin/cuu/Value?r</ref>. T is the temperature, room temperature 298.15K is used here.
Equilibrium constant K can be calculated: 5533.018. The S,S conformation is a in large excess. The enantiomeric excess of S,S conformation is 99.98%.

The following is the transition state energies of the reaction Jacobsen catalyst and cis-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! S,R!! R,S
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.185100 || -3383.177857
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.142495 ||-3383.135845
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.141551|| -3383.134901
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.259559 || -3383.250270
|-
|Free energy Difference (Hartee)|| -0.009289 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -24.388 ||''' '''
|-
|Equilibrium Constant K|| 18744.52 ||''' '''
|-
|Enantiomeric excess|| 99.99% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. Equilibrium constant K can be calculated: 18744.52. The S,R conformation is a in large excess. The enantiomeric excess of S,R conformation is 99.99%.

=== Non covalent interaction analysis ===

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f0/Output-1jh_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Output-1_denjh.cub.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

[[Image:Jmol1jh.gif]]

This image is the Non covalent interaction electron cloud analysis of the transition state of tran-methyl styrene reacting with Jacobsen catalyst. Colour green in the graph means interaction and red means repulsion. As it is shown in the graph, the major colour is green. The alkene is reacting with the catalyst by maximizing the interaction. The red atom in the catalyst is bonding to the double bond of methyl styrene. From the orientation of the two reactants in the transition state, the product can be predicted to be S,S conformation.
The following is the reaction scheme that can predicted from the transition state graph above.
[[Image:Transition_statejh.PNG]]

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

[[Image:S,s_q.PNG]]

== Reference ==
<references />

Rep:Mod:jh46111

2013-11-21T15:18:52Z

Jh4611: /* Non covalent interaction analysis */

==Part I==
===Hydrogenation of Cyclopentadiene Dimer===

The Diels-Alder Reaction of two Cyclopentadiene molecules can form two forms of dimers, one is Endo (Molecule 1) and the other is Exo (Molecule 2). Molecule 3 and 4 are the products after hydrogenation. The fact that Endo form is the major product of the reaction is concluded from experiments. The energy of Endo, Exo forms and their hydrogenated forms can be calculated by Avogadro programme using energy calculation method MMFF94s; the energies are listed in Table 2.

[[Image:1-4jhh.PNG]]
{| class="wikitable" border="1"
|+ Table 1 Structures of Molecules
! No. !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule1jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_2jh.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_3jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 22 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_4jh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 2 Energies of Molecules
! Property !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Total energy (kcal/mol) || 55.37342 || 58.19067|| 50.44566 || 41.34098
|-
| Total electronic energy (kcal/mol)|| 13.01368 ||14.18454 || 5.11949 || 5.14770
|-
|Total VdW's energy (kcal/mol)|| 12.80149|| 12.35877 || 13.63843 || 10.54000
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.01475 || 0.02183 || 0.01311 || 0.00053
|-
|Total torsional energy (kcal/mol)|| -2.73093 || -2.94949 || -1.46888 || -0.31691
|-
|Total stretch bending energy (kcal/mol)|| -2.04135 || -2.08221 || -2.10211 || -1.64420
|-
|Total angle bending energy (kcal/mol)|| 30.77274 || 33.18926 || 31.93395 || 24.80178
|-
|Total bond stretching energy (kcal/mol)|| 3.54304 || 3.46797 || 3.31167 || 2.81207
|}

After running the energy calculation of the 4 molecules listed above, 2 observations can be seen.
1. Total Energy of Molecule 1(Endo) is lower than the Total Energy of Molecule 2(Exo). Comparing different kinds of energies, it has been found that the main difference is due to the angle bending energy, 30.77274kcal/mol vs 33.18926kcal/mol.
2. Total Energy of Molecule 3 is higher than that of Molecule 4. The main difference is also due to angle bending energy, 31.93395kcal/mol vs 24.80178kcal/mol.

The rise of angle bending energy is because of the bond angles deviate from the natural occurring ones, such as 120° in sp<sup>2</sup> and 109.5° in sp<sup>3</sup>. By measuring the bond angles in the molecules, the deviations can be concluded in the Table 3. It is shown clearly that there is more Angle Deviation of Molecule 1 than that of Molecule 2; more Angle Deviation of Molecule 3 than Molecule 4.

{| class="wikitable" border="1"
|+ Table 3 Angles of Molecule 1 & 2
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 1)|| 114.9 (+5.4) ||110.5 (+1)|| 102.5 (-7)
|-
| Angle/Deviation (Molecule 2)|| 117.8 (+8.3)|| 113.0 (+3.5)|| 100.2 (-9.3)
|}

{| class="wikitable" border="1"
|+ Table 4 Angles of Molecule 3 & 4
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19/22,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 3)|| 118.8 (+9.3) ||111.7 (+2.2)|| 100.1 (-9.4)
|-
| Angle/Deviation (Molecule 4)|| 118.6 (+9.1)|| 110.5 (+1)|| 101.1 (-8.4)
|}

The reason that Endo form is the major product in experiment. The reason for this is due to the lower energy of Transition state of Endo form. Endo form has higher energy which mean it is more unstable. This Diels-Alder reaction is under kinetic control instead of thermodynamic control as the more unstable Endo form is the major product.

Molecule 3 & 4 are the production of hydrogenation from Molecule 2. The Total Energies of Molecule 3 & 4 are both lower than that of Molecule 2. It means the hydrogenation is favored.

=== Atropisomerism in an Intermediate related to the Synthesis of Taxol ===

[[Image:Molecule9-10jh.PNG]]

Molecule 9 and 10 <ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319;{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>are atropisomers and they give Molecule 9(saturated) and 10(saturated) after hydrogenation. Comparison can be done between the saturated form and unsaturated form of 9 and 10.

{| class="wikitable" border="1"
|+ Table 5 Structures of Molecules
! No. !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script> <uploadedFileContents>Molecule_9jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule_10jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule17_chair.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule10_saturatedjh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 6 Energies of Molecules
! Property !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Total energy (kcal/mol) || 70.54467 || 66.29108 || 81.75656 || 73.77833
|-
| Total electronic energy (kcal/mol)|| 0.30395 ||-0.06889 || 0.0000 || 0.0000
|-
|Total VdW's energy (kcal/mol)|| 33.11930|| 35.06832 || 32.71947 || 32.80239
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.97422 || 0.25399 || 70.54467 || 0.23332
|-
|Total torsional energy (kcal/mol)|| 0.31308 || 3.65335 || 9.47264 || 9.21881
|-
|Total stretch bending energy (kcal/mol)|| -0.08187 || 0.30222 || 0.30222 || 0.32484
|-
|Total angle bending energy (kcal/mol)|| 28.25720 || 32.05685 || 32.05685 || 24.29611
|-
|Total bond stretching energy (kcal/mol)|| 7.65878 || 6.95138 || 6.95138 || 6.90286
|}

{| class="wikitable" border="1"
|+ Table 7 Angles of Molecule 9 & 10
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C7,C3,C6 || H18,C11,C5|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 120
|-
| Angle/Deviation (Molecule 3)|| 118.5 (+9) ||107.9 (+1.6)|| 123.4 (-3.4)
|-
| Angle/Deviation (Molecule 4)|| 116.4 (+6.9)|| 108.8 (+0.7)|| 122.3 (-2.3)
|}

Same arguments here as of Molecule 1 to 4. Molecule 9 has higher energy than Molecule 10, among all types of energies, total angle bending energy contributes the most. It means the angles deviated more for Molecule 9, the details of deviations show in the table below.
Molecule 9 & 10(saturated) are the products of hydrogenation of Molecule 9 & 10 respectively. Olefin strain<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891{{DOI|10.1021/ja00398a003}}</ref> energy should be taken into account in this case. Olefin strain is the difference between the strain energy of olefin and its saturated product. The strain energies of saturated molecules are higher than the unsaturated molcules. This is because olefins are locating in the brigehead of the molecules and as a result, the rate of hydrogenation from Molecule 9 & 10 to their saturated forms is low.

=== Derivative Molecules from Taxol ===

{| class="wikitable" border="1"
|+ Table 8 Structures of Molecules
! No. !! Molecule 17 boat!! Molecule 17 chair!! Molecule 18 boat!! Molecule 18 chair
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17twist_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 9 Energies of Molecules
! Property !! Molecule 17 boat!! Molecule 17 chair !! Molecule 18 boat!! Molecule 18 chair
|-
| Total energy (kcal/mol) || 114.33657 || 104.98391 || 102.28716 || 100.46235
|-
| Total electronic energy (kcal/mol)|| -7.05008 ||-7.22117 || -6.24215 || -6.05131
|-
|Total VdW's energy (kcal/mol)|| 54.37213|| 52.21497 || 50.49934 || 49.45308
|-
|Total out-of-plane bending energy (kcal/mol)|| 1.18784 || 1.02419 || 96.99088 || 0.90018
|-
|Total torsional energy (kcal/mol)|| 14.28618 || 10.98776 || 13.58885 || 9.76322
|-
|Total stretch bending energy (kcal/mol)|| 0.76536 || 0.31639 || 0.48412 || 0.63651
|-
|Total angle bending energy (kcal/mol)|| 35.01470 || 31.52244 || 28.54054 || 30.70962
|-
|Total bond stretching energy (kcal/mol)|| 15.89062 || 15.97568 || 14.39227 || 15.05105
|}

It can be concluded from Table 8 that Molecule 17 has higher energy than Molecule 18 and the chair forms have lower energy than the boat forms.

Table 10 shows the energies of Molecule 17 & 18 chair forms.

{| class="wikitable" border="1"
|+ Table 10 Energies of Molecule 17 & 18
! Property !! Molecule 17 chair!! Molecule 18 chair
|-
| Sum of electronic and thermal Energies (kJ/mol) || -1615.412 || -1651.417
|-
| Sum of electronic and thermal Energies (kJ/mol)|| -1615.390 ||-1651.396
|-
|Sum of electronic and thermal Enthalpies (kJ/mol)|| -1615.389|| -1651.395
|-
|Sum of electronic and thermal Energies (kJ/mol)|| -1615.459 || -1651.464
|}

{| class="wikitable" border="1"
|+ Table 11 <sup>1</sup>H and <sup>13</sup>C NMR for Molecule 17 & 18
! No. !! Molecule 17 NMR!! Molecule 18 NMR
|-
| Structure || [[Image:MOLECULE_17_NMRjh.PNG|500px]] || [[Image:MOLECULE_18_NMRjh.PNG|500px]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 17
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m17_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m17_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 18
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m18_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m18_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

For Table 11, the NMR data are calculated by first optimising energy by Avogadro then introduced to Gaussian. B3LYP/6-31G (d,p)basis, chloroform solvent are used.

By comparing <sup>1</sup>H NMR spectra, the computed chemical shifts are generally larger than the chemical shifts in literature<ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>. The hydrogen atoms on the methyl group near carbonyl bond are more desheided. For <sup>13</sup>C NMR, the computed chemical shifts match the those in literature.

== Part 2 ==

=== Two Catalysts ===

Properties analysis of alkene epoxide

Two catalysts can be used to epoxide alkene: Shi <ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338;{{DOI|10.1021/jo900739q}}</ref>and Jacobsen catalyst<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>.

[[Image:Two_catalysts.PNG]]

For Shi catalyst, the C-O bond length in the anomeric centre is different.

{| class="wikitable" border="1"
|+ Table 12Shi Catalyst
|-
| Structure || [[Image:Ocojhh.PNG]] || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>350</size><script>measure 10 16; measure 8 16; measure 1 2; measure 2 15; measure 3 4; measure 4 15</script><uploadedFileContents>OCOjhh.mol</uploadedFileContents>
</jmolApplet></jmol>|| [[Image:Ejh.PNG]]
|}

The C-O bond length in the Shi catalyst varies and differs from the ideal C-O single bond length: 1.43Å.
There are three O-C-O centres and the bond lengths are shown in the graph above.

The lone pair on oxygen can overlap with the anti-bonding orbital of C-O bond when the orientation is anti-periplanar: LP<sub>O</sub>/σ<sup>*</sup><sub>C-O</sub>. There are six pairs of overlap in total which are shown on the graph above.
The C-O bond will compress when its its oxygen donates lone pair; the C-O bond will extend when other oxygen donates lone pair. This can answer the question why the C-O bond is different within the same anomeric centre.

For Jacobsen catalyst, the structure can be depicted as square pyramid.

[[Image:Jacojh.PNG]]

<jmol><jmolApplet><title>ah</title><color>white</color>
<size>350</size><uploadedFileContents>TOVNIB01jh.mol</uploadedFileContents></jmolApplet></jmol>

For a 5-coordinated Mn, trigonal bipyramidal should be the ideal stucture. Here for Jacobsen catalyst, square plane pyramid is preferred due to the steric effect. The H atoms in the tBu group close to each other, the distances are shown in the graph which are slightly larger than the two times of the van der Waals radius of hydrogen: 2 x 1.20Å =2.40Å. These are attraction interaction which can stabilize the molecule.

=== Two alkenes ===

The following 2 alkenes can be oxidized to epoxide when treated with catalyst.

[[Image:Reaction schemejh.PNG]]

The epoxides of methyl styrene and stilbene have two forms: R,R and S,S. Here are the structures in 3D.

{| class="wikitable" border="1"
|+ Table 13 Structures of Molecules
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S!! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> 2rr.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> 2_ss.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Rrr_3.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Ss_3.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

The <sup>1</sup>H and <sup>13</sup>C NMR of tran-methyl styrene oxide and Stilbene oxide are listed below.
[[Image:NMR_of_H_alkene_2.PNG]][[Image:Nmr_1jh.PNG]]
[[Image:NMR_of_C_alkene_2.PNG]][[Image:Nmr2jh.PNG]]
[[Image:NMR_of_H_alkene_3.PNG]][[Image:Nmr3jh.PNG]]
[[Image:NMR_of_C_alkene_3.PNG]][[Image:Nmr4jh.PNG]]

The alkene that under epoxiation can remain the E/Z stereochemistry. However, the epoxiation has enantimochemistry and the result product of the epoxide can be assigned as R,R or S,S (epoxidation is syn-reaction). As a result, techniques can be used to determine the stereochemistry of the final product. There are three ways can be used to show which enantiomer resulted: Reaxys used to know the optical rotation value in literature, calculated chiroptical properties of the product and properties of transition state for the reaction.

==== The reported literature for optical rotations====
Literature from Reaxys, the optical rotation:

{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! methyl-Styrene oxide !! R,R !! S,S
|-
| Optical rotation || 44.3 deg <ref>Wong,O.Andrea;Wang,Bin ;Zhao,Mei-Xin and Shi,Yian,''Journal of Organic Chemistry'', '''2009''', ''74'', 6335-6338. {{DOI|10.1021/jo900739q}}</ref>
||-41.8 deg <ref>Lin,Hui;Liu,Yan;Wu,Zhong-Liu,''Tetrahedron:Asymmetry'', '''2011''', ''22'', 134-137.{{DOI|10.1016/j.tetasy.2010.12.022}}</ref>
|-
| Concentration || 0.32 g/100ml
|| 1g/100mL
|-
| Temperature|| 25°C
|| 25°C
|-
| Solvent || chloroform
|| chloroform
|-
| Wavelength || 589nm
||589nm
|}
{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! Siltbene oxide !! R,R !! S,S
|-
| Optical rotation || 296 deg <ref>Solladie-Cavallo, Arlette; Diep-Vohuule, Anh; Sunjic, Vitomir; Vinkovic, Vladimir
Tetrahedron: Asymmetry, 1996 , vol. 7, # 6 p. 1783 - 1788{{DOI|10.1016/0957-4166(96)00213-3}}</ref>
||-291 deg <ref>Read; Campbell Journal of the Chemical Society, 1930 , p. 2377 Nature (London, United Kingdom), 1930 , vol. 125, p. 16{{DOI|10.1039/jr9300002377}}</ref>
|-
| Concentration || 1.01 g/100ml
|| 0.6g/100mL
|-
| Temperature|| 22°C
|| 15°C
|-
| Solvent || ethanol
|| acetone
|-
| Wavelength || 589nm
||589nm
|}

==== The calculated chiroptical properties of the product ====

By comparing the values of the computed chiroptical properties and the values gained from the experiment or literature, the specified enantiomer of epoxides can be predicted. The three chiroptical properties are:
1. The optical rotation at specified range of wavelength.
2. The electronic circular dichroism (ECD)
3. The vibrational circular dichroism(VCD)<ref>M. J. Fuchter, Ya-Pei Lo and H. S. Rzepa, J. Org. Chem., 2013,</ref>

1.The QM-Optimized geometry is used and input into Cambridge variation on B3LYP density functional method. Polar(optrot) calculated the [alpha]<sub>D</sub> optical rotation components of the epoxides.
[alpha]D optical rotation at wavelength range 589nm has the following vaules:

Methyl-styrene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 46.78 deg and [Alpha] ( 5890.0 A) = -46.78 deg repectively.
Silbene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 297.68 deg[Alpha], and(5890.0 A) = -298.24 deg respectively.
Both of the optical rotation data roughly match the literature data.
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! methyl-Styrene !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation ||46.78 deg ||-46.78 deg || 44.3 deg ||-41.8 deg
|}
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! Siltbene oxide !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation || 297.68 deg ||-298.24 deg || 296 deg ||-291 deg
|}

2.The ECD is useless for epoxides as there are no chromophore these epoxides

3.The VCD spectrum of methyl-styrene and siltbene and their oxides are attached here:

{| class="wikitable" border="1"
|+ VCD Spectrum of methyl styrene oxide
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S
|-
| Structure || [[File:Vcd_specturm_rr2.PNG|400px|left|thumb|The methyl-styrene oxide R,R]]
||[[File:Vcd_spectrum_ss2.PNG|400px|right|thumb|The methyl-styrene oxide S,S]]
|}

{| class="wikitable" border="1"
|+ VCD Spectrum of Stilbene oxide
! No. !! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || [[File:Vcd_spectrum_rr3.PNG|400px|left|thumb|The Siltbene oxide R,R]] ||
[[File:Vcd_spectrum_ss3.PNG|400px|right|thumb|The Siltbene oxide S,S]]
|}

As it can be seen from the VCD Spectrum above, the pair of enantimoers have similar but opposite spectrum. Since the R,R and S,S conformers are mirror images to each other, the vibrations in VCD Spectrum is opposite as well. This technique can be used to assign the stereochemistry of the molecule but it is not available in Imperial College.

==== Using the (calculated) properties of transition state for the reaction ====
The enantiomeric excess and relative population of the two two conformers of a molecule can be calculated by the following method.

The following is the transition state energies of the reaction Jacobsen catalyst and trans-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! R,R<ref>{{DOI|10.6084/m9.figshare.856651}}</ref>!! S,S<ref>{{DOI|10042/25945}}</ref>
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.183068 || -3383.188478
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.141188 ||-3383.145943
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.140244|| -3383.144999
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.254344 || -3383.262481
|-
|Free energy Difference (Hartee)|| -0.008137 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -21.36367 ||''' '''
|-
|Equilibrium Constant K|| 5533.018 ||''' '''
|-
|Enantiomeric excess|| 99.98% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. R is ideal gas constant= 8.314J/mol*K<ref>http://physics.nist.gov/cgi-bin/cuu/Value?r</ref>. T is the temperature, room temperature 298.15K is used here.
Equilibrium constant K can be calculated: 5533.018. The S,S conformation is a in large excess. The enantiomeric excess of S,S conformation is 99.98%.

The following is the transition state energies of the reaction Jacobsen catalyst and cis-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! S,R!! R,S
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.185100 || -3383.177857
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.142495 ||-3383.135845
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.141551|| -3383.134901
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.259559 || -3383.250270
|-
|Free energy Difference (Hartee)|| -0.009289 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -24.388 ||''' '''
|-
|Equilibrium Constant K|| 18744.52 ||''' '''
|-
|Enantiomeric excess|| 99.99% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. Equilibrium constant K can be calculated: 18744.52. The S,R conformation is a in large excess. The enantiomeric excess of S,R conformation is 99.99%.

=== Non covalent interaction analysis ===

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f0/Output-1jh_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Output-1_denjh.cub.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

This image is the Non covalent interaction electron cloud analysis of the transition state of tran-methyl styrene reacting with Jacobsen catalyst. Colour green in the graph means interaction and red means repulsion. As it is shown in the graph, the major colour is green. The alkene is reacting with the catalyst by maximizing the interaction. The red atom in the catalyst is bonding to the double bond of methyl styrene. From the orientation of the two reactants in the transition state, the product can be predicted to be S,S conformation.
The following is the reaction scheme that can predicted from the transition state graph above.
[[Image:Transition_statejh.PNG]]

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

[[Image:S,s_q.PNG]]

== Reference ==
<references />

File:Output-1jh den.cub.jvxl

2013-11-21T15:17:16Z

Jh4611:

File:Output-1 denjh.cub.xyz

2013-11-21T15:16:53Z

Jh4611:

Rep:Mod:jh46111

2013-11-21T15:07:10Z

Jh4611: /* Non covalent interaction analysis */

==Part I==
===Hydrogenation of Cyclopentadiene Dimer===

The Diels-Alder Reaction of two Cyclopentadiene molecules can form two forms of dimers, one is Endo (Molecule 1) and the other is Exo (Molecule 2). Molecule 3 and 4 are the products after hydrogenation. The fact that Endo form is the major product of the reaction is concluded from experiments. The energy of Endo, Exo forms and their hydrogenated forms can be calculated by Avogadro programme using energy calculation method MMFF94s; the energies are listed in Table 2.

[[Image:1-4jhh.PNG]]
{| class="wikitable" border="1"
|+ Table 1 Structures of Molecules
! No. !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule1jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_2jh.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_3jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 22 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_4jh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 2 Energies of Molecules
! Property !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Total energy (kcal/mol) || 55.37342 || 58.19067|| 50.44566 || 41.34098
|-
| Total electronic energy (kcal/mol)|| 13.01368 ||14.18454 || 5.11949 || 5.14770
|-
|Total VdW's energy (kcal/mol)|| 12.80149|| 12.35877 || 13.63843 || 10.54000
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.01475 || 0.02183 || 0.01311 || 0.00053
|-
|Total torsional energy (kcal/mol)|| -2.73093 || -2.94949 || -1.46888 || -0.31691
|-
|Total stretch bending energy (kcal/mol)|| -2.04135 || -2.08221 || -2.10211 || -1.64420
|-
|Total angle bending energy (kcal/mol)|| 30.77274 || 33.18926 || 31.93395 || 24.80178
|-
|Total bond stretching energy (kcal/mol)|| 3.54304 || 3.46797 || 3.31167 || 2.81207
|}

After running the energy calculation of the 4 molecules listed above, 2 observations can be seen.
1. Total Energy of Molecule 1(Endo) is lower than the Total Energy of Molecule 2(Exo). Comparing different kinds of energies, it has been found that the main difference is due to the angle bending energy, 30.77274kcal/mol vs 33.18926kcal/mol.
2. Total Energy of Molecule 3 is higher than that of Molecule 4. The main difference is also due to angle bending energy, 31.93395kcal/mol vs 24.80178kcal/mol.

The rise of angle bending energy is because of the bond angles deviate from the natural occurring ones, such as 120° in sp<sup>2</sup> and 109.5° in sp<sup>3</sup>. By measuring the bond angles in the molecules, the deviations can be concluded in the Table 3. It is shown clearly that there is more Angle Deviation of Molecule 1 than that of Molecule 2; more Angle Deviation of Molecule 3 than Molecule 4.

{| class="wikitable" border="1"
|+ Table 3 Angles of Molecule 1 & 2
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 1)|| 114.9 (+5.4) ||110.5 (+1)|| 102.5 (-7)
|-
| Angle/Deviation (Molecule 2)|| 117.8 (+8.3)|| 113.0 (+3.5)|| 100.2 (-9.3)
|}

{| class="wikitable" border="1"
|+ Table 4 Angles of Molecule 3 & 4
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19/22,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 3)|| 118.8 (+9.3) ||111.7 (+2.2)|| 100.1 (-9.4)
|-
| Angle/Deviation (Molecule 4)|| 118.6 (+9.1)|| 110.5 (+1)|| 101.1 (-8.4)
|}

The reason that Endo form is the major product in experiment. The reason for this is due to the lower energy of Transition state of Endo form. Endo form has higher energy which mean it is more unstable. This Diels-Alder reaction is under kinetic control instead of thermodynamic control as the more unstable Endo form is the major product.

Molecule 3 & 4 are the production of hydrogenation from Molecule 2. The Total Energies of Molecule 3 & 4 are both lower than that of Molecule 2. It means the hydrogenation is favored.

=== Atropisomerism in an Intermediate related to the Synthesis of Taxol ===

[[Image:Molecule9-10jh.PNG]]

Molecule 9 and 10 <ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319;{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>are atropisomers and they give Molecule 9(saturated) and 10(saturated) after hydrogenation. Comparison can be done between the saturated form and unsaturated form of 9 and 10.

{| class="wikitable" border="1"
|+ Table 5 Structures of Molecules
! No. !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script> <uploadedFileContents>Molecule_9jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule_10jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule17_chair.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule10_saturatedjh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 6 Energies of Molecules
! Property !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Total energy (kcal/mol) || 70.54467 || 66.29108 || 81.75656 || 73.77833
|-
| Total electronic energy (kcal/mol)|| 0.30395 ||-0.06889 || 0.0000 || 0.0000
|-
|Total VdW's energy (kcal/mol)|| 33.11930|| 35.06832 || 32.71947 || 32.80239
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.97422 || 0.25399 || 70.54467 || 0.23332
|-
|Total torsional energy (kcal/mol)|| 0.31308 || 3.65335 || 9.47264 || 9.21881
|-
|Total stretch bending energy (kcal/mol)|| -0.08187 || 0.30222 || 0.30222 || 0.32484
|-
|Total angle bending energy (kcal/mol)|| 28.25720 || 32.05685 || 32.05685 || 24.29611
|-
|Total bond stretching energy (kcal/mol)|| 7.65878 || 6.95138 || 6.95138 || 6.90286
|}

{| class="wikitable" border="1"
|+ Table 7 Angles of Molecule 9 & 10
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C7,C3,C6 || H18,C11,C5|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 120
|-
| Angle/Deviation (Molecule 3)|| 118.5 (+9) ||107.9 (+1.6)|| 123.4 (-3.4)
|-
| Angle/Deviation (Molecule 4)|| 116.4 (+6.9)|| 108.8 (+0.7)|| 122.3 (-2.3)
|}

Same arguments here as of Molecule 1 to 4. Molecule 9 has higher energy than Molecule 10, among all types of energies, total angle bending energy contributes the most. It means the angles deviated more for Molecule 9, the details of deviations show in the table below.
Molecule 9 & 10(saturated) are the products of hydrogenation of Molecule 9 & 10 respectively. Olefin strain<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891{{DOI|10.1021/ja00398a003}}</ref> energy should be taken into account in this case. Olefin strain is the difference between the strain energy of olefin and its saturated product. The strain energies of saturated molecules are higher than the unsaturated molcules. This is because olefins are locating in the brigehead of the molecules and as a result, the rate of hydrogenation from Molecule 9 & 10 to their saturated forms is low.

=== Derivative Molecules from Taxol ===

{| class="wikitable" border="1"
|+ Table 8 Structures of Molecules
! No. !! Molecule 17 boat!! Molecule 17 chair!! Molecule 18 boat!! Molecule 18 chair
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17twist_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 9 Energies of Molecules
! Property !! Molecule 17 boat!! Molecule 17 chair !! Molecule 18 boat!! Molecule 18 chair
|-
| Total energy (kcal/mol) || 114.33657 || 104.98391 || 102.28716 || 100.46235
|-
| Total electronic energy (kcal/mol)|| -7.05008 ||-7.22117 || -6.24215 || -6.05131
|-
|Total VdW's energy (kcal/mol)|| 54.37213|| 52.21497 || 50.49934 || 49.45308
|-
|Total out-of-plane bending energy (kcal/mol)|| 1.18784 || 1.02419 || 96.99088 || 0.90018
|-
|Total torsional energy (kcal/mol)|| 14.28618 || 10.98776 || 13.58885 || 9.76322
|-
|Total stretch bending energy (kcal/mol)|| 0.76536 || 0.31639 || 0.48412 || 0.63651
|-
|Total angle bending energy (kcal/mol)|| 35.01470 || 31.52244 || 28.54054 || 30.70962
|-
|Total bond stretching energy (kcal/mol)|| 15.89062 || 15.97568 || 14.39227 || 15.05105
|}

It can be concluded from Table 8 that Molecule 17 has higher energy than Molecule 18 and the chair forms have lower energy than the boat forms.

Table 10 shows the energies of Molecule 17 & 18 chair forms.

{| class="wikitable" border="1"
|+ Table 10 Energies of Molecule 17 & 18
! Property !! Molecule 17 chair!! Molecule 18 chair
|-
| Sum of electronic and thermal Energies (kJ/mol) || -1615.412 || -1651.417
|-
| Sum of electronic and thermal Energies (kJ/mol)|| -1615.390 ||-1651.396
|-
|Sum of electronic and thermal Enthalpies (kJ/mol)|| -1615.389|| -1651.395
|-
|Sum of electronic and thermal Energies (kJ/mol)|| -1615.459 || -1651.464
|}

{| class="wikitable" border="1"
|+ Table 11 <sup>1</sup>H and <sup>13</sup>C NMR for Molecule 17 & 18
! No. !! Molecule 17 NMR!! Molecule 18 NMR
|-
| Structure || [[Image:MOLECULE_17_NMRjh.PNG|500px]] || [[Image:MOLECULE_18_NMRjh.PNG|500px]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 17
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m17_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m17_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 18
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m18_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m18_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

For Table 11, the NMR data are calculated by first optimising energy by Avogadro then introduced to Gaussian. B3LYP/6-31G (d,p)basis, chloroform solvent are used.

By comparing <sup>1</sup>H NMR spectra, the computed chemical shifts are generally larger than the chemical shifts in literature<ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>. The hydrogen atoms on the methyl group near carbonyl bond are more desheided. For <sup>13</sup>C NMR, the computed chemical shifts match the those in literature.

== Part 2 ==

=== Two Catalysts ===

Properties analysis of alkene epoxide

Two catalysts can be used to epoxide alkene: Shi <ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338;{{DOI|10.1021/jo900739q}}</ref>and Jacobsen catalyst<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>.

[[Image:Two_catalysts.PNG]]

For Shi catalyst, the C-O bond length in the anomeric centre is different.

{| class="wikitable" border="1"
|+ Table 12Shi Catalyst
|-
| Structure || [[Image:Ocojhh.PNG]] || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>350</size><script>measure 10 16; measure 8 16; measure 1 2; measure 2 15; measure 3 4; measure 4 15</script><uploadedFileContents>OCOjhh.mol</uploadedFileContents>
</jmolApplet></jmol>|| [[Image:Ejh.PNG]]
|}

The C-O bond length in the Shi catalyst varies and differs from the ideal C-O single bond length: 1.43Å.
There are three O-C-O centres and the bond lengths are shown in the graph above.

The lone pair on oxygen can overlap with the anti-bonding orbital of C-O bond when the orientation is anti-periplanar: LP<sub>O</sub>/σ<sup>*</sup><sub>C-O</sub>. There are six pairs of overlap in total which are shown on the graph above.
The C-O bond will compress when its its oxygen donates lone pair; the C-O bond will extend when other oxygen donates lone pair. This can answer the question why the C-O bond is different within the same anomeric centre.

For Jacobsen catalyst, the structure can be depicted as square pyramid.

[[Image:Jacojh.PNG]]

<jmol><jmolApplet><title>ah</title><color>white</color>
<size>350</size><uploadedFileContents>TOVNIB01jh.mol</uploadedFileContents></jmolApplet></jmol>

For a 5-coordinated Mn, trigonal bipyramidal should be the ideal stucture. Here for Jacobsen catalyst, square plane pyramid is preferred due to the steric effect. The H atoms in the tBu group close to each other, the distances are shown in the graph which are slightly larger than the two times of the van der Waals radius of hydrogen: 2 x 1.20Å =2.40Å. These are attraction interaction which can stabilize the molecule.

=== Two alkenes ===

The following 2 alkenes can be oxidized to epoxide when treated with catalyst.

[[Image:Reaction schemejh.PNG]]

The epoxides of methyl styrene and stilbene have two forms: R,R and S,S. Here are the structures in 3D.

{| class="wikitable" border="1"
|+ Table 13 Structures of Molecules
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S!! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> 2rr.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> 2_ss.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Rrr_3.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Ss_3.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

The <sup>1</sup>H and <sup>13</sup>C NMR of tran-methyl styrene oxide and Stilbene oxide are listed below.
[[Image:NMR_of_H_alkene_2.PNG]][[Image:Nmr_1jh.PNG]]
[[Image:NMR_of_C_alkene_2.PNG]][[Image:Nmr2jh.PNG]]
[[Image:NMR_of_H_alkene_3.PNG]][[Image:Nmr3jh.PNG]]
[[Image:NMR_of_C_alkene_3.PNG]][[Image:Nmr4jh.PNG]]

The alkene that under epoxiation can remain the E/Z stereochemistry. However, the epoxiation has enantimochemistry and the result product of the epoxide can be assigned as R,R or S,S (epoxidation is syn-reaction). As a result, techniques can be used to determine the stereochemistry of the final product. There are three ways can be used to show which enantiomer resulted: Reaxys used to know the optical rotation value in literature, calculated chiroptical properties of the product and properties of transition state for the reaction.

==== The reported literature for optical rotations====
Literature from Reaxys, the optical rotation:

{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! methyl-Styrene oxide !! R,R !! S,S
|-
| Optical rotation || 44.3 deg <ref>Wong,O.Andrea;Wang,Bin ;Zhao,Mei-Xin and Shi,Yian,''Journal of Organic Chemistry'', '''2009''', ''74'', 6335-6338. {{DOI|10.1021/jo900739q}}</ref>
||-41.8 deg <ref>Lin,Hui;Liu,Yan;Wu,Zhong-Liu,''Tetrahedron:Asymmetry'', '''2011''', ''22'', 134-137.{{DOI|10.1016/j.tetasy.2010.12.022}}</ref>
|-
| Concentration || 0.32 g/100ml
|| 1g/100mL
|-
| Temperature|| 25°C
|| 25°C
|-
| Solvent || chloroform
|| chloroform
|-
| Wavelength || 589nm
||589nm
|}
{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! Siltbene oxide !! R,R !! S,S
|-
| Optical rotation || 296 deg <ref>Solladie-Cavallo, Arlette; Diep-Vohuule, Anh; Sunjic, Vitomir; Vinkovic, Vladimir
Tetrahedron: Asymmetry, 1996 , vol. 7, # 6 p. 1783 - 1788{{DOI|10.1016/0957-4166(96)00213-3}}</ref>
||-291 deg <ref>Read; Campbell Journal of the Chemical Society, 1930 , p. 2377 Nature (London, United Kingdom), 1930 , vol. 125, p. 16{{DOI|10.1039/jr9300002377}}</ref>
|-
| Concentration || 1.01 g/100ml
|| 0.6g/100mL
|-
| Temperature|| 22°C
|| 15°C
|-
| Solvent || ethanol
|| acetone
|-
| Wavelength || 589nm
||589nm
|}

==== The calculated chiroptical properties of the product ====

By comparing the values of the computed chiroptical properties and the values gained from the experiment or literature, the specified enantiomer of epoxides can be predicted. The three chiroptical properties are:
1. The optical rotation at specified range of wavelength.
2. The electronic circular dichroism (ECD)
3. The vibrational circular dichroism(VCD)<ref>M. J. Fuchter, Ya-Pei Lo and H. S. Rzepa, J. Org. Chem., 2013,</ref>

1.The QM-Optimized geometry is used and input into Cambridge variation on B3LYP density functional method. Polar(optrot) calculated the [alpha]<sub>D</sub> optical rotation components of the epoxides.
[alpha]D optical rotation at wavelength range 589nm has the following vaules:

Methyl-styrene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 46.78 deg and [Alpha] ( 5890.0 A) = -46.78 deg repectively.
Silbene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 297.68 deg[Alpha], and(5890.0 A) = -298.24 deg respectively.
Both of the optical rotation data roughly match the literature data.
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! methyl-Styrene !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation ||46.78 deg ||-46.78 deg || 44.3 deg ||-41.8 deg
|}
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! Siltbene oxide !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation || 297.68 deg ||-298.24 deg || 296 deg ||-291 deg
|}

2.The ECD is useless for epoxides as there are no chromophore these epoxides

3.The VCD spectrum of methyl-styrene and siltbene and their oxides are attached here:

{| class="wikitable" border="1"
|+ VCD Spectrum of methyl styrene oxide
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S
|-
| Structure || [[File:Vcd_specturm_rr2.PNG|400px|left|thumb|The methyl-styrene oxide R,R]]
||[[File:Vcd_spectrum_ss2.PNG|400px|right|thumb|The methyl-styrene oxide S,S]]
|}

{| class="wikitable" border="1"
|+ VCD Spectrum of Stilbene oxide
! No. !! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || [[File:Vcd_spectrum_rr3.PNG|400px|left|thumb|The Siltbene oxide R,R]] ||
[[File:Vcd_spectrum_ss3.PNG|400px|right|thumb|The Siltbene oxide S,S]]
|}

As it can be seen from the VCD Spectrum above, the pair of enantimoers have similar but opposite spectrum. Since the R,R and S,S conformers are mirror images to each other, the vibrations in VCD Spectrum is opposite as well. This technique can be used to assign the stereochemistry of the molecule but it is not available in Imperial College.

==== Using the (calculated) properties of transition state for the reaction ====
The enantiomeric excess and relative population of the two two conformers of a molecule can be calculated by the following method.

The following is the transition state energies of the reaction Jacobsen catalyst and trans-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! R,R<ref>{{DOI|10.6084/m9.figshare.856651}}</ref>!! S,S<ref>{{DOI|10042/25945}}</ref>
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.183068 || -3383.188478
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.141188 ||-3383.145943
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.140244|| -3383.144999
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.254344 || -3383.262481
|-
|Free energy Difference (Hartee)|| -0.008137 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -21.36367 ||''' '''
|-
|Equilibrium Constant K|| 5533.018 ||''' '''
|-
|Enantiomeric excess|| 99.98% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. R is ideal gas constant= 8.314J/mol*K<ref>http://physics.nist.gov/cgi-bin/cuu/Value?r</ref>. T is the temperature, room temperature 298.15K is used here.
Equilibrium constant K can be calculated: 5533.018. The S,S conformation is a in large excess. The enantiomeric excess of S,S conformation is 99.98%.

The following is the transition state energies of the reaction Jacobsen catalyst and cis-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! S,R!! R,S
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.185100 || -3383.177857
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.142495 ||-3383.135845
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.141551|| -3383.134901
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.259559 || -3383.250270
|-
|Free energy Difference (Hartee)|| -0.009289 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -24.388 ||''' '''
|-
|Equilibrium Constant K|| 18744.52 ||''' '''
|-
|Enantiomeric excess|| 99.99% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. Equilibrium constant K can be calculated: 18744.52. The S,R conformation is a in large excess. The enantiomeric excess of S,R conformation is 99.99%.

=== Non covalent interaction analysis ===

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/6/69/Output-1_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Output-1_den.cub.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

This image is the Non covalent interaction electron cloud analysis of the transition state of tran-methyl styrene reacting with Jacobsen catalyst. Colour green in the graph means interaction and red means repulsion. As it is shown in the graph, the major colour is green. The alkene is reacting with the catalyst by maximizing the interaction. The red atom in the catalyst is bonding to the double bond of methyl styrene. From the orientation of the two reactants in the transition state, the product can be predicted to be S,S conformation.
The following is the reaction scheme that can predicted from the transition state graph above.
[[Image:Transition_statejh.PNG]]

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

[[Image:S,s_q.PNG]]

== Reference ==
<references />

File:Output-1 den.cub.jvxl

2013-11-21T14:59:52Z

Jh4611: uploaded a new version of "File:Output-1 den.cub.jvxl"

File:Output-1 den.cub.xyz

2013-11-21T14:58:32Z

Jh4611: uploaded a new version of "File:Output-1 den.cub.xyz"

Rep:Mod:jh46111

2013-11-21T13:50:09Z

Jh4611: /* Non covalent interaction analysis */

==Part I==
===Hydrogenation of Cyclopentadiene Dimer===

The Diels-Alder Reaction of two Cyclopentadiene molecules can form two forms of dimers, one is Endo (Molecule 1) and the other is Exo (Molecule 2). Molecule 3 and 4 are the products after hydrogenation. The fact that Endo form is the major product of the reaction is concluded from experiments. The energy of Endo, Exo forms and their hydrogenated forms can be calculated by Avogadro programme using energy calculation method MMFF94s; the energies are listed in Table 2.

[[Image:1-4jhh.PNG]]
{| class="wikitable" border="1"
|+ Table 1 Structures of Molecules
! No. !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule1jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_2jh.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_3jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 22 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_4jh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 2 Energies of Molecules
! Property !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Total energy (kcal/mol) || 55.37342 || 58.19067|| 50.44566 || 41.34098
|-
| Total electronic energy (kcal/mol)|| 13.01368 ||14.18454 || 5.11949 || 5.14770
|-
|Total VdW's energy (kcal/mol)|| 12.80149|| 12.35877 || 13.63843 || 10.54000
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.01475 || 0.02183 || 0.01311 || 0.00053
|-
|Total torsional energy (kcal/mol)|| -2.73093 || -2.94949 || -1.46888 || -0.31691
|-
|Total stretch bending energy (kcal/mol)|| -2.04135 || -2.08221 || -2.10211 || -1.64420
|-
|Total angle bending energy (kcal/mol)|| 30.77274 || 33.18926 || 31.93395 || 24.80178
|-
|Total bond stretching energy (kcal/mol)|| 3.54304 || 3.46797 || 3.31167 || 2.81207
|}

After running the energy calculation of the 4 molecules listed above, 2 observations can be seen.
1. Total Energy of Molecule 1(Endo) is lower than the Total Energy of Molecule 2(Exo). Comparing different kinds of energies, it has been found that the main difference is due to the angle bending energy, 30.77274kcal/mol vs 33.18926kcal/mol.
2. Total Energy of Molecule 3 is higher than that of Molecule 4. The main difference is also due to angle bending energy, 31.93395kcal/mol vs 24.80178kcal/mol.

The rise of angle bending energy is because of the bond angles deviate from the natural occurring ones, such as 120° in sp<sup>2</sup> and 109.5° in sp<sup>3</sup>. By measuring the bond angles in the molecules, the deviations can be concluded in the Table 3. It is shown clearly that there is more Angle Deviation of Molecule 1 than that of Molecule 2; more Angle Deviation of Molecule 3 than Molecule 4.

{| class="wikitable" border="1"
|+ Table 3 Angles of Molecule 1 & 2
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 1)|| 114.9 (+5.4) ||110.5 (+1)|| 102.5 (-7)
|-
| Angle/Deviation (Molecule 2)|| 117.8 (+8.3)|| 113.0 (+3.5)|| 100.2 (-9.3)
|}

{| class="wikitable" border="1"
|+ Table 4 Angles of Molecule 3 & 4
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19/22,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 3)|| 118.8 (+9.3) ||111.7 (+2.2)|| 100.1 (-9.4)
|-
| Angle/Deviation (Molecule 4)|| 118.6 (+9.1)|| 110.5 (+1)|| 101.1 (-8.4)
|}

The reason that Endo form is the major product in experiment. The reason for this is due to the lower energy of Transition state of Endo form. Endo form has higher energy which mean it is more unstable. This Diels-Alder reaction is under kinetic control instead of thermodynamic control as the more unstable Endo form is the major product.

Molecule 3 & 4 are the production of hydrogenation from Molecule 2. The Total Energies of Molecule 3 & 4 are both lower than that of Molecule 2. It means the hydrogenation is favored.

=== Atropisomerism in an Intermediate related to the Synthesis of Taxol ===

[[Image:Molecule9-10jh.PNG]]

Molecule 9 and 10 <ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319;{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>are atropisomers and they give Molecule 9(saturated) and 10(saturated) after hydrogenation. Comparison can be done between the saturated form and unsaturated form of 9 and 10.

{| class="wikitable" border="1"
|+ Table 5 Structures of Molecules
! No. !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script> <uploadedFileContents>Molecule_9jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule_10jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule17_chair.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule10_saturatedjh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 6 Energies of Molecules
! Property !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Total energy (kcal/mol) || 70.54467 || 66.29108 || 81.75656 || 73.77833
|-
| Total electronic energy (kcal/mol)|| 0.30395 ||-0.06889 || 0.0000 || 0.0000
|-
|Total VdW's energy (kcal/mol)|| 33.11930|| 35.06832 || 32.71947 || 32.80239
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.97422 || 0.25399 || 70.54467 || 0.23332
|-
|Total torsional energy (kcal/mol)|| 0.31308 || 3.65335 || 9.47264 || 9.21881
|-
|Total stretch bending energy (kcal/mol)|| -0.08187 || 0.30222 || 0.30222 || 0.32484
|-
|Total angle bending energy (kcal/mol)|| 28.25720 || 32.05685 || 32.05685 || 24.29611
|-
|Total bond stretching energy (kcal/mol)|| 7.65878 || 6.95138 || 6.95138 || 6.90286
|}

{| class="wikitable" border="1"
|+ Table 7 Angles of Molecule 9 & 10
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C7,C3,C6 || H18,C11,C5|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 120
|-
| Angle/Deviation (Molecule 3)|| 118.5 (+9) ||107.9 (+1.6)|| 123.4 (-3.4)
|-
| Angle/Deviation (Molecule 4)|| 116.4 (+6.9)|| 108.8 (+0.7)|| 122.3 (-2.3)
|}

Same arguments here as of Molecule 1 to 4. Molecule 9 has higher energy than Molecule 10, among all types of energies, total angle bending energy contributes the most. It means the angles deviated more for Molecule 9, the details of deviations show in the table below.
Molecule 9 & 10(saturated) are the products of hydrogenation of Molecule 9 & 10 respectively. Olefin strain<ref>W. F. Maier, P. Von Rague Schleyer, J. Am. Chem. Soc., 1981, 103, 1891{{DOI|10.1021/ja00398a003}}</ref> energy should be taken into account in this case. Olefin strain is the difference between the strain energy of olefin and its saturated product. The strain energies of saturated molecules are higher than the unsaturated molcules. This is because olefins are locating in the brigehead of the molecules and as a result, the rate of hydrogenation from Molecule 9 & 10 to their saturated forms is low.

=== Derivative Molecules from Taxol ===

{| class="wikitable" border="1"
|+ Table 8 Structures of Molecules
! No. !! Molecule 17 boat!! Molecule 17 chair!! Molecule 18 boat!! Molecule 18 chair
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17twist_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 9 Energies of Molecules
! Property !! Molecule 17 boat!! Molecule 17 chair !! Molecule 18 boat!! Molecule 18 chair
|-
| Total energy (kcal/mol) || 114.33657 || 104.98391 || 102.28716 || 100.46235
|-
| Total electronic energy (kcal/mol)|| -7.05008 ||-7.22117 || -6.24215 || -6.05131
|-
|Total VdW's energy (kcal/mol)|| 54.37213|| 52.21497 || 50.49934 || 49.45308
|-
|Total out-of-plane bending energy (kcal/mol)|| 1.18784 || 1.02419 || 96.99088 || 0.90018
|-
|Total torsional energy (kcal/mol)|| 14.28618 || 10.98776 || 13.58885 || 9.76322
|-
|Total stretch bending energy (kcal/mol)|| 0.76536 || 0.31639 || 0.48412 || 0.63651
|-
|Total angle bending energy (kcal/mol)|| 35.01470 || 31.52244 || 28.54054 || 30.70962
|-
|Total bond stretching energy (kcal/mol)|| 15.89062 || 15.97568 || 14.39227 || 15.05105
|}

It can be concluded from Table 8 that Molecule 17 has higher energy than Molecule 18 and the chair forms have lower energy than the boat forms.

Table 10 shows the energies of Molecule 17 & 18 chair forms.

{| class="wikitable" border="1"
|+ Table 10 Energies of Molecule 17 & 18
! Property !! Molecule 17 chair!! Molecule 18 chair
|-
| Sum of electronic and thermal Energies (kJ/mol) || -1615.412 || -1651.417
|-
| Sum of electronic and thermal Energies (kJ/mol)|| -1615.390 ||-1651.396
|-
|Sum of electronic and thermal Enthalpies (kJ/mol)|| -1615.389|| -1651.395
|-
|Sum of electronic and thermal Energies (kJ/mol)|| -1615.459 || -1651.464
|}

{| class="wikitable" border="1"
|+ Table 11 <sup>1</sup>H and <sup>13</sup>C NMR for Molecule 17 & 18
! No. !! Molecule 17 NMR!! Molecule 18 NMR
|-
| Structure || [[Image:MOLECULE_17_NMRjh.PNG|500px]] || [[Image:MOLECULE_18_NMRjh.PNG|500px]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 17
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m17_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m17_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

{| class="wikitable" border="1"
|+ NMR Spectrum of Molecule 18
! No. !! <sup>1</sup>H NMR!! <sup>13</sup>C NMR
|-
| Spectrums || [[File:Nmr_m18_H.PNG|400px|left|thumb|<sup>1</sup>H NMR]] ||
[[File:Nmr_m18_C.PNG|400px|right|thumb|<sup>13</sup>C NMR]]
|}

For Table 11, the NMR data are calculated by first optimising energy by Avogadro then introduced to Gaussian. B3LYP/6-31G (d,p)basis, chloroform solvent are used.

By comparing <sup>1</sup>H NMR spectra, the computed chemical shifts are generally larger than the chemical shifts in literature<ref>S. W. Elmore and L. Paquette, Tetrahedron Letters, 1991, 319{{DOI|10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0 10.1016/S0040-4039(00)92617-0}}</ref>. The hydrogen atoms on the methyl group near carbonyl bond are more desheided. For <sup>13</sup>C NMR, the computed chemical shifts match the those in literature.

== Part 2 ==

=== Two Catalysts ===

Properties analysis of alkene epoxide

Two catalysts can be used to epoxide alkene: Shi <ref>O. A. Wong , B. Wang , M-X Zhao and Y. Shi J. Org. Chem., 2009, 74, 335–6338;{{DOI|10.1021/jo900739q}}</ref>and Jacobsen catalyst<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>.

[[Image:Two_catalysts.PNG]]

For Shi catalyst, the C-O bond length in the anomeric centre is different.

{| class="wikitable" border="1"
|+ Table 12Shi Catalyst
|-
| Structure || [[Image:Ocojhh.PNG]] || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>350</size><script>measure 10 16; measure 8 16; measure 1 2; measure 2 15; measure 3 4; measure 4 15</script><uploadedFileContents>OCOjhh.mol</uploadedFileContents>
</jmolApplet></jmol>|| [[Image:Ejh.PNG]]
|}

The C-O bond length in the Shi catalyst varies and differs from the ideal C-O single bond length: 1.43Å.
There are three O-C-O centres and the bond lengths are shown in the graph above.

The lone pair on oxygen can overlap with the anti-bonding orbital of C-O bond when the orientation is anti-periplanar: LP<sub>O</sub>/σ<sup>*</sup><sub>C-O</sub>. There are six pairs of overlap in total which are shown on the graph above.
The C-O bond will compress when its its oxygen donates lone pair; the C-O bond will extend when other oxygen donates lone pair. This can answer the question why the C-O bond is different within the same anomeric centre.

For Jacobsen catalyst, the structure can be depicted as square pyramid.

[[Image:Jacojh.PNG]]

<jmol><jmolApplet><title>ah</title><color>white</color>
<size>350</size><uploadedFileContents>TOVNIB01jh.mol</uploadedFileContents></jmolApplet></jmol>

For a 5-coordinated Mn, trigonal bipyramidal should be the ideal stucture. Here for Jacobsen catalyst, square plane pyramid is preferred due to the steric effect. The H atoms in the tBu group close to each other, the distances are shown in the graph which are slightly larger than the two times of the van der Waals radius of hydrogen: 2 x 1.20Å =2.40Å. These are attraction interaction which can stabilize the molecule.

=== Two alkenes ===

The following 2 alkenes can be oxidized to epoxide when treated with catalyst.

[[Image:Reaction schemejh.PNG]]

The epoxides of methyl styrene and stilbene have two forms: R,R and S,S. Here are the structures in 3D.

{| class="wikitable" border="1"
|+ Table 13 Structures of Molecules
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S!! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> 2rr.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> 2_ss.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Rrr_3.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Ss_3.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

The <sup>1</sup>H and <sup>13</sup>C NMR of tran-methyl styrene oxide and Stilbene oxide are listed below.
[[Image:NMR_of_H_alkene_2.PNG]][[Image:Nmr_1jh.PNG]]
[[Image:NMR_of_C_alkene_2.PNG]][[Image:Nmr2jh.PNG]]
[[Image:NMR_of_H_alkene_3.PNG]][[Image:Nmr3jh.PNG]]
[[Image:NMR_of_C_alkene_3.PNG]][[Image:Nmr4jh.PNG]]

The alkene that under epoxiation can remain the E/Z stereochemistry. However, the epoxiation has enantimochemistry and the result product of the epoxide can be assigned as R,R or S,S (epoxidation is syn-reaction). As a result, techniques can be used to determine the stereochemistry of the final product. There are three ways can be used to show which enantiomer resulted: Reaxys used to know the optical rotation value in literature, calculated chiroptical properties of the product and properties of transition state for the reaction.

==== The reported literature for optical rotations====
Literature from Reaxys, the optical rotation:

{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! methyl-Styrene oxide !! R,R !! S,S
|-
| Optical rotation || 44.3 deg <ref>Wong,O.Andrea;Wang,Bin ;Zhao,Mei-Xin and Shi,Yian,''Journal of Organic Chemistry'', '''2009''', ''74'', 6335-6338. {{DOI|10.1021/jo900739q}}</ref>
||-41.8 deg <ref>Lin,Hui;Liu,Yan;Wu,Zhong-Liu,''Tetrahedron:Asymmetry'', '''2011''', ''22'', 134-137.{{DOI|10.1016/j.tetasy.2010.12.022}}</ref>
|-
| Concentration || 0.32 g/100ml
|| 1g/100mL
|-
| Temperature|| 25°C
|| 25°C
|-
| Solvent || chloroform
|| chloroform
|-
| Wavelength || 589nm
||589nm
|}
{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! Siltbene oxide !! R,R !! S,S
|-
| Optical rotation || 296 deg <ref>Solladie-Cavallo, Arlette; Diep-Vohuule, Anh; Sunjic, Vitomir; Vinkovic, Vladimir
Tetrahedron: Asymmetry, 1996 , vol. 7, # 6 p. 1783 - 1788{{DOI|10.1016/0957-4166(96)00213-3}}</ref>
||-291 deg <ref>Read; Campbell Journal of the Chemical Society, 1930 , p. 2377 Nature (London, United Kingdom), 1930 , vol. 125, p. 16{{DOI|10.1039/jr9300002377}}</ref>
|-
| Concentration || 1.01 g/100ml
|| 0.6g/100mL
|-
| Temperature|| 22°C
|| 15°C
|-
| Solvent || ethanol
|| acetone
|-
| Wavelength || 589nm
||589nm
|}

==== The calculated chiroptical properties of the product ====

By comparing the values of the computed chiroptical properties and the values gained from the experiment or literature, the specified enantiomer of epoxides can be predicted. The three chiroptical properties are:
1. The optical rotation at specified range of wavelength.
2. The electronic circular dichroism (ECD)
3. The vibrational circular dichroism(VCD)<ref>M. J. Fuchter, Ya-Pei Lo and H. S. Rzepa, J. Org. Chem., 2013,</ref>

1.The QM-Optimized geometry is used and input into Cambridge variation on B3LYP density functional method. Polar(optrot) calculated the [alpha]<sub>D</sub> optical rotation components of the epoxides.
[alpha]D optical rotation at wavelength range 589nm has the following vaules:

Methyl-styrene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 46.78 deg and [Alpha] ( 5890.0 A) = -46.78 deg repectively.
Silbene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 297.68 deg[Alpha], and(5890.0 A) = -298.24 deg respectively.
Both of the optical rotation data roughly match the literature data.
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! methyl-Styrene !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation ||46.78 deg ||-46.78 deg || 44.3 deg ||-41.8 deg
|}
{| class="wikitable" border="1"
|+ Literature data and computed data comparison
! Siltbene oxide !! R,R (computed) !! S,S (computed)!! R,R (literature) !! S,S (literature)
|-
| Optical rotation || 297.68 deg ||-298.24 deg || 296 deg ||-291 deg
|}

2.The ECD is useless for epoxides as there are no chromophore these epoxides

3.The VCD spectrum of methyl-styrene and siltbene and their oxides are attached here:

{| class="wikitable" border="1"
|+ VCD Spectrum of methyl styrene oxide
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S
|-
| Structure || [[File:Vcd_specturm_rr2.PNG|400px|left|thumb|The methyl-styrene oxide R,R]]
||[[File:Vcd_spectrum_ss2.PNG|400px|right|thumb|The methyl-styrene oxide S,S]]
|}

{| class="wikitable" border="1"
|+ VCD Spectrum of Stilbene oxide
! No. !! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || [[File:Vcd_spectrum_rr3.PNG|400px|left|thumb|The Siltbene oxide R,R]] ||
[[File:Vcd_spectrum_ss3.PNG|400px|right|thumb|The Siltbene oxide S,S]]
|}

As it can be seen from the VCD Spectrum above, the pair of enantimoers have similar but opposite spectrum. Since the R,R and S,S conformers are mirror images to each other, the vibrations in VCD Spectrum is opposite as well. This technique can be used to assign the stereochemistry of the molecule but it is not available in Imperial College.

==== Using the (calculated) properties of transition state for the reaction ====
The enantiomeric excess and relative population of the two two conformers of a molecule can be calculated by the following method.

The following is the transition state energies of the reaction Jacobsen catalyst and trans-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! R,R<ref>{{DOI|10.6084/m9.figshare.856651}}</ref>!! S,S<ref>{{DOI|10042/25945}}</ref>
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.183068 || -3383.188478
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.141188 ||-3383.145943
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.140244|| -3383.144999
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.254344 || -3383.262481
|-
|Free energy Difference (Hartee)|| -0.008137 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -21.36367 ||''' '''
|-
|Equilibrium Constant K|| 5533.018 ||''' '''
|-
|Enantiomeric excess|| 99.98% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. R is ideal gas constant= 8.314J/mol*K<ref>http://physics.nist.gov/cgi-bin/cuu/Value?r</ref>. T is the temperature, room temperature 298.15K is used here.
Equilibrium constant K can be calculated: 5533.018. The S,S conformation is a in large excess. The enantiomeric excess of S,S conformation is 99.98%.

The following is the transition state energies of the reaction Jacobsen catalyst and cis-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! S,R!! R,S
|-
| Sum of electronic and zero-point Energies (Hartree) || -3383.185100 || -3383.177857
|-
| Sum of electronic and thermal Energies (Hartree)|| -3383.142495 ||-3383.135845
|-
|Sum of electronic and thermal Enthalpies (Hartree)|| -3383.141551|| -3383.134901
|-
|Sum of electronic and thermal Free Energies (Hartree)|| -3383.259559 || -3383.250270
|-
|Free energy Difference (Hartee)|| -0.009289 ||''' '''
|-
|Free energy Difference (kJ/mol)|| -24.388 ||''' '''
|-
|Equilibrium Constant K|| 18744.52 ||''' '''
|-
|Enantiomeric excess|| 99.99% ||''' '''
|}

ΔG=-RTlnK is the equation applied here. Equilibrium constant K can be calculated: 18744.52. The S,R conformation is a in large excess. The enantiomeric excess of S,R conformation is 99.99%.

=== Non covalent interaction analysis ===

[[Image:Jmoljh.gif‎]] [[Image:Jmol1jh.gif]]

This image is the Non covalent interaction electron cloud analysis of the transition state of tran-methyl styrene reacting with Jacobsen catalyst. Colour green in the graph means interaction and red means repulsion. As it is shown in the graph, the major colour is green. The alkene is reacting with the catalyst by maximizing the interaction. The red atom in the catalyst is bonding to the double bond of methyl styrene. From the orientation of the two reactants in the transition state, the product can be predicted to be S,S conformation.

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

== Reference ==
<references />

File:Jmol1jh.gif

2013-11-21T13:42:36Z

Jh4611:

File:Jmoljh.gif

2013-11-21T13:32:37Z

Jh4611:

2013-11-20T13:39:17Z

Jh4611: /* Derivative Molecules from Taxol */

==Part I==
===Hydrogenation of Cyclopentadiene Dimer===

The Diels-Alder Reaction of two Cyclopentadiene molecules can form two forms of dimers, one is Endo (Molecule 1) and the other is Exo (Molecule 2). Molecule 3 and 4 are the products after hydrogenation. The fact that Endo form is the major product of the reaction is concluded from experiments. The energy of Endo, Exo forms and their hydrogenated forms can be calculated by Avogadro programme using energy calculation method MMFF94s; the energies are listed in Table 2.

[[Image:1-4jhh.PNG]]
{| class="wikitable" border="1"
|+ Table 1 Structures of Molecules
! No. !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule1jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_2jh.mol</uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 19 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_3jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>220</size><script>measure 3 6 8;measure 22 8 6; measure 5 4 7</script><uploadedFileContents>Molecule_4jh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 2 Energies of Molecules
! Property !! Molecule 1(Endo)!! Molecule 2(Exo) !! Molecule 3 !! Molecule 4
|-
| Total energy (kcal/mol) || 55.37342 || 58.19067|| 50.44566 || 41.34098
|-
| Total electronic energy (kcal/mol)|| 13.01368 ||14.18454 || 5.11949 || 5.14770
|-
|Total VdW's energy (kcal/mol)|| 12.80149|| 12.35877 || 13.63843 || 10.54000
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.01475 || 0.02183 || 0.01311 || 0.00053
|-
|Total torsional energy (kcal/mol)|| -2.73093 || -2.94949 || -1.46888 || -0.31691
|-
|Total stretch bending energy (kcal/mol)|| -2.04135 || -2.08221 || -2.10211 || -1.64420
|-
|Total angle bending energy (kcal/mol)|| 30.77274 || 33.18926 || 31.93395 || 24.80178
|-
|Total bond stretching energy (kcal/mol)|| 3.54304 || 3.46797 || 3.31167 || 2.81207
|}

After running the energy calculation of the 4 molecules listed above, 2 observations can be seen.
1. Total Energy of Molecule 1(Endo) is lower than the Total Energy of Molecule 2(Exo). Comparing different kinds of energies, it has been found that the main difference is due to the angle bending energy, 30.77274kcal/mol vs 33.18926kcal/mol.
2. Total Energy of Molecule 3 is higher than that of Molecule 4. The main difference is also due to angle bending energy, 31.93395kcal/mol vs 24.80178kcal/mol.

The rise of angle bending energy is because of the bond angles deviate from the natural occurring ones, such as 120° in sp<sup>2</sup> and 109.5° in sp<sup>3</sup>. By measuring the bond angles in the molecules, the deviations can be concluded in the Table 3. It is shown clearly that there is more Angle Deviation of Molecule 1 than that of Molecule 2; more Angle Deviation of Molecule 3 than Molecule 4.

{| class="wikitable" border="1"
|+ Table 3 Angles of Molecule 1 & 2
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 1)|| 114.9 (+5.4) ||110.5 (+1)|| 102.5 (-7)
|-
| Angle/Deviation (Molecule 2)|| 117.8 (+8.3)|| 113.0 (+3.5)|| 100.2 (-9.3)
|}

{| class="wikitable" border="1"
|+ Table 4 Angles of Molecule 3 & 4
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C3,C6,C8 || H19/22,C8,C6|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 109.5
|-
| Angle/Deviation (Molecule 3)|| 118.8 (+9.3) ||111.7 (+2.2)|| 100.1 (-9.4)
|-
| Angle/Deviation (Molecule 4)|| 118.6 (+9.1)|| 110.5 (+1)|| 101.1 (-8.4)
|}

The reason that Endo form is the major product in experiment. The reason for this is due to the lower energy of Transition state of Endo form. Endo form has higher energy which mean it is more unstable. This Diels-Alder reaction is under kinetic control instead of thermodynamic control as the more unstable Endo form is the major product.

Molecule 3 & 4 are the production of hydrogenation from Molecule 2. The Total Energies of Molecule 3 & 4 are both lower than that of Molecule 2. It means the hydrogenation is favored.

=== Atropisomerism in an Intermediate related to the Synthesis of Taxol ===

[[Image:Molecule9-10jh.PNG]]

Molecule 9 and 10 are atropisomers and they give Molecule 9(saturated) and 10(saturated) after hydrogenation. Comparison can be done between the saturated form and unsaturated form of 9 and 10.

{| class="wikitable" border="1"
|+ Table 5 Structures of Molecules
! No. !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Structure || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script> <uploadedFileContents>Molecule_9jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule_10jh.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule17_chair.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>250</size><script>measure 7 3 6; measure 5 4 7; measure 5 11 35 </script><uploadedFileContents>Molecule10_saturatedjh.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 6 Energies of Molecules
! Property !! Molecule 9!! Molecule 10 !! Molecule 9 (saturated)!! Molecule 10 (saturated)
|-
| Total energy (kcal/mol) || 70.54467 || 66.29108 || 81.75656 || 73.77833
|-
| Total electronic energy (kcal/mol)|| 0.30395 ||-0.06889 || 0.0000 || 0.0000
|-
|Total VdW's energy (kcal/mol)|| 33.11930|| 35.06832 || 32.71947 || 32.80239
|-
|Total out-of-plane bending energy (kcal/mol)|| 0.97422 || 0.25399 || 70.54467 || 0.23332
|-
|Total torsional energy (kcal/mol)|| 0.31308 || 3.65335 || 9.47264 || 9.21881
|-
|Total stretch bending energy (kcal/mol)|| -0.08187 || 0.30222 || 0.30222 || 0.32484
|-
|Total angle bending energy (kcal/mol)|| 28.25720 || 32.05685 || 32.05685 || 24.29611
|-
|Total bond stretching energy (kcal/mol)|| 7.65878 || 6.95138 || 6.95138 || 6.90286
|}

{| class="wikitable" border="1"
|+ Table 7 Angles of Molecule 9 & 10
! Property !! Angle 1!! Angle 2 !! Angle 3
|-
| Atoms involved || C7,C3,C6 || H18,C11,C5|| C5,C4,C7
|-
| Natural occurring|| 109.5|| 109.5 || 120
|-
| Angle/Deviation (Molecule 3)|| 118.5 (+9) ||107.9 (+1.6)|| 123.4 (-3.4)
|-
| Angle/Deviation (Molecule 4)|| 116.4 (+6.9)|| 108.8 (+0.7)|| 122.3 (-2.3)
|}

Same arguments here as of Molecule 1 to 4. Molecule 9 has higher energy than Molecule 10, among all types of energies, total angle bending energy contributes the most. It means the angles deviated more for Molecule 9, the details of deviations show in the table below.
Molecule 9 & 10(saturated) are the products of hydrogenation of Molecule 9 & 10 respectively. Olefin strain energy should be taken into account in this case. Olefin strain is the difference between the strain energy of olefin and its saturated product. The strain energies of saturated molecules are higher than the unsaturated molcules. This is because olefins are locating in the brigehead of the molecules and as a result, the rate of hydrogenation from Molecule 9 & 10 to their saturated forms is low.

=== Derivative Molecules from Taxol ===

{| class="wikitable" border="1"
|+ Table 8 Structures of Molecules
! No. !! Molecule 17 boat!! Molecule 17 chair!! Molecule 18 boat!! Molecule 18 chair
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17twist_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule17chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_boatjh.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Molecule_18_chair_form.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

{| class="wikitable" border="1"
|+ Table 9 Energies of Molecules
! Property !! Molecule 17 boat!! Molecule 17 chair !! Molecule 18 boat!! Molecule 18 chair
|-
| Total energy (kcal/mol) || 114.33657 || 104.98391 || 102.28716 || 100.46235
|-
| Total electronic energy (kcal/mol)|| -7.05008 ||-7.22117 || -6.24215 || -6.05131
|-
|Total VdW's energy (kcal/mol)|| 54.37213|| 52.21497 || 50.49934 || 49.45308
|-
|Total out-of-plane bending energy (kcal/mol)|| 1.18784 || 1.02419 || 96.99088 || 0.90018
|-
|Total torsional energy (kcal/mol)|| 14.28618 || 10.98776 || 13.58885 || 9.76322
|-
|Total stretch bending energy (kcal/mol)|| 0.76536 || 0.31639 || 0.48412 || 0.63651
|-
|Total angle bending energy (kcal/mol)|| 35.01470 || 31.52244 || 28.54054 || 30.70962
|-
|Total bond stretching energy (kcal/mol)|| 15.89062 || 15.97568 || 14.39227 || 15.05105
|}

It can be concluded from Table 8 that Molecule 17 has higher energy than Molecule 18 and the chair forms have lower energy than the boat forms.

Table 10 shows the energies of Molecule 17 & 18 chair forms.

{| class="wikitable" border="1"
|+ Table 10 Energies of Molecule 17 & 18
! Property !! Molecule 17 chair!! Molecule 18 chair
|-
| Sum of electronic and thermal Energies (kJ/mol) || -1615.412 || -1651.417
|-
| Sum of electronic and thermal Energies (kJ/mol)|| -1615.390 ||-1651.396
|-
|Sum of electronic and thermal Enthalpies (kJ/mol)|| -1615.389|| -1651.395
|-
|Sum of electronic and thermal Energies (kJ/mol)|| -1615.459 || -1651.464
|}

{| class="wikitable" border="1"
|+ Table 11 <sup>1</sup>H and <sup>13</sup>C NMR for Molecule 17 & 18
! No. !! Molecule 17 NMR!! Molecule 18 NMR
|-
| Structure || [[Image:MOLECULE_17_NMRjh.PNG|500px]] || [[Image:MOLECULE_18_NMRjh.PNG|500px]]
|}

Nmr_m17_H.PNG
Nmr_m17_C.PNG
Nmr_m18_H.PNG
Nmr_m18_C.PNG

For Table 11, the NMR data are calculated by first optimising energy by Avogadro then introduced to Gaussian. B3LYP/6-31G (d,p)basis, chloroform solvent are used.

By comparing <sup>1</sup>H NMR spectra, the computed chemical shifts are generally larger than the chemical shifts in literature. The hydrogen atoms on the methyl group near carbonyl bond are more desheided. For <sup>13</sup>C NMR, the computed chemical shifts match the those in literature.

== Part 2 ==

=== Two Catalysts ===

Properties analysis of alkene epoxide

Two catalysts can be used to epoxide alkene: Shi and Jacobsen catalyst.

[[Image:Two_catalysts.PNG]]

For Shi catalyst, the C-O bond length in the anomeric centre is different.

{| class="wikitable" border="1"
|+ Table 12Shi Catalyst
|-
| Structure || [[Image:Ocojhh.PNG]] || <jmol><jmolApplet><title>ah_test</title><color>white</color>
<size>350</size><script>measure 10 16; measure 8 16; measure 1 2; measure 2 15; measure 3 4; measure 4 15</script><uploadedFileContents>OCOjhh.mol</uploadedFileContents>
</jmolApplet></jmol>|| [[Image:Ejh.PNG]]
|}

The C-O bond length in the Shi catalyst varies and differs from the ideal C-O single bond length: 1.43Å.
There are three O-C-O centres and the bond lengths are shown in the graph above.

The lone pair on oxygen can overlap with the anti-bonding orbital of C-O bond when the orientation is anti-periplanar: LP<sub>O</sub>/σ<sup>*</sup><sub>C-O</sub>. There are six pairs of overlap in total which are shown on the graph above.
The C-O bond will compress when its its oxygen donates lone pair; the C-O bond will extend when other oxygen donates lone pair. This can answer the question why the C-O bond is different within the same anomeric centre.

For Jacobsen catalyst, the structure can be depicted as square pyramid.

[[Image:Jacojh.PNG]]

<jmol><jmolApplet><title>ah</title><color>white</color>
<size>350</size><uploadedFileContents>TOVNIB01jh.mol</uploadedFileContents></jmolApplet></jmol>

For a 5-coordinated Mn, trigonal bipyramidal should be the ideal stucture. Here for Jacobsen catalyst, square plane pyramid is preferred due to the steric effect. The H atoms in the tBu group close to each other, the distances are shown in the graph which are slightly larger than the two times of the van der Waals radius of hydrogen: 2 x 1.20Å =2.40Å. These are attraction interaction which can stabilize the molecule.

=== Two alkenes ===

The following 2 alkenes can be oxidized to epoxide when treated with catalyst.

[[Image:Reaction schemejh.PNG]]

The epoxides of methyl styrene and stilbene have two forms: R,R and S,S. Here are the structures in 3D.

{| class="wikitable" border="1"
|+ Table 13 Structures of Molecules
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S!! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || <jmol><jmolApplet><title>a</title><color>white</color>
<size>220</size><uploadedFileContents> 2rr.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>b</title><color>white</color>
<size>220</size><uploadedFileContents> 2_ss.mol </uploadedFileContents>
</jmolApplet></jmol>|| <jmol><jmolApplet><title>c</title><color>white</color>
<size>220</size><uploadedFileContents> Rrr_3.mol </uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>d</title><color>white</color>
<size>220</size><uploadedFileContents> Ss_3.mol </uploadedFileContents>
</jmolApplet></jmol>
|}

The <sup>1</sup>H and <sup>13</sup>C NMR of tran-methyl styrene oxide and Stilbene oxide are listed below.
[[Image:NMR_of_H_alkene_2.PNG]][[Image:Nmr_1jh.PNG]]
[[Image:NMR_of_C_alkene_2.PNG]][[Image:Nmr2jh.PNG]]
[[Image:NMR_of_H_alkene_3.PNG]][[Image:Nmr3jh.PNG]]
[[Image:NMR_of_C_alkene_3.PNG]][[Image:Nmr4jh.PNG]]

The alkene that under epoxiation can remain the E/Z stereochemistry. However, the epoxiation has enantimochemistry and the result product of the epoxide can be assigned as R,R or S,S (epoxidation is syn-reaction). As a result, techniques can be used to determine the stereochemistry of the final product. There are three ways can be used to show which enantiomer resulted: Reaxys used to know the optical rotation value in literature, calculated chiroptical properties of the product and properties of transition state for the reaction.

==== The reported literature for optical rotations====
Literature from Reaxys, the optical rotation:

{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! methyl-Styrene oxide !! R,R !! S,S
|-
| Optical rotation || 296 deg
||-278nm
|-
| Concentration || 1.01 g/100ml
|| 0.6g/100mL
|-
| Temperature|| 22°C
|| 20°C
|-
| Solvent || ethanol
|| ethanol
|-
| Wavelength || 589nm
||589nm
|}

{| class="wikitable" border="1"
|+ Literature data for optical rotation of epoxides
! Siltbene oxide !! R,R !! S,S
|-
| Optical rotation || 296 deg
||-278nm
|-
| Concentration || 1.01 g/100ml
|| 0.6g/100mL
|-
| Temperature|| 22°C
|| 20°C
|-
| Solvent || ethanol
|| ethanol
|-
| Wavelength || 589nm
||589nm
|}

R,R Solladie-Cavallo, Arlette; Diep-Vohuule, Anh; Sunjic, Vitomir; Vinkovic, Vladimir
Tetrahedron: Asymmetry, 1996 , vol. 7, # 6 p. 1783 - 1788
S,S Capriati, Vito; Florio, Saverio; Luisi, Renzo; Perna, Filippo Maria; Salomone, Antonio; Gasparrini, Francesco
Organic Letters, 2005 , vol. 7, # 22 p. 4895 - 4898

==== The calculated chiroptical properties of the product ====

By comparing the values of the computed chiroptical properties and the values gained from the experiment or literature, the specified enantiomer of epoxides can be predicted. The three chiroptical properties are:
1. The optical rotation at specified range of wavelength.
2. The electronic circular dichroism (ECD)
3. The vibrational circular dichroism(VCD)

1.The QM-Optimized geometry is used and input into Cambridge variation on B3LYP density functional method. Polar(optrot) calculated the [alpha]<sub>D</sub> optical rotation components of the epoxides.
[alpha]D optical rotation at wavelength range 589nm has the following vaules:

Methyl-styrene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 46.78 deg and [Alpha] ( 5890.0 A) = -46.78 deg repectively.
Silbene oxide, R,R & S,S structures have optical rotation: [Alpha] ( 5890.0 A) = 297.68 deg[Alpha], and(5890.0 A) = -298.24 deg respectively.

2.The ECD is useless for epoxides as there are no chromophore in epoxides

3.The VCD spectrum of methyl-styrene and siltbene and their oxides are attached here:

{| class="wikitable" border="1"
|+ VCD Spectrum of methyl styrene oxide
! No. !! methyl styrene oxide R,R !! methyl styrene oxide S,S
|-
| Structure || [[File:Vcd_specturm_rr2.PNG|400px|left|thumb|The methyl-styrene oxide R,R]]
||[[File:Vcd_spectrum_ss2.PNG|400px|right|thumb|The methyl-styrene oxide S,S]]
|}

{| class="wikitable" border="1"
|+ VCD Spectrum of Stilbene oxide
! No. !! Stilbene oxide R,R!! Stilbene oxide S,S
|-
| Structure || [[File:Vcd_spectrum_rr3.PNG|400px|left|thumb|The Siltbene oxide R,R]] ||
[[File:Vcd_spectrum_ss3.PNG|400px|right|thumb|The Siltbene oxide S,S]]
|}

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

The following is the transition state energies of the reaction Jacobsen catalyst and trans-methyl styrene.

{| class="wikitable" border="1"
|+ TS Energies of trans-methyl styrene when treated with Jacobsen catalyst
! enantimoers !! R,R!! S,S
|-
| Sum of electronic and zero-point Energies (kJ/mol) || -3383.183068 || -3383.188478
|-
| Sum of electronic and thermal Energies (kJ/mol)|| -3383.141188 ||-3383.145943
|-
|Sum of electronic and thermal Enthalpies (kJ/mol)|| -3383.140244|| -3383.144999
|-
|Sum of electronic and thermal Free Energies (kJ/mol)|| -3383.254344 || -3383.262481
|}

ΔG=-RTlnK is the equation applied here. ΔG is the difference of the free energy: (-3383.254344+3383.262481= -0.008137kJ/mol)
R is ideal gas constant= 8.314J/mol*K. T is the temperature, room temperature 298.15K is used here.
Equilibrium constant K can be calculated: 1.003288. The S,S conformation is a slight excess.

File:Nmr m18 H.PNG

2013-11-20T13:38:18Z

Jh4611:

File:Nmr m18 C.PNG

2013-11-20T13:38:17Z

Jh4611:

File:Nmr m17 H.PNG

2013-11-20T13:38:17Z

Jh4611:

2013-11-19T21:07:54Z

Jh4611: