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Rep:Mod:NBC1C

2013-11-22T17:54:24Z

Bn711: /* Atropisomerism in an Intermediate related to the Synthesis of Taxol */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

There are other isomers present, for example, the twist boat structures. However, they're less stable because of higher energies.

{| class="wikitable" border="1"
|+
!Structure
|| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9TWSITCHAIR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Total Energy /kcal/mol
||76.46449|| 63.93652
|}

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

β-methyl styrene and trans-stilbene are chosen for this section and their epoxides products are analyzed. By comparing the calculated NMR data with literature values, the calculated values are indicated to be reasonable.

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

The following molecule is suggested for further investigation. It is know that D-pulegone is commercially available on Sigma-Aldrich, more details can be found [http://www.sigmaaldrich.com/catalog/product/aldrich/w296309?lang=en&region=GB here]

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

{| class="wikitable" border="1"
|+ Epoxide
!!!(R)Pulegone Oxide!!(S)Pulegone Oxide
|-
! Structure
|| [[Image:Bn711newcanEp.jpg|thumb|200px]]||[[Image:Bn711newcanEpo.jpg|thumb|200px]]
|-
!Optical Rotation Literature, Solvent: Ethanol
||786.5 (293 nm)<ref name="lastref">W. Reusch, C. K. Johnson, '' J. Org. Chem.'', '''1963''', ''28'', 2557-2560. {{DOI|10.1021/jo01045a016}}</ref>||-1177.9 (327 nm)<ref name="lastref"></ref>
|}

Literature value is listed above for future reference.

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T17:50:04Z

Bn711: /* Atropisomerism in an Intermediate related to the Synthesis of Taxol */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

There are other isomers present, for example, the twist boat structures. However, they're less stable because of higher energies.

{| class="wikitable" border="1"
|+
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9TWSITCHAIR.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

β-methyl styrene and trans-stilbene are chosen for this section and their epoxides products are analyzed. By comparing the calculated NMR data with literature values, the calculated values are indicated to be reasonable.

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

The following molecule is suggested for further investigation. It is know that D-pulegone is commercially available on Sigma-Aldrich, more details can be found [http://www.sigmaaldrich.com/catalog/product/aldrich/w296309?lang=en&region=GB here]

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

{| class="wikitable" border="1"
|+ Epoxide
!!!(R)Pulegone Oxide!!(S)Pulegone Oxide
|-
! Structure
|| [[Image:Bn711newcanEp.jpg|thumb|200px]]||[[Image:Bn711newcanEpo.jpg|thumb|200px]]
|-
!Optical Rotation Literature, Solvent: Ethanol
||786.5 (293 nm)<ref name="lastref">W. Reusch, C. K. Johnson, '' J. Org. Chem.'', '''1963''', ''28'', 2557-2560. {{DOI|10.1021/jo01045a016}}</ref>||-1177.9 (327 nm)<ref name="lastref"></ref>
|}

Literature value is listed above for future reference.

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T17:46:41Z

Bn711: /* Atropisomerism in an Intermediate related to the Synthesis of Taxol */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

There are other isomers present, for example, the twist boat structure. However, it is less stable because of a higher energy.

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9TWSITCHAIR.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

β-methyl styrene and trans-stilbene are chosen for this section and their epoxides products are analyzed. By comparing the calculated NMR data with literature values, the calculated values are indicated to be reasonable.

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

The following molecule is suggested for further investigation. It is know that D-pulegone is commercially available on Sigma-Aldrich, more details can be found [http://www.sigmaaldrich.com/catalog/product/aldrich/w296309?lang=en&region=GB here]

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

{| class="wikitable" border="1"
|+ Epoxide
!!!(R)Pulegone Oxide!!(S)Pulegone Oxide
|-
! Structure
|| [[Image:Bn711newcanEp.jpg|thumb|200px]]||[[Image:Bn711newcanEpo.jpg|thumb|200px]]
|-
!Optical Rotation Literature, Solvent: Ethanol
||786.5 (293 nm)<ref name="lastref">W. Reusch, C. K. Johnson, '' J. Org. Chem.'', '''1963''', ''28'', 2557-2560. {{DOI|10.1021/jo01045a016}}</ref>||-1177.9 (327 nm)<ref name="lastref"></ref>
|}

Literature value is listed above for future reference.

==References==

<references/>

File:Bn711Taxol9TWSITCHAIR.mol

2013-11-22T17:43:41Z

Bn711:

Rep:Mod:NBC1C

2013-11-22T17:20:05Z

Bn711: /* Atropisomerism in an Intermediate related to the Synthesis of Taxol */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

There are other isomers present, for example, the twist boat structure. However, it is less stable because of a higher energy.

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

β-methyl styrene and trans-stilbene are chosen for this section and their epoxides products are analyzed. By comparing the calculated NMR data with literature values, the calculated values are indicated to be reasonable.

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

The following molecule is suggested for further investigation. It is know that D-pulegone is commercially available on Sigma-Aldrich, more details can be found [http://www.sigmaaldrich.com/catalog/product/aldrich/w296309?lang=en&region=GB here]

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

{| class="wikitable" border="1"
|+ Epoxide
!!!(R)Pulegone Oxide!!(S)Pulegone Oxide
|-
! Structure
|| [[Image:Bn711newcanEp.jpg|thumb|200px]]||[[Image:Bn711newcanEpo.jpg|thumb|200px]]
|-
!Optical Rotation Literature, Solvent: Ethanol
||786.5 (293 nm)<ref name="lastref">W. Reusch, C. K. Johnson, '' J. Org. Chem.'', '''1963''', ''28'', 2557-2560. {{DOI|10.1021/jo01045a016}}</ref>||-1177.9 (327 nm)<ref name="lastref"></ref>
|}

Literature value is listed above for future reference.

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T17:14:30Z

Bn711: /* NMR properties of products */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

β-methyl styrene and trans-stilbene are chosen for this section and their epoxides products are analyzed. By comparing the calculated NMR data with literature values, the calculated values are indicated to be reasonable.

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

The following molecule is suggested for further investigation. It is know that D-pulegone is commercially available on Sigma-Aldrich, more details can be found [http://www.sigmaaldrich.com/catalog/product/aldrich/w296309?lang=en&region=GB here]

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

{| class="wikitable" border="1"
|+ Epoxide
!!!(R)Pulegone Oxide!!(S)Pulegone Oxide
|-
! Structure
|| [[Image:Bn711newcanEp.jpg|thumb|200px]]||[[Image:Bn711newcanEpo.jpg|thumb|200px]]
|-
!Optical Rotation Literature, Solvent: Ethanol
||786.5 (293 nm)<ref name="lastref">W. Reusch, C. K. Johnson, '' J. Org. Chem.'', '''1963''', ''28'', 2557-2560. {{DOI|10.1021/jo01045a016}}</ref>||-1177.9 (327 nm)<ref name="lastref"></ref>
|}

Literature value is listed above for future reference.

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T17:04:22Z

Bn711: /* NMR properties of products */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

The following molecule is suggested for further investigation. It is know that D-pulegone is commercially available on Sigma-Aldrich, more details can be found [http://www.sigmaaldrich.com/catalog/product/aldrich/w296309?lang=en&region=GB here]

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

{| class="wikitable" border="1"
|+ Epoxide
!!!(R)Pulegone Oxide!!(S)Pulegone Oxide
|-
! Structure
|| [[Image:Bn711newcanEp.jpg|thumb|200px]]||[[Image:Bn711newcanEpo.jpg|thumb|200px]]
|-
!Optical Rotation Literature, Solvent: Ethanol
||786.5 (293 nm)<ref name="lastref">W. Reusch, C. K. Johnson, '' J. Org. Chem.'', '''1963''', ''28'', 2557-2560. {{DOI|10.1021/jo01045a016}}</ref>||-1177.9 (327 nm)<ref name="lastref"></ref>
|}

Literature value is listed above for future reference.

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T16:43:07Z

Bn711: /* New Candidate */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

The following molecule is suggested for further investigation. It is know that D-pulegone is commercially available on Sigma-Aldrich, more details can be found [http://www.sigmaaldrich.com/catalog/product/aldrich/w296309?lang=en&region=GB here]

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

{| class="wikitable" border="1"
|+ Epoxide
!!!(R)Pulegone Oxide!!(S)Pulegone Oxide
|-
! Structure
|| [[Image:Bn711newcanEp.jpg|thumb|200px]]||[[Image:Bn711newcanEpo.jpg|thumb|200px]]
|-
!Optical Rotation Literature, Solvent: Ethanol
||786.5 (293 nm)<ref name="lastref">W. Reusch, C. K. Johnson, '' J. Org. Chem.'', '''1963''', ''28'', 2557-2560. {{DOI|10.1021/jo01045a016}}</ref>||-1177.9 (327 nm)<ref name="lastref"></ref>
|}

Literature value is listed above for future reference.

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T16:42:29Z

Bn711: /* New Candidate */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

The following molecule is suggest for further investigation. It is know that D-pulegone is commercially available on Sigma-Aldrich, more details can be found [http://www.sigmaaldrich.com/catalog/product/aldrich/w296309?lang=en&region=GB here]

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

{| class="wikitable" border="1"
|+ Epoxide
!!!(R)Pulegone Oxide!!(S)Pulegone Oxide
|-
! Structure
|| [[Image:Bn711newcanEp.jpg|thumb|200px]]||[[Image:Bn711newcanEpo.jpg|thumb|200px]]
|-
!Optical Rotation Literature, Solvent: Ethanol
||786.5 (293 nm)<ref name="lastref">W. Reusch, C. K. Johnson, '' J. Org. Chem.'', '''1963''', ''28'', 2557-2560. {{DOI|10.1021/jo01045a016}}</ref>||-1177.9 (327 nm)<ref name="lastref"></ref>
|}

Literature value is listed above for future reference.

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T16:31:51Z

Bn711: /* New Candidate */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

{| class="wikitable" border="1"
|+ Epoxide
!(R)Pulegone Oxide!!(S)Pulegone Oxide
|-
! Structure
|| [[Image:Bn711newcanEp.jpg|thumb|200px]]||[[Image:Bn711newcanEpo.jpg|thumb|200px]]
|-
!Optical Rotation Literature, Solvent: Ethanol
||786.5 (293 nm)||-1177.9 (327 nm)
|}

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

327 nm ethanol 25 °C

------------------------------

==References==

<references/>

File:Bn711newcanEpo.jpg

2013-11-22T16:28:56Z

Bn711:

File:Bn711newcanEp.jpg

2013-11-22T16:28:56Z

Bn711:

Rep:Mod:NBC1C

2013-11-22T16:26:15Z

Bn711: /* New Candidate */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

{| class="wikitable" border="1"
|+ New Candidate
!Name
||D-pulegone
|-
! Structure
|| [[Image:Bn711newcan.jpg|thumb|200px]]
|-
! Reaxys Registry Number
|| 3588094
|-
! CAS Registry Number
|| 89-82-7
|}

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

File:Bn711newcan.jpg

2013-11-22T16:16:40Z

Bn711: uploaded a new version of "File:Bn711newcan.jpg"

File:Bn711newcan.jpg

2013-11-22T15:47:46Z

Bn711:

Rep:Mod:NBC1C

2013-11-22T15:27:05Z

Bn711: /* QTAIM */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|450px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

Arrow 3 in the graph indicates a BCP (bond critical point). There are other types of critical points in the diagram, but they're not considered in this experiment. Arrow 1 indicates a weak non-covalent BCP, which is associated with weak interaction between oxygen and hydrogen. Electronic topology (QTAIM) confirms the suggestion from previous section, because there are two BCP (arrow 1 and 2) associate with the pink oxygen atom.

-----------------------------------

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

File:Bn711QTAIM.PNG

2013-11-22T15:16:41Z

Bn711: uploaded a new version of "File:Bn711QTAIM.PNG"

Rep:Mod:NBC1C

2013-11-22T15:07:07Z

Bn711: /* Investigating the non-covalent interactions in the active-site of the reaction transition state */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between the oxygen atom (in colour pink) of active catalyst and substrate molecule, indicating a strong interaction between them, which is a origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T14:57:48Z

Bn711: /* Investigating the non-covalent interactions in the active-site of the reaction transition state */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

(R,R)trans-β-methyl styrene transition state (Shi catalyst, group 4) is used for non-covalent interactions (NCI) analysis, giving the following result.

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=2,atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between two oxygen atoms (in colour pink) of active catalyst and substrate, indicating a strong interaction between them, which is the origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T14:52:34Z

Bn711: /* Investigating the non-covalent interactions in the active-site of the reaction transition state */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>select atomno=2,atomno=4; color pink; isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

Colours in the diagram represent the attractiveness of the interaction, blue is very attractive, green is mildly attractive, yellow is mildly repulsive and red is strongly repulsive. There are large green areas between two oxygen atoms (in colour pink) of active catalyst and substrate, indicating a strong interaction between them, which is the origin of stereoselectivity.

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T14:18:56Z

Bn711: /* The two catalytic systems */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4">E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T14:17:33Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4"></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T14:10:59Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%<ref name="ref4></ref>.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

The vibrational circular dichroism (VCD)of each diastereomer is calculated using GaussView. Results is shown in the table below.
{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

It's easy to notice that results for VCD of diastereomers are completely opposite to each other, this is because diastereomers are mirror image to each other. The electronic circular dichroism (ECD) is not practical in this experiment because there's no chromophore in the molecule.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T13:49:48Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | Trans-β-methyl Styrene Epoxide (Group 4 Data)
|-
! R,R ||S,S
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (R,R)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! S,R ||R,S || S,S ||R,R
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (S,R)
|colspan="2" style="text-align: center;" |99.98% (S,S)
|}

It can be seen from the tables that, for trans-β-methyl styrene, (R,R)trans-β-methyl styrene epoxide will be synthesized when Shi catalyst is used, with an enantiomeric excess of 99.94%. However, when Jacobsen catalyst is used, the dominate product will be (S,S)trans-β-methyl styrene epoxide, with an enantiomeric excess of 99.98%. This difference is caused by the stereoselectivity difference of the two catalysts. For (S,R)cis-β-methyl styrene, calculated value of enantiomeric excess is 99.98%, which is a reasonable result compared to literature value of 92%.

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T12:55:22Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculations are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | β-methyl Styrene Epoxide (Group 4 Data)
|-
! RR ||SS
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (RR)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! SR ||RS || SS ||RR
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (SR)
|colspan="2" style="text-align: center;" |99.98% (SS)
|}

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-22T11:28:08Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculation are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | β-methyl Styrene Epoxide (Group 4 Data)
|-
! RR ||SS
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (RR)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! SR ||RS || SS ||RR
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (SR)
|colspan="2" style="text-align: center;" |99.98% (SS)
|}

By comparing transition states in different energies, it is discovered that the most stable form of transition state is the one with the best "overlap" between alkene and the catalyst. For example, (R,R)β-methyl styrene epoxide (group 4) is more table than that of group 2 because the benzene ring has a better "overlap" with Shi catalyst.

{| class="wikitable" border="1"
|+ Example: (R,R)β-methyl Styrene Epoxide
! !!Group 4 !! Group 3
|-
!Structure
|| [[Image:Bn711stable.PNG|thumb|250px]] ||[[Image:Bn711less_stable.PNG|thumb|250px]]
|-
!Relative Energy kJ/mol
|style="text-align: center;" | 0
|style="text-align: center;" |8.3254605
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

File:Bn711less stable.PNG

2013-11-22T11:06:21Z

Bn711:

File:Bn711stable.PNG

2013-11-22T11:06:20Z

Bn711:

Rep:Mod:NBC1C

2013-11-22T10:47:19Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

Free energy difference between two diastereomeric transition states is calculated by using data from the most stable group of transition states. K is then calculated using the equation, <math>K=e^{-\frac{\Delta G}{RT}}</math>. Summaries of calculation are shown in the tables below.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | β-methyl Styrene Epoxide (Group 4 Data)
|-
! RR ||SS
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (RR)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! SR ||RS || SS ||RR
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (SR)
|colspan="2" style="text-align: center;" |99.98% (SS)
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T21:37:47Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

<math>K=e^{-\frac{\Delta G}{RT}}</math> <br/>

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | β-methyl Styrene Epoxide (Group 4 Data)
|-
! RR ||SS
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94% (RR)
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! SR ||RS || SS ||RR
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98% (SR)
|colspan="2" style="text-align: center;" |99.98% (SS)
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T21:36:33Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

<math>K=e^{-\frac{\Delta G}{RT}}</math> <br/>

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | β-methyl Styrene Epoxide (Group 4 Data)
|-
! RR ||SS
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Population
||99.97%||0.03%
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.94%
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl Styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 1 Data)
|-
! SR ||RS || SS ||RR
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Population
||99.99%||0.01%||99.99%||0.01%
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.98%
|colspan="2" style="text-align: center;" |99.98%
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T21:05:31Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | β-methyl Styrene Epoxide (Group 4 Data)
|-
! RR ||SS
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.97%
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 2 Data)
|-
! SR ||RS || SS ||RR
|-
!Free Energy /Hartree
||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS, SS-RR) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.99%
|colspan="2" style="text-align: center;" |99.99%
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide !! Trans-Stilbene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T21:04:16Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | β-methyl Styrene Epoxide (Group 4 Data)
|-
! RR ||SS
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.97%
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Cis-β-methyl styrene (Group 1 Data)
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 2 Data)
|-
! SR ||RS || SS ||RR
|-
!Free Energy /Hartree ||-3383.259559|| -3383.251060||-3383.262481|| -3383.253816
|-
!Free Energy Difference (SR-RS) /kJ/mol
|colspan="2" style="text-align: center;" | -22.3141245
|colspan="2" style="text-align: center;" | -22.7499575
|-
!K
|colspan="2" style="text-align: center;" |8118.494422
|colspan="2" style="text-align: center;" |9679.254069
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.99%
|colspan="2" style="text-align: center;" |99.99%
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide !! Trans-Stilbene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T20:40:39Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

{|class="wikitable" border="1"
|+ Shi Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" | β-methyl Styrene Epoxide (Group 4 Data)
|-
! RR ||SS
|-
!Free Energy /Hartree
||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.97%
|}

{|class="wikitable" border="1"
|+ Jacobsen Epoxidation
! rowspan="2" |
! colspan="2" style="text-align: center;" |Trans-β-methyl Styrene (Group 2)
|-
! RR ||SS || RR ||SS
|-
!Free Energy /Hartree ||-1343.032443|| -1343.024742||-1343.032443|| -1343.024742
|-
!Free Energy Difference (RR-SS) /kJ/mol
|colspan="2" style="text-align: center;" | -20.2189755
|colspan="2" style="text-align: center;" | -20.2189755
|-
!K
|colspan="2" style="text-align: center;" |3596.649285
|colspan="2" style="text-align: center;" |3596.649285
|-
!Enantiomeric Excess
|colspan="2" style="text-align: center;" |99.97%
|colspan="2" style="text-align: center;" |99.97%
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide !! Trans-Stilbene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T20:20:30Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

2478.8191

{| class="wikitable" border="1"
|+ caption
! !! trans-β-methyl styrene!!heading
|-
!Free Energy /Hartree ||-1343.032443|| -1343.024742
|-
!Free Energy Difference(RR-SS) /kJ/mol || -20.2189755
|-
!K
||3596.649285
|-
!Enantiomeric Excess
||99.97%
|}

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide !! Trans-Stilbene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T17:33:21Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! β-methyl Styrene Epoxide !! Trans-Stilbene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|400px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|400px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|400px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|400px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T17:20:48Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

{| class="wikitable" border="1"
|+ VCD Spectrum
!!! β-methyl Styrene Epoxide !! Trans-Stilbene Epoxide
|-
! SS
||[[Image:Bn711SSmethyl_styrene_epoxideVCD.svg|thumb|300px]]||[[Image:Bn711SSTransStilbene_oxideVCD.svg|thumb|300px]]
|-
! RR
|| [[Image:Bn711RRmethyl_styrene_epoxide_VCD.svg|thumb|300px]]||[[Image:Bn711RRTransStilbene_oxideVCD.svg|thumb|300px]]
|}

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

File:Bn711SSTransStilbene oxideVCD.svg

2013-11-21T17:06:15Z

Bn711:

File:Bn711SSmethyl styrene epoxideVCD.svg

2013-11-21T17:06:14Z

Bn711:

File:Bn711RRTransStilbene oxideVCD.svg

2013-11-21T17:06:14Z

Bn711:

File:Bn711RRmethyl styrene epoxide VCD.svg

2013-11-21T17:06:13Z

Bn711:

Rep:Mod:NBC1C

2013-11-21T16:51:43Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform. It should be noticed that all values in this section are taken at 589 nm.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T16:04:31Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products. Different literature values are also being compared to each other, generally, the deviation is small when the same solvent is used.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T16:00:26Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|-
!Others Literature Optical Rotation
||-50.1° (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref>|| +131° (Benzene)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref>||-384° (Ethyl Acetate,15 °C)<ref name="SStrans"></ref>||
+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref>
|}

Overall, the calculated results demonstrate a good match with literature values, therefore structures shown above are the correct assignments of absolute configurations of epoxide products.

It is found that different solvents have a profound impact on the optical rotation value. For example, literature value for (R,R)β-methyl styrene epoxide is +47°<ref name="RRstyrene"></ref>, which is a great match with calculated value (+46.77°), the literature value increases to +131° <ref name="RRstyreneREF"></ref> when product is dissolved in benzene instead of chloroform. More examples of solvent effects are also shown in the table above.

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T15:33:38Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

Optical rotation of epoxide products are calculated and compared with literature values, giving the table shown below. The solvent used for calculation is chloroform.

{|class="wikitable" border="1"
|+ Optical Rotation
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|}

ethyl acetate -384 deg 15 °C <ref name="SStrans"></ref>

20 g/100ml benzene 131(+47)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref> deg 25°C

-50.1 (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref> http://www.sciencedirect.com/science/article/pii/S0040402001883496

+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref> http://pubs.acs.org/doi/abs/10.1021/jo960718q

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T15:25:42Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

{|class="wikitable" border="1"
|+ and 4
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|}

ethyl acetate -384 deg 15 °C <ref name="SStrans"></ref>

20 g/100ml benzene 131(+47)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref> deg 25°C

-50.1 (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//10.1016/S0040-4020(01)88349-6}}</ref> http://www.sciencedirect.com/science/article/pii/S0040402001883496

+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref> http://pubs.acs.org/doi/abs/10.1021/jo960718q

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T15:23:11Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

{|class="wikitable" border="1"
|+ and 4
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|}

ethyl acetate -384 deg 15 °C <ref name="SStrans"></ref>

20 g/100ml benzene 131(+47)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref> deg 25°C

-50.1 (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//pii/S0040402001883496}}</ref> http://www.sciencedirect.com/science/article/pii/S0040402001883496

+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref> http://pubs.acs.org/doi/abs/10.1021/jo960718q

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T15:21:01Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

{|class="wikitable" border="1"
|+ and 4
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|}

ethyl acetate -384 deg 15 °C <ref name="SStrans"></ref>

20 g/100ml benzene 131(+47)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref> deg 25°C

-50.1 (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//00404020/92}}</ref> http://www.sciencedirect.com/science/article/pii/S0040402001883496

+361°(PhH)<ref name="SStransREsdF">H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref> http://pubs.acs.org/doi/abs/10.1021/jo960718q

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T15:20:15Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

{|class="wikitable" border="1"
|+ and 4
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|}

20 g/100ml benzene 131(+47)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref> deg 25°C

-50.1 (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//00404020/92}}</ref> http://www.sciencedirect.com/science/article/pii/S0040402001883496

+361°(PhH)<ref name="SStransREsdF"H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref> http://pubs.acs.org/doi/abs/10.1021/jo960718q

===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>

Rep:Mod:NBC1C

2013-11-21T15:18:19Z

Bn711: /* Assigning the absolute configuration of the product */

==The Hydrogenation of Cyclopentadiene Dimer==

It should be noticed that all the optimisations in this experiment are carried out using Avogadro.

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer1 !! Isomer2!!Isomer3!!Isomer4
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 10;measure 4 10 14;measure 4 10 17;measure 12 19 17;zoom 5;measure 2 3 7;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene1.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 4 6 13;measure 4 6 10;zoom 5;;measure 6 13 15;measure 1 2 3;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711cyclopentadiene2.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;measure 10 8 5;measure 15 13 6;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene3.mol</uploadedFileContents>
</jmolApplet></jmol>
||
<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>measure 1 4 6;measure 6 4 5;measure 4 1 2;zoom 5;measure 9 8 14;measure 9 8 5;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Cyclopentadiene4.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
||3.54278||3.46716|| 3.30864 ||2.82304
|-
!Total angle bending energy/ kcal/mol
||30.77303||33.19917|| 30.86391||24.68554
|-
!Total stretch bending energy / kcal/mol
||-2.04132||-2.08202|| -1.92667 ||-1.65717
|-
!Total torsional energy/ kcal/mol
|| -2.73109||-2.94992||0.05990||-0.37838
|-
!Total out-of-plane bending energy/ kcal/mol
||0.01495|| 0.02190|| 0.01539|| 0.00028
|-
!Total van der Waals energy/ kcal/mol
||12.80140||12.35073||13.28110||10.63716
|-
!Total electrostatic energy/ kcal/mol
||13.01372||14.18365||5.12099||5.14702
|-
!Total energy/ kcal/mol
||55.37347|| 58.19066||50.72283||41.25749
|}

[[Image:Thermodyamic versus kinetic control.png|thumb|200px| kinetic/thermodynamic reaction pathway<ref name="control"> ''Generalised energy profile diagram for kinetic versus thermodynamic product reaction'', '''2012'''<.http://en.wikipedia.org/wiki/File:Thermodyamic_versus_kinetic_control.png></ref>]]

As can be seen in the table above, same settings of force field and algorithm are used in order to allow the comparison of energies. As a result, isomer 1 (exo structure, 55.37347 kcal/mol) is lower in energy than isomer 2 (endo structure, 58.19066 kcal/mol), indicating isomer 1 is the more stable and thermodynamically favored product and isomer 2 is the kinetic product which is favored under kinetic control. Isomer 2 is formed faster than isomer 1 because of the lower activation energy of isomer 2, yet it is less stable due to the higher molecular energy.

Total angle bending energy contributes most to the total energy among other dissection energies, the difference between total angle bending energies of isomer 1 and 2 is also the largest, which accounts for the major energy difference between isomer 1 and 2. Angle bending energy of isomer 2 (33.19917 kcal/mol) is larger than that of isomer 1 (30.77303 kcal/mol), this can be explained by the fact that measured angles have larger deviation from ideal hybridisation angles(sp<sup>2</sup> C :120°, sp<sup>3</sup> C:109.5°).

By comparing the total energy of isomer 3 with that of isomer 4, isomer 4 shows a lower energy than isomer 3. Therefore, isomer 4 is the product under thermodynamic control. There are little difference between the dissection energies of isomer 3 and 4 except for the angle bending energy. The energy difference in angle bending energy can be explained in the same theory as above.

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

{| class="wikitable" border="1"
|+ Hydrogenation of Cyclopentadiene Dimer
! !! Isomer9 !!Isomer 9*!!Isomer 10!!Isomer 10*
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9derv.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol10deri.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
! Force Field
|| MMFF94s|| MMFF94s|| MMFF94s|| MMFF94s
|-
!Algorithm
||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients||Conjugate Gradients
|-
!Total bond stretching energy/ kcal/mol
|| 7.63349|| 6.94603||7.60077|| 6.57496
|-
!Total angle bending energy/ kcal/mol
|| 28.28144||32.04138 ||18.83483||24.73710
|-
!Total stretch bending energy / kcal/mol
||-0.08450||0.29925 ||-0.13931|| 0.42627
|-
!Total torsional energy/ kcal/mol
|| 0.38399||9.49812 ||0.21789||8.48774
|-
!Total out-of-plane bending energy/ kcal/mol
|| 0.97300|| 0.25592||0.84256||0.06353
|-
!Total van der Waals energy/ kcal/mol
||33.06924||32.71211 ||33.24867||31.13566
|-
!Total electrostatic energy/ kcal/mol
|| 0.30709|| 0.00000||-0.05465|| 0.00000
|-
!Total energy/ kcal/mol
||70.56377|| 81.75280 ||60.55077|| 71.42526
|}

<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol9twistboat.mol</uploadedFileContents>
</jmolApplet></jmol>

Energy: 76.46449

''Which of the two atropisomers is the more stable?''

Isomer 9 has an energy of 70.56377 kcal/mol and the energy of isomer 10 is 10.013 kcal/mol less than that. Therefore, isomer 10 is more stable because it is lower in energy.

''Why the alkene reacts slowly?''

The difference between the strain energy of an olefin and that of its hydrogenated derivative is defined as olefin strain energy (OS). Isomer 9 and 10 are bridgehead olefins, which can be divided into three groups based on their olefin strain energies. OS ≤ 17 kcal/mol are called isolable bridgehead olefins, which are kinetically stable at room temperature. Olefins with OS higher than 17 kcal/mol are less stable.<ref name="ja9825332">W. F. Maier and P. v. R. Schleyer, "Evaluation and Prediction of the Stability of Bridgehead Olefins", ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> The OS for isomer 9 is 9.11413 kcal/mol and the OS for isomer 10 is 8.26985 kcal/mol. Both of the values are smaller than 17 kcal/mol which means they're stable and reacts slowly.

==Spectroscopy of an intermediate related to the synthesis of Taxol==

Molecule 17 and 18 are optimised using Avogadro (force field: MFF94s) and then a setting of B3LYP/6-31G(d,p) is used to compute their corresponding NMRs. Chloroform is chosen as the solvent when doing the calculation. However, the solvent used in literature is C<sub>6</sub>D<sub>6</sub><ref name="spectra"></ref>.

{| class="wikitable" border="1"
|+ Molecule 17&18 Analysis
! !! Molecule 17 ||Molecule 18
|-
! Structure
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol17.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>250</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Taxol18.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculation type
||FREQ||FREQ
|-
!Calculation Method
||RB3LYP||RB3LYP
|-
!Basis Set
||6-31G(D,P)||6-31G(D,P)
|-
!Total Energy/ a.u.
||-1651.88240714||-1651.88157369
|-
!Sum of electronic and thermal free energies/a.u.
||-1651.461189||-1651.460740
|-
!.log File
||[[Media:Bn711Taxol17log.log| here]]||[[Media:Bn711Taxol18log.log| here]]
|}

{| class="wikitable" border="1"
|+ Molecule 17 NMR
! <sup>1</sup>H NMR !! <sup>13</sup>C NMR
|-
| [[Image:Bn711Taxol17HNMR.svg|thumb|300px|<sup>1</sup>H NMR]] || [[Image:Bn711Taxol17CNMR.svg|thumb|300px|<sup>13</sup>C NMR]]
|}

[[Image:Bn711M17C13.JPG|right|600px|thumb|Molecule 17 <sup>13</sup>C NMR Analysis]]

{| class="wikitable" border="1"
|+ Molecule 17 <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Corrected Shift/ ppm!!Literature Shift<ref name="spectra">L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, ''J. Am. Chem. Soc.,'', '''1990''', ''112'', 277-283. {{DOI|10.1021/ja00157a043}}</ref>/ ppm!!Degeneracy
|-
| 9||216.1047298||219.6605406||211.49||1
|-
| 3||145.124741||145.124741||148.72||1
|-
| 5||124.6849266||124.6849266||120.9||1
|-
| 11||90.64759911||84.64759911||74.61||1
|-
| 8||60.63933078||60.63933078||60.53||1
|-
| 10||57.04499698||57.04499698||51.3||1
|-
| 2||52.47751049||52.47751049||50.94||1
|-
| 1||51.54743778||51.54743778||45.53||1
|-
| 6||46.69312938||46.69312938||43.28||1
|-
| 46||45.95379184||42.95379184||40.82||1
|-
| 12||42.17199765||42.17199765||38.73||1
|-
| 45||40.57497339||37.57497339||36.78||1
|-
| 7||35.3285884||35.3285884||35.47||1
|-
| 4||31.01138079||31.01138079||30.84||1
|-
| 13||29.35321102||29.35321102||30||1
|-
| 21||29.32217151||29.32217151||25.56||1
|-
| 36||27.09236319||27.09236319||25.35||1
|-
| 28||26.40358177||26.40358177||22.21||1
|-
| 14||22.90364275||22.90364275||21.39||1
|-
| 32||19.72646||19.72646||19.83||1
|}

Chemical shifts for atom 9, 45 and 46 of molecule 17 are corrected because of their attachments to heavy elements and the corresponding spin-orbit coupling errors. Corrected value for atom 9 is calculated by using the equation δ<sub>corr</sub> = 0.96δ<sub>calc</sub> + 12.2. The corrections for atom 45 and 46 (C-S) is estimated to be -3 ppm based on the correction for C-Cl (-3 ppm), because no corresponding literature value is found and sulfur and chlorine atoms are next to each other within the same period in periodic table.

An analysis is taken by taking the difference between each corrected <sup>13</sup>C shifts and literature values, the graph is plotted above. It can be seen that while the majority of the deviations are under 5 ppm, there are still some deviations have values above that. For example, atom 9 has a deviation of 8.1705406 ppm. But it should be noticed that atom 9 of molecule 17 connects to 2 sulfur atoms, and the NMR shift correction for atoms connect with sulfur atom is estimated. Besides, there could be a bigger impact on the atom 9 since it connects with 2 sulfur atoms, which makes the value unreliable. Due to the reason that most of the values show a good match with literature values, it can be deduced that the literature values with large deviation with this experiment are wrong.

{| class="wikitable" border="1"
|+ Molecule 17 <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="spectra"></ref>/ ppm!!Degeneracy
|-
| 17||5.150921272||5.21||1
|-
| 50||3.308126287
| rowspan="5" | 3.00-2.70||1
|-
| 49||3.221071967||1
|-
| 20||3.158522394||1
|-
| 47,48||3.028805078||2
|-
| 40,19||2.72977565||2
|-
| 34||2.635042805
| rowspan="2" |2.70-2.35||1
|-
| 37,38,22,18||2.396951168||4
|-
| 39,42||2.276827035
| rowspan="5" |2.20-1.70||2
|-
| 25,16||2.129430447||2
|-
| 23||1.954108422||1
|-
| 26||1.903859149||1
|-
| 53||1.744331831||1
|-
| 41,27,29||1.59509974||1.58||3
|-
| 24||1.489509991
| rowspan="2"|1.50-1.20||1
|-
| 51||1.164851679||1
|-
| 31,35,30||0.915513841||1.10||3
|-
| 33||0.82411982||1.07||1
|-
| 52||0.591931279||1.03||1
|}

<sup>1</sup>H NMR of molecule 17 is also analyzed and compared with literature values. In general, it shows a bad match with literature. The deviation of chemical shifts have a tendency of increasing as the chemical shifts become less positive. Therefore no conclusion can be drawn regarding which set of data is correct.

==Analysis of the properties of the synthesised alkene epoxides==
===The two catalytic systems===

Cambridge crystal database (CCDC) is searched by using the Conquest program, the following structures of pre-catalysts 21 and 23 are found. Mercury program is then used to measure the C-O bond lengths of three anomeric centres of Shi catalyst.

{| class="wikitable" border="1"
|+ The two catalytic systems
! Shi Catalyst (21) !! Jacobsen Catalyst (23)
|-
| <jmol><jmolApplet><title>Cyclopentadiene1</title><color>black</color>
<size>300</size><script>measure 16 10;measure 8 16;measure 15 2;measure 15 4;measure 3 4; measure 12 3;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71121.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Cyclopentadiene1</title><color>Black</color>
<size>300</size><script>measure 49 88;MEASURE 45 92;measure 45 3; measure 92 42;zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn71123H.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

It can be seen on the diagram that on each anomeric centres(O-C-O), one C-O bond length is longer than another. Even though the diagram displays an equal bond length for the C-O bonds in the middle anomeric centre, Mercury program shows a more accurate result, one C-O bond is 1.415 Å while another is 1.423 Å. The difference between the C-O bond lengths can be explained by anomeric effect. Hyperconjugation between the lone pair on the oxygen atom and the σ* orbital for the C-O bond strengthens the C-O bond which makes it shorter. In the contrary, another C-O bond is lengthened because of the extra electron density on the σ* orbital.

By analyzing the two adjacent t-butyl groups on the rings of Jacobsen catalyst, it is found that the hydrogen atoms of one methyl group are quite close to the hydrogen atoms on the opposite methyl group of t-butyl. With one distance of 2.08 Å which is shorter than the Van der Waals radii (2.20 Å <ref name="VdW">M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and
D. G. Truhlar ''J. Phys. Chem.'', '''2009''', ''113'', 5810. {{DOI|/10.1021/jp8111556}}</ref>) for two hydrogen atoms, indicating an interaction exists between the two hydrogen atoms. This leads to an enhanced catalyst selectivity due to the fact that t-butyl groups prevent substrate approach metal centre from its side<ref name="ref4>E. N. Jacobsen , W. Zhang , A. R. Muci ,J. R. Ecker , L. Deng,''J. Am. Chem. Soc.'', '''1991''', ''113'', 7063–7064; {{DOI|10.1021/ja00018a068}}</ref>. It is interesting to notice that some H atoms from t-butyl groups have a close proximity to the oxygen atoms (e.g. 2.22 Å), which means the interaction between H an O might also contributes to the selectivity of catalyst.

===NMR properties of products===

{| class="wikitable" border="1"
|+ Epoxides
! !!β-methyl styrene epoxide !! trans-Stilbene epoxide
|-
!Strucutre
|| <jmol><jmolApplet><title>Epoxides</title><color>black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711Bstyreneexpoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>300</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711tran_sstilbene_Epoxide.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!<sup>1</sup>H NMR
||[[Image:Trans-Stilbene_oxide_1H.svg|thumb|250px]]||[[Image:Bn711styreneepoxideHNMR.svg|thumb|250px]]
|-
!<sup>13</sup>C NMR
||[[Image:Trans-Stilbene_oxide_13C.svg|thumb|250px]]||[[Image:Bn711styreneepoxideCNMR.svg|thumb|250px]]
|-
!D-Space
||{{DOI|/10042/26177}}||{{DOI|/10042/26178}}
|}
{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="methylstyNMR">M. Sangaa, I. R. Younisa, P. S. Tirumalaia, T. M. Blanda, M. Banaszewskab, G. W. Konatb, T. S. Tracyc, P. M. Gannetta, P. S. Callery ''Toxicology and Applied Pharmacology'', '''2006''', ''211'', 152. {{DOI|/10.1016/j.taap.2005.06.017}}</ref> / ppm!!Degeneracy
|-
| 14||7.5005789387
| rowspan="5" | 7.17-7.28||3
|-
| 11||7.4965353149||3
|-
| 13||7.4764056286||3
|-
| 12||7.4215078669||1
|-
| 15||7.3072832156 ||1
|-
| 16||3.4146796724||3.688||1
|-
| 17||2.7878820719||3.243||1
|-
| 19|| 1.6782269670
| rowspan="3" |1.287||1
|-
| 18||1.5872817485||1
|-
| 20||0.7169440684 ||1
|}

{| class="wikitable" border="1"
|+ β-methyl styrene epoxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Degeneracy
|-
| 5||134.9753965424||1
|-
| 1||124.0725177924||1
|-
| 3||123.3280431186||1
|-
| 4||122.7961719799||1
|-
| 2|| 122.7269092928||1
|-
| 6||118.4861712952||1
|-
| 9||62.3200384786||1
|-
| 7|| 60.5763422400||1
|-
| 10|| 18.8378278486||1
|}

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>13</sup>C NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR">M. W. C. Robinson, A. M. Davies, R. Buckle, I. Mabbett, S. H. Taylora and A. E. Graham ''Org. Biomol. Chem.'', '''2009''', ''7'', 2562. {{DOI|/10.1039/B900719A}}</ref> / ppm!!Degeneracy
|-
| 5||134.0880446109
| rowspan="2" | 137.6||2
|-
| 9||134.0879314162||2
|-
| 11||124.2199442902
| rowspan="2" |129.0||2
|-
| 1||124.2199347937||2
|-
| 3||123.5184078463
| rowspan="6" |128.8 ||2
|-
| 13||123.5183926697||2
|-
| 12||123.2119589779||2
|-
| 2||123.2119101109||2
|-
| 14||123.0785722351||2
|-
| 4||123.0784012095||2
|-
| 10|| 118.2628347616
| rowspan="2" |126.2||2
|-
| 6||118.2627684281 ||2
|-
| 7||66.4265991815
| rowspan="2" |63.3||2
|-
| 8||66.4265484152 ||2
|}

6 and 10 out a lot???????????????????????????

{| class="wikitable" border="1"
|+ Trans-Stilbene oxide <sup>1</sup>H NMR Analysis
!Atom Number!!Shift/ ppm!!Literature Shift<ref name="transstilNMR"></ref> / ppm!!Degeneracy
|-
| 21||7.5704385557
| rowspan="10" | 7.57-7.34 (10H)||2
|-
| 15||7.5704374374||2
|-
| 18||7.5069643263||8
|-
| 24||7.5069578119||8
|-
| 17||7.4896480510||8
|-
| 23|| 7.4896464357||8
|-
| 22||7.4691926261||8
|-
| 16|| 7.4691895198||8
|-
| 19||7.4507152761||8
|-
| 20||7.4507076434 ||8
|-
| 27|| 3.5377977258
| rowspan="2" |3.91 (2H)||2
|-
| 26||3.5377374275 ||2
|}

===Assigning the absolute configuration of the product===

{|class="wikitable" border="1"
|+ and 4
! rowspan="2" |
! colspan="2" style="text-align: center;" |β-methyl Styrene Epoxide
! colspan="2" style="text-align: center;" |Trans-Stilbene Epoxide
|-
! SS ||RR || SS ||RR
|-
!Structure
||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711styreneepoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideSS.mol</uploadedFileContents>
</jmolApplet></jmol> ||<jmol><jmolApplet><title>Epoxides</title><color>Black</color>
<size>200</size><script>zoom 5;moveto 4 0 2 0 90 120;</script>
<uploadedFileContents>Bn711transEpoxideRR.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
!Calculated Optical Rotation Solvent:CHCl<sub>3</sub>
||-46.77°||+46.77°||-298.00° ||+298.00°
|-
!Literature Optical Rotation Solvent:CHCl<sub>3</sub>
||-48.5° <ref name="SSstyrene">P. Besse, Michel F. Renard, H. Veschambre, ''Tetrahedron: Asymmetry'', '''1994''', ''5'', 1268. {{DOI|//10.1016/0957-4166(94)80167-3}}</ref> ||+47°<ref name="RRstyrene">G. Fronza, C. Fuganti, P. Grasselli, and A. Mele ''J. Org. Chem.'', '''1991''', ''56'', 6023. {{DOI|//10.1021/jo00021a011}}</ref> || -249° ( 15 °C)<ref name="SStrans">J. Read, I. G. M. Campbell ''J. Chem. Soc.'', '''1930''', 2382. {{DOI|//10.1039/JR9300002377}}</ref>||+ 250.8°<ref name="RRtrans">D. J. Fox, D. S. Pedersen, A. B. Petersen, S. Warren, ''Org. Biomol. Chem.'', '''2006''', ''4'', 3117-3119.</ref>
|}

20 g/100ml benzene 131(+47)<ref name="RRstyreneREF">M. Rosenberger, W. Jackson, G. Saucy, ''Helvetica Chimica Acta'', '''1980''', ''63'', 1665 - 1674.</ref> deg 25°C

-50.1 (CHCl<sub>3</sub>)<ref name="SSstyreneREF">H. C. Kolb, K. B. Sharpless, ''Tetrahedron'', '''1992''', ''48'', 10521.{{DOI|//00404020/92}}</ref> http://www.sciencedirect.com/science/article/pii/S0040402001883496

ethyl acetate -384 deg 15 °C <ref name="SStrans"></ref>

+361°(PhH)<ref name="SStransREsdF"H. T. Chang, K. B. Sharpless, ''J. Org. Chem.'', '''1996''', ''61'', 6457.{{DOI|//10.1021/jo960718q}}</ref> http://pubs.acs.org/doi/abs/10.1021/jo960718q
<references/>
===Investigating the non-covalent interactions in the active-site of the reaction transition state===

<jmol>
<jmolApplet>
<title>Orbital</title><color>black</color><size>300</size>
<script>isosurface color orange purple "images/8/83/Bn711transBSRR%24_den.cub.jvxl" translucent;</script>
<uploadedFileContents>Bn711transBSRR$ den.cub.xyz </uploadedFileContents>
</jmolApplet>
</jmol>

===QTAIM===

[[Image:Bn711QTAIM.PNG|thumb|500px|Transition states for Shi epoxidation of trans-β-methyl styrene (R,R) ]]

==New Candidate==

pulegone epoxide

Reaxys Registry Number: 81906

CAS Registry Number: 7599-90-8

Type of Substance: heterocyclic

Molecular Formula: C10H16O2

Linear Structure Formula: C10H16O2

Molecular Weight: 168.236

786.5 293 nm ethanol 25 °C

W. Reusch, C. K. Johnson, J. Org. Chem., 1963, 28 (10), pp 2557–2560 DOI: 10.1021/jo01045a016

-1177.9 327 nm ethanol 25 °C

------------------------------

==References==

<references/>