==Confirmational Analysis of Cyclopentadiene Dimer==
Cyclopentadiene dimerises to give product 1 and 2. Through further hydrogenation, derivatives 3 and 4 are produced. 
[[File:Capture_total.PNG]]
 
Whether the endo or the exo form dominate depends on whether the reaction is under kinetic or thermodynamic control. Therefore calculations are carried out to obtain values for total bond stretching, angle bending, torsional, van der Waals and electrostatic energies. MMFF94s method is used. The values are listed below in the table.

{| class="wikitable" border="1"
|+ Table 1: Energy values of dimers 1-4
! Property !! Dimer 1 (exo) !! Dimer 2 (endo)!! Dimer 3!! Dimer 4
|-
| Stretch kcal/mol || 3.54305 || 3.46741 || 3.31169 ||2.82305
|-
| Bend kcal/mol || 30.77271 || 33.19144 || 31.93522 || 24.68537
|-
| Torsion kcal/mol || -2.73105 ||-2.94939 || -1.46912 || -0.37837
|-
| van der Waals kcal/mol || 12.80155 || 12.35716 || 13.63750 ||10.63729
|-
| Electrostatic kcal/mol || 13.01372 || 14.18422 ||5.11952 ||5.14702
|-
| Total energy kcal/mol || 55.37344 || 58.19070 || 50.44568 || 41.25749
|-
| Structure ||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>Form 1 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>Form 2 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>3 JMOL.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>4 JMOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
'''Analysis''' For molecules 1 and 2, it is evident that the exo form is lower in energy, it is the thermodynamic product. However the endo form is produced specifically. This means the kinetic product dominates. From the table above we can see that the angle bending energy contributes largely to the difference in total energy. This could be due to less strained angles in the endo form at sp2 and sp3 carbon centres (since typical angle values for sp2 carbon is 120o and for sp3 carbon is 109o) .
 For molecules 3 and 4, from the energy values we can see that dimer 4 should be the thermodynamic product. From the angles, it it obvious that dimer 3 should be the kinetic product.
 

==Atropisomerism in an Intermediate related to the Synthesis of Taxol==
The two intermediates (9 and 10) in the formation of taxol are optimised and analysed using MMFF94s method.
[[File:Capture_9_and_10.PNG]]
 
The energies of the two atropisomers are given in the table below.
{| class="wikitable" border="1"
|+ Table 2: Energy values of isomers 9-10
! Property !! Isomer 9 !! Isomer 10
|-
| Stretch kcal/mol || 7.65325 || 7.75545
|-
| Bend kcal/mol || 28.28188 || 18.98819
|-
| Torsion kcal/mol || 0.26912 ||3.79387
|-
| van der Waals kcal/mol || 33.14267 || 34.99601
|-
| Electrostatic kcal/mol || 0.30295 || -0.05982
|-
| Total energy kcal/mol || 70.54025 || 66.29283
|-
| Structure|| <jmol><jmolApplet><title>9</title><color>white</color>
<size>230</size><script>measure 6 4 24; measure 16 9 15</script>
<uploadedFileContents>9_JMOL3.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>10</title><color>white</color>
<size>230</size><script>measure 6 4 24; measure 16 9 15</script>
<uploadedFileContents>10_JMOL2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

 It is evident that isomer 10 (down) has the lower energy therefor it is the thermodynamic product. This is due to less contribution from the angle bending energy. From the angles labelled in structures we can see that isomer 10 has a less strained structure. Therefore it could be the kinetic product as well. 
'''Products after hydrogenation'''<ref>W. F. Maier, P. Von Rague Schleyer, ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.{{DOI|10.1021/ja00398a003}}</ref> 
The energies of the products from hydrogenation of isomers 9 and 10 are also analysed using the same method.
[[File:9 and 10 single.PNG]]
{| class="wikitable" border="1"
|+ Table 3: Energy values of saturated forms
! Property !! Isomer 9 (saturated) !! Isomer 10 (saturated)
|-
| Stretch kcal/mol || 7.22403 || 7.35327
|-
| Bend kcal/mol || 23.32429 || 30.23447
|-
| Torsion kcal/mol || 8.10832 ||6.51434
|-
| van der Waals kcal/mol || 33.55023 || 33.94051
|-
| Electrostatic kcal/mol || 0.00000 || 0.00000
|-
| Total energy kcal/mol || 72.32844 || 78.49372
|}
The saturated products have higher energies than the unsaturated one. This means for the hydrogenation of isomers 9 and 10, the products are less stable than the reactants. Therefore it is an unfavourable process.

==Spectroscopic Simulation using Quantum Mechanics <ref>Spectroscopic data: L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, J. Am. ''Chem. Soc.'','''1990''', ''112'', 277-283 {{DOI|10.1021/ja00157a043}}</ref>==
Molecules 17 and 18 are derivatives from molecules 9 and 10 above. For isomer 18, the structure is optimized, and 1H and 13C spectra are simulated using gaussian. [[File:Capture_17_and_18.PNG]]
 
{| class="wikitable" border="1"
|+ Table 4:Molecules 17 and 18
! !!Molecule 17 !!Molecule 18
|-
| Jmol image || <jmol><jmolApplet><title>18</title><color>white</color>
<size>230</size>
<uploadedFileContents>17jmol.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>18</title><color>white</color>
<size>230</size>
<uploadedFileContents>18 run 3 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
| Bond stretching energy kcal/mol|| 15.89829|| 14.44122
|-
| Angle bending energy kcal/mol|| 35.38739 || 28.81334
|-
| Torsion kcal/mol|| 14.35822 || 13.37805
|-
| van der Waals kcal/mol|| 53.68261 || 50.45971
|-
| Electrostatic kcal/mol|| -7.12920|| -6.21523
|-
| Total energy kcal/mol|| 113.98747 || 102.38268
|-
| Sum of electronic and thermal free energies /hartree|| -1651.446638 || -1651.462758
|}

{| class="wikitable" border="1"
|+ Table 5: Molecules 18 spectra
! !! Images
|-
| 1H NMR|| [[File:H nmr.PNG|800px]]
|-
| 13C NMR|| [[File:C nmr.PNG|800px]]

|}
 
{| class="wikitable" border="1"
|+ Table 6 data of 1H NMR
! Atom number!!Chemical shift!! Integration !!Reference values (300 MHz, C6D6 )
|-
| 25-H || 5.3799000000 || 1 || rowspan="31"| 5.21 (m, 1 H), 3.00-2.70 (m, 6 H), 2.70-2.35(m, 4 H), 2.20-1.70 (m, 6 H), 1.58 (t, J = 5.4 Hz, 1 H), 1.50-1.20 (m, 3 H), 1.10 (s, 3 H), 1.07(s, 3 H), 1.03 (s, 3 H)
|-
| 53-H || 3.3549000000 || 1
|-
| 52-H || 3.1421000000 || 1
|-
| 50-H || 3.0461000000 || 1
|-
| 51-H || 2.9783000000 || 1
|-
| 39-H || 2.8347000000 || 1
|-
| 37-H || 2.5414000000 || 1
|-
| 29-H || 2.4458000000 || 1
|-
| 38-H || 2.4396000000 || 2
|-
| 41-H || 2.2127000000 || 1
|-
| 27-H || 2.1244000000 || 1
|-
| 19-H || 2.0957000000 || 2
|-
| 26-H || 1.9936000000 || 1
|-
| 42-H || 1.9921000000 || 2
|-
| 45-H || 1.9888000000 || 3
|-
| 30-H || 1.9628000000 || 4
|-
| 28-H || 1.8624000000 || 1
|-
| 43-H || 1.7942000000 || 1
|-
| 47-H || 1.7491000000 || 2
|-
| 44-H || 1.6772000000 || 1
|-
| 19-H || 2.0957000000 || 2
|-
| 31-H || 1.5435000000 || 1
|-
| 34-H || 1.5162000000 || 2
|-
| 40-H || 1.4073000000 || 1
|-
| 49-H || 1.3150000000 || 1
|-
| 35-H || 1.1656000000 || 1
|-
| 46-H || 1.1176000000 || 2
|-
| 48-H || 1.0804000000 || 3
|-
| 36-H || 1.0476000000 || 4
|-
| 33-H || 0.9840000000 || 1
|-
| 32-H || 0.9728000000 || 2
|}

{| class="wikitable" border="1"
|+ Table 7: data of 13C NMR
! Atom number!!Chemical shift!! Integration !!Reference values (75 MHz, C6D6 )
|-
| 12-C || 212.2430000000 || 1 || rowspan="20"|211.49, 148.72, 120.90, 74.61, 60.53, 51.30, 50.94, 45.53, 43.28, 40.82, 38.73, 36.78, 35.47, 30.84.30.00, 25.56, 25.35, 22.21, 21.39, 19.83
|-
| 2-C || 148.8953000000 || 1
|-
| 3-C || 118.5509000000 || 1
|-
| 14-C || 89.0565000000 || 1
|-
| 10-C || 67.5747000000 || 1
|-
| 11-C || 56.3146000000 || 1
|-
| 5-C || 55.5376000000 || 1
|-
| 6-C || 50.0936000000 || 1
|-
| 23-C || 46.8216000000 || 1
|-
| 22-C || 44.4718000000 || 1
|-
| 15-C || 41.2998000000 || 1
|-
| 13-C || 37.6775000000 || 1
|-
| 17-C || 36.2823000000 || 1
|-
| 9-C || 32.0825000000 || 1
|-
| 18-C || 29.0650000000 || 1
|-
| 1-C || 28.6982000000 || 1
|-
| 7-C || 25.8648000000 || 1
|-
| 4-C || 25.2119000000 || 1
|-
| 8-C || 23.2836000000 || 1
|-
| 16-C || 21.7432000000 || 1
|}

Comment on NMR spectra: the calculated values generally agree well with experimental data, with some differences in integration numbers. This could be caused by peaks merging together during measurements due to similar chemical shifts. Therefore each hydrogen or carbon cannot be read separately.

From the energy values we can see that molecule 18 has lower energy. This could be the reason why 17 can be completely changed into 18. But due to similarity in energy values, the process takes a long time, and energy need to be put in.
 

==Analysis of the properties of the synthesised alkene epoxides==
===Molecule 21===
The pre-catalyst 21 is used in the Shi asymmetric Fructose catalysis. [[File:bond.PNG|200px|right]]It is searched in the Cambridge crystal database (CCDC) to obtain information about bond lengths in this molecule. Two molecules are found in Mercury.

<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>500</size><script>measure 44 52; measure 46 52; measure 40 51; measure 51 38; measure 39 40; measure 48 39; measure 10 16; measure 8 16; measure 3 4; measure 3 12; measure 4 15; measure 2 15</script>
<uploadedFileContents>NELQEA01.xyz</uploadedFileContents>
</jmolApplet></jmol>
 
C-O bond lengths (with O-C-O substructures) are labelled. 
Typical C-O bond length is 1.43 Å <ref name="data">CRC Handbook of Chemistry and Physics 65Th Ed.</ref>. The difference in bond lengths in this molecule can be explained by enomeric effect<ref>R. U. Lemieux, S. Koto, and D. Voisin,"The Exo-Anomeric Effect",''ACS Symposium Series'' '''1979''', ''87'', 17-29.{{DOI|10.1021/bk-1979-0087.ch002}}</ref>. The lone pair on the oxygen in the 6-membered ring donates to the anti-periplanar antibonding σ* orbital of the C-O bond (bond a). This results in shortened bond length in bond a. For bonds f and e, where enomeric effect doesn't possess, bond lengths are longer and close to normal C-O bond length value. 

===Molecule 23===
The stable pre-catalyst 23 is used in the Jacobsen asymmetric catalysis. Two molecules are found in Mercury. [[File:Capture23.PNG|200px|right]]
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>500</size><script>measure 139 186; measure 143 182; measure 46 92; measure 51 88</script>
<uploadedFileContents>TOVNIB01.xyz</uploadedFileContents>
</jmolApplet></jmol>
 Within the distance of 2.4 Å, molecules would have interactions. However repulsive interactions occur within 2.1 Å <ref name="data"></ref>.For molecule 23, from the labelled through space distances we can see that only 1 out of the 4 labelled bonds has disfavoured interactions. Therefore overall the molecule can be considered as stabilized.
 

==Analysis of styrene and stilbene epoxides==
==== Styrene epoxide (1) (R conformer) ====
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Styrene jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Styrene C.PNG|700px]]

1H NMR
[[File:Styrene H.PNG|700px]] 

ECD spectra 
[[File:Styrene ECD.PNG|700px]] 

VCD spectra 
[[File:Styrene VCD.PNG|700px]]
 

 
'''NCI (non-covalent-interaction) analysis''' [[File:Labelled1.PNG]] Arrow 1 points to the attractive interaction between styrene and the catalyst 22. Arrow 2 points out the bond that is formed in the transition state between the two molecules.
 
'''Electronic topology (QTAIM)''' [[File:QTAIM.PNG]] The solid lines with a yellow dot in the middle indicates a BCP (bond critical point). The dashed line with a yellow dot in the middle indicates a non-covalent BCP (eg. between hydrogen and oxygen).

==== Styrene epoxide (2) (S conformer) ====
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>styrene2 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Styrene2 C.PNG|700px]]

1H NMR
[[File:Styrene2 H.PNG|700px]] 

ECD spectra 
[[File:Styrene2 ECD.PNG|700px]] 

VCD spectra 
[[File:Styrene2 VCD.PNG|700px]] 

==== Trans-stilbene epoxide(RR) ====
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>stilbene nmr.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Stilbene_Cnmr.PNG|700px]]

1H NMR
[[File:Stilbene_Hnmr.PNG|700px]] 

ECD spectra 
[[File:Stilbene ECD.PNG|700px]] 

VCD spectra 
[[File:Stilbene VCD.PNG|700px]]
 
 

===Trans-stilbene epoxide (SS)===
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>stilbene 2 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Stilbene2_cnmr.PNG|700px]]
 
1H NMR
[[File:Stilbene2_hnmr.PNG|700px]] 
{| class="wikitable" border="1"
|+ Table 8: Optical rotation values
! !! R-Styrene!!S-Styrene!!RR-Stilbene!!SS-Stilbene
|-
| Calculated value / deg || 48.89||-30.39||298.01||-298.06
|-
| Literature value / deg || 44.8<ref>Kuladip Sarma et al., "A novel method for the synthesis of chiral epoxides from
styrene derivatives using chiral acids in presence of Pseudomonas lipase G6 [PSL G6] and hydrogen peroxide", ''Tetrahedron'', '''2007''', ''63'',735–8741 {{DOI|10.1002/chin.200751136}} </ref>||-33.2<ref>E. J. Corey et al, "An Efficient and Catalytically Enantioselective
Route to (S )- (-)-Phenyloxirane", ''J Org Chem'', '''1988''', ''53'',2861-2863 {{DOI|10.1021/jo00247a044}}</ref>||361.0<ref>Philip C. Bulman Page et al, "Asymmetric organocatalysis of epoxidation by iminium salts under non-aqueous conditions", ''Tetrahedron'', '''2007''', ''63'',5386–5393{{DOI|10.1021/jo035820j}}</ref>||-205.2<ref>Niwa,Takashi and Nakada,Masahisa;''Journal of the American Chemistry'', '''2012''', ''134'', 13538-13541 {{DOI|10.1021/ja304219s}}</ref>
|}

The optical rotation values for R and S conformers of styrene and stilbene both show similar values with opposite signs. This is a signature of different conformers existing.
 

===Using the calculated properties of transition state for the reaction===
{| class="wikitable" border="1"
|+ Table 9: energy values for styrene and trans-stilbene epoxides
! !! R-Styrene!!S-Styrene!!RR-Stilbene!!SS-Stilbene
|-
| Total energy / kcal/mol || 23.90614||24.54131||44.66384||44.66336
|}
 

Styrene
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''R /hartree'''
| align="center" style="background:#f0f0f0;"|'''S /hartree'''
| align="center" style="background:#f0f0f0;"|'''Difference /hartree'''
| align="center" style="background:#f0f0f0;"|'''Energy in j/mol'''
| align="center" style="background:#f0f0f0;"|'''K'''
| align="center" style="background:#f0f0f0;"|'''enantiomeric excess'''
|-
| -1303.730703||-1303.733828||0.003125||8203.126562||0.036549452||0.035260693
|-
| -1303.730238||-1303.724178||-0.00606||-15907.50303||612.1550372||0.998369091
|-
| -1303.736813||-1303.727673||-0.00914||-23992.50457||15969.30616||0.999937384
|-
| -1303.738044||-1303.738503||0.000459||1204.87523||0.615057815||0.380827119
|-
|
|}

 
Trans-stilbene
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''RR /hartree'''
| align="center" style="background:#f0f0f0;"|'''SS /hartree'''
| align="center" style="background:#f0f0f0;"|'''Difference /hartree'''
| align="center" style="background:#f0f0f0;"|'''Energy in j/mol'''
| align="center" style="background:#f0f0f0;"|'''K'''
| align="center" style="background:#f0f0f0;"|'''enantiomeric excess'''
|-
| -1534.687808||-1534.68344||-0.004368||-11466.00218||102.0346414||0.990294526
|-
| -1534.687252||-1534.685089||-0.002163||-5677.876081||9.879077234||0.908080439
|-
| -1534.700037||-1534.693818||-0.006219||-16324.87811||724.4060173||0.998621462
|-
| -1534.699901||-1534.691858||-0.008043||-21112.87902||4998.040213||0.999799962
|-
|
|}

 
Jacobsen catalyst
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''S,R /hartree'''
| align="center" style="background:#f0f0f0;"|'''R,S /hartree'''
| align="center" style="background:#f0f0f0;"|'''Difference /hartree'''
| align="center" style="background:#f0f0f0;"|'''energy in j/mol'''
| align="center" style="background:#f0f0f0;"|'''K'''
| align="center" style="background:#f0f0f0;"|'''enantiomeric excess'''
|-
| -3383.259559||-3383.25106||-0.008499||-22309.87925||8100.3572||0.999876564
|-
| -3383.253442||-3383.25027||-0.003172||-8326.501586||28.75632659||0.966393701
|-
| S,S /hartree||R,R /hartree||||||||
|-
| -3383.262481||-3383.253816||-0.008665||-22745.62933||9657.037968||0.999896459
|-
| -3383.257847||-3383.254344||-0.003503||-9195.376751||40.82752619||0.976092299
|-
|
|}

(K= exp(-ΔG/RT), enatiomeric excess= K/(1+K)<ref>Schneebeli et al. "Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations", ''J Am Chem Soc.'', '''2009''', ''131(11)'',3965–3973 {{DOI|10.1021/ja806951r}}</ref>)

 
For styrene, we can see that the R conformer has the lower energy, therefore it should be the main enatiomer. This generally agrees with the enatiomeric excess (ee) calculated from the data given. However the ee data for stilbene is unusual. The RR and SS form has similar energy but RR is obviously the main enatiomer. This may be due to some other factors which computational calculations
don't include. 

==Suggested new candidate for investigation==
(1R,4R,5R,9S)-4,5-epoxy-8-hydroxy-14-caryophyllanal<ref>Abraham, Wolf-Rainer; Ernst, Ludger; Arfmann, Hans-Adolf
Phytochemistry (Elsevier), '''1990''',''29'',757-763{{DOI|10.1016/0031-9422(90)80013-7}}</ref> 
[[File:Capture new.PNG]] 
Experimental conditions: Concentration: 1g/100ml Solvent: CHCl3
{| class="wikitable" border="1"
|+ Optical rotation values
! Wavelength !! 589!!578!!546!!436!!365
|-
| α || -148.6o||-153.2o||-174.8o||-309.3o||525.0o
|}

==References==
<references/>

2013-11-21T13:53:22Z

Yh3511: /* Spectroscopic Simulation using Quantum Mechanics */

==Confirmational Analysis of Cyclopentadiene Dimer==
Cyclopentadiene dimerises to give product 1 and 2. Through further hydrogenation, derivatives 3 and 4 are produced. 
[[File:Capture_total.PNG]]
 
Whether the endo or the exo form dominate depends on whether the reaction is under kinetic or thermodynamic control. Therefore calculations are carried out to obtain values for total bond stretching, angle bending, torsional, van der Waals and electrostatic energies. MMFF94s method is used. The values are listed below in the table.

{| class="wikitable" border="1"
|+ Table 1: Energy values of dimers 1-4
! Property !! Dimer 1 (exo) !! Dimer 2 (endo)!! Dimer 3!! Dimer 4
|-
| Stretch kcal/mol || 3.54305 || 3.46741 || 3.31169 ||2.82305
|-
| Bend kcal/mol || 30.77271 || 33.19144 || 31.93522 || 24.68537
|-
| Torsion kcal/mol || -2.73105 ||-2.94939 || -1.46912 || -0.37837
|-
| van der Waals kcal/mol || 12.80155 || 12.35716 || 13.63750 ||10.63729
|-
| Electrostatic kcal/mol || 13.01372 || 14.18422 ||5.11952 ||5.14702
|-
| Total energy kcal/mol || 55.37344 || 58.19070 || 50.44568 || 41.25749
|-
| Structure ||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>Form 1 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>Form 2 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>3 JMOL.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>4 JMOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
'''Analysis''' For molecules 1 and 2, it is evident that the exo form is lower in energy, it is the thermodynamic product. However the endo form is produced specifically. This means the kinetic product dominates. From the table above we can see that the angle bending energy contributes largely to the difference in total energy. This could be due to less strained angles in the endo form at sp2 and sp3 carbon centres (since typical angle values for sp2 carbon is 120o and for sp3 carbon is 109o) .
 For molecules 3 and 4, from the energy values we can see that dimer 4 should be the thermodynamic product. From the angles, it it obvious that dimer 3 should be the kinetic product.
 

==Atropisomerism in an Intermediate related to the Synthesis of Taxol==
The two intermediates (9 and 10) in the formation of taxol are optimised and analysed using MMFF94s method.
[[File:Capture_9_and_10.PNG]]
 
The energies of the two atropisomers are given in the table below.
{| class="wikitable" border="1"
|+ Table 2: Energy values of isomers 9-10
! Property !! Isomer 9 !! Isomer 10
|-
| Stretch kcal/mol || 7.65325 || 7.75545
|-
| Bend kcal/mol || 28.28188 || 18.98819
|-
| Torsion kcal/mol || 0.26912 ||3.79387
|-
| van der Waals kcal/mol || 33.14267 || 34.99601
|-
| Electrostatic kcal/mol || 0.30295 || -0.05982
|-
| Total energy kcal/mol || 70.54025 || 66.29283
|-
| Structure|| <jmol><jmolApplet><title>9</title><color>white</color>
<size>230</size><script>measure 6 4 24; measure 16 9 15</script>
<uploadedFileContents>9_JMOL3.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>10</title><color>white</color>
<size>230</size><script>measure 6 4 24; measure 16 9 15</script>
<uploadedFileContents>10_JMOL2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

 It is evident that isomer 10 (down) has the lower energy therefor it is the thermodynamic product. This is due to less contribution from the angle bending energy. From the angles labelled in structures we can see that isomer 10 has a less strained structure. Therefore it could be the kinetic product as well. 
'''Products after hydrogenation'''<ref>W. F. Maier, P. Von Rague Schleyer, ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.</ref> 
The energies of the products from hydrogenation of isomers 9 and 10 are also analysed using the same method.
[[File:9 and 10 single.PNG]]
{| class="wikitable" border="1"
|+ Table 3: Energy values of saturated forms
! Property !! Isomer 9 (saturated) !! Isomer 10 (saturated)
|-
| Stretch kcal/mol || 7.22403 || 7.35327
|-
| Bend kcal/mol || 23.32429 || 30.23447
|-
| Torsion kcal/mol || 8.10832 ||6.51434
|-
| van der Waals kcal/mol || 33.55023 || 33.94051
|-
| Electrostatic kcal/mol || 0.00000 || 0.00000
|-
| Total energy kcal/mol || 72.32844 || 78.49372
|}
The saturated products have higher energies than the unsaturated one. This means for the hydrogenation of isomers 9 and 10, the products are less stable than the reactants. Therefore it is an unfavourable process.

==Spectroscopic Simulation using Quantum Mechanics ==
Molecules 17 and 18 are derivatives from molecules 9 and 10 above. For isomer 18, the structure is optimized, and 1H and 13C spectra are simulated using gaussian. [[File:Capture_17_and_18.PNG]]
 
{| class="wikitable" border="1"
|+ Table 4:Molecules 17 and 18
! !!Molecule 17 !!Molecule 18
|-
| Jmol image || <jmol><jmolApplet><title>18</title><color>white</color>
<size>230</size>
<uploadedFileContents>17jmol.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>18</title><color>white</color>
<size>230</size>
<uploadedFileContents>18 run 3 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
| Bond stretching energy kcal/mol|| 15.89829|| 14.44122
|-
| Angle bending energy kcal/mol|| 35.38739 || 28.81334
|-
| Torsion kcal/mol|| 14.35822 || 13.37805
|-
| van der Waals kcal/mol|| 53.68261 || 50.45971
|-
| Electrostatic kcal/mol|| -7.12920|| -6.21523
|-
| Total energy kcal/mol|| 113.98747 || 102.38268
|}

{| class="wikitable" border="1"
|+ Table 5: Molecules 18 spectra
! !! Images
|-
| 1H NMR|| [[File:H nmr.PNG|800px]]
|-
| 13C NMR|| [[File:C nmr.PNG|800px]]

|}
 
{| class="wikitable" border="1"
|+ Table for 1H NMR
! Atom number!!Chemical shift!! Integration !!Reference values (300 MHz, C6D6 <ref>Spectroscopic data: L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, J. Am. ''Chem. Soc.'','''1990''', ''112'', 277-283</ref>)
|-
| 25-H || 5.3799000000 || 1 || rowspan="31"| 5.21 (m, 1 H), 3.00-2.70 (m, 6 H), 2.70-2.35(m, 4 H), 2.20-1.70 (m, 6 H), 1.58 (t, J = 5.4 Hz, 1 H), 1.50-1.20 (m, 3 H), 1.10 (s, 3 H), 1.07(s, 3 H), 1.03 (s, 3 H)
|-
| 53-H || 3.3549000000 || 1
|-
| 52-H || 3.1421000000 || 1
|-
| 50-H || 3.0461000000 || 1
|-
| 51-H || 2.9783000000 || 1
|-
| 39-H || 2.8347000000 || 1
|-
| 37-H || 2.5414000000 || 1
|-
| 29-H || 2.4458000000 || 1
|-
| 38-H || 2.4396000000 || 2
|-
| 41-H || 2.2127000000 || 1
|-
| 27-H || 2.1244000000 || 1
|-
| 19-H || 2.0957000000 || 2
|-
| 26-H || 1.9936000000 || 1
|-
| 42-H || 1.9921000000 || 2
|-
| 45-H || 1.9888000000 || 3
|-
| 30-H || 1.9628000000 || 4
|-
| 28-H || 1.8624000000 || 1
|-
| 43-H || 1.7942000000 || 1
|-
| 47-H || 1.7491000000 || 2
|-
| 44-H || 1.6772000000 || 1
|-
| 19-H || 2.0957000000 || 2
|-
| 31-H || 1.5435000000 || 1
|-
| 34-H || 1.5162000000 || 2
|-
| 40-H || 1.4073000000 || 1
|-
| 49-H || 1.3150000000 || 1
|-
| 35-H || 1.1656000000 || 1
|-
| 46-H || 1.1176000000 || 2
|-
| 48-H || 1.0804000000 || 3
|-
| 36-H || 1.0476000000 || 4
|-
| 33-H || 0.9840000000 || 1
|-
| 32-H || 0.9728000000 || 2
|}

{| class="wikitable" border="1"
|+ Table for 13C NMR
! Atom number!!Chemical shift!! Integration !!Reference values (75 MHz, C6D6 <ref>Spectroscopic data: L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, J. Am. ''Chem. Soc.'','''1990''', ''112'', 277-283</ref>)
|-
| 12-C || 212.2430000000 || 1 || rowspan="20"|211.49, 148.72, 120.90, 74.61, 60.53, 51.30, 50.94, 45.53, 43.28, 40.82, 38.73, 36.78, 35.47, 30.84.30.00, 25.56, 25.35, 22.21, 21.39, 19.83
|-
| 2-C || 148.8953000000 || 1
|-
| 3-C || 118.5509000000 || 1
|-
| 14-C || 89.0565000000 || 1
|-
| 10-C || 67.5747000000 || 1
|-
| 11-C || 56.3146000000 || 1
|-
| 5-C || 55.5376000000 || 1
|-
| 6-C || 50.0936000000 || 1
|-
| 23-C || 46.8216000000 || 1
|-
| 22-C || 44.4718000000 || 1
|-
| 15-C || 41.2998000000 || 1
|-
| 13-C || 37.6775000000 || 1
|-
| 17-C || 36.2823000000 || 1
|-
| 9-C || 32.0825000000 || 1
|-
| 18-C || 29.0650000000 || 1
|-
| 1-C || 28.6982000000 || 1
|-
| 7-C || 25.8648000000 || 1
|-
| 4-C || 25.2119000000 || 1
|-
| 8-C || 23.2836000000 || 1
|-
| 16-C || 21.7432000000 || 1
|}

Comment on NMR spectra: the calculated values generally agree well with experimental data, with some differences in integration numbers. This could be caused by peaks merging together during measurements due to similar chemical shifts. Therefore each hydrogen or carbon cannot be read separately.

For 18: Sum of electronic and thermal free Energies (ΔG)= -1651.462785 Hartree 
 

==Analysis of the properties of the synthesised alkene epoxides==
===Molecule 21===
The pre-catalyst 21 is used in the Shi asymmetric Fructose catalysis. [[File:bond.PNG|200px|right]]It is searched in the Cambridge crystal database (CCDC) to obtain information about bond lengths in this molecule. Two molecules are found in Mercury.

<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>500</size><script>measure 44 52; measure 46 52; measure 40 51; measure 51 38;measure 47 48; measure 39 40; measure 48 39; measure 10 16; measure 8 16; measure 3 4; measure 3 12; measure 4 15; measure 2 15; measure 48 39 40 </script>
<uploadedFileContents>NELQEA01.xyz</uploadedFileContents>
</jmolApplet></jmol>
 
C-O bond lengths (with O-C-O substructures) are labelled. 
Typical C-O bond length is 1.43 Å <ref>CRC Handbook of Chemistry and Physics 65Th Ed.</ref>. Both bond a and bond b are slightly shorter than this value. This could be due to p orbital overlap of the two oxygen atoms.

 

===Molecule 23===
The stable pre-catalyst 23 is used in the Jacobsen asymmetric catalysis. Two molecules are found in Mercury. [[File:Capture23.PNG|200px|right]]
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>500</size><script>measure 139 186; measure 143 182; measure 46 92; measure 51 88</script>
<uploadedFileContents>TOVNIB01.xyz</uploadedFileContents>
</jmolApplet></jmol>
 Within the distance of 2.4 Å, molecules would have interactions. However repulsive interactions occur within 2.1 Å <ref>?</ref>.For molecule 23, from the labelled through space distances we can see that only 1 out of the 4 labelled bonds has disfavoured interactions. Therefore overall the molecule can be considered as stabilized.
 

==Analysis of styrene and stilbene epoxides==
==== Styrene epoxide (1) (R conformer) ====
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Styrene jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Styrene C.PNG|700px]]

1H NMR
[[File:Styrene H.PNG|700px]] 

ECD spectra 
[[File:Styrene ECD.PNG|700px]] 

VCD spectra 
[[File:Styrene VCD.PNG|700px]]
 
[Alpha] (5890.0A)= 48.89 deg (lit. 44.8 deg <ref>Kuladip Sarma et al., "A novel method for the synthesis of chiral epoxides from
styrene derivatives using chiral acids in presence of Pseudomonas lipase G6 [PSL G6] and hydrogen peroxide", ''Tetrahedron'', '''2007''', ''63'',735–8741 </ref>)
 
'''NCI (non-covalent-interaction) analysis''' [[File:Labelled1.PNG]] Arrow 1 points to the attractive interaction between styrene and the catalyst 22. Arrow 2 points out the bond that is formed in the transition state between the two molecules.
 
'''Electronic topology (QTAIM)''' [[File:QTAIM.PNG]] The solid lines with a yellow dot in the middle indicates a BCP (bond critical point). The dashed line with a yellow dot in the middle indicates a non-covalent BCP.

==== Styrene epoxide (2) (S conformer) ====
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>styrene2 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Styrene2 C.PNG|700px]]

1H NMR
[[File:Styrene2 H.PNG|700px]] 

ECD spectra 
[[File:Styrene2 ECD.PNG|700px]] 

VCD spectra 
[[File:Styrene2 VCD.PNG|700px]] 

[Alpha](5890.0 A) = 30.39 deg (lit. 33.2 deg <ref>E. J. Corey et al, "An Efficient and Catalytically Enantioselective
Route to (S )- (-)-Phenyloxirane", ''J Org Chem'', '''1988''', ''53'',2861-2863 </ref>)

==== Trans-stilbene epoxide(RR) ====
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>stilbene nmr.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Stilbene_Cnmr.PNG|700px]]

1H NMR
[[File:Stilbene_Hnmr.PNG|700px]] 

ECD spectra 
[[File:Stilbene ECD.PNG|700px]] 

VCD spectra 
[[File:Stilbene VCD.PNG|700px]]
 
[Alpha](5890.0 A)= 298.01 deg (lit. 361.0 deg <ref>Philip C. Bulman Page et al, "Asymmetric organocatalysis of epoxidation by iminium salts under non-aqueous conditions", ''Tetrahedron'', '''2007''', ''63'',5386–5393</ref>)
 

===Trans-stilbene epoxide (SS)===
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>stilbene 2 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Stilbene2_cnmr.PNG|700px]]

1H NMR
[[File:Stilbene2_hnmr.PNG|700px]] 

===Using the calculated properties of transition state for the reaction===
Styrene
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''R /hartree'''
| align="center" style="background:#f0f0f0;"|'''S /hartree'''
| align="center" style="background:#f0f0f0;"|'''Difference /hartree'''
| align="center" style="background:#f0f0f0;"|'''Energy in j/mol'''
| align="center" style="background:#f0f0f0;"|'''K'''
| align="center" style="background:#f0f0f0;"|'''enantiomeric excess'''
|-
| -1303.730703||-1303.733828||0.003125||8203.126562||0.036549452||0.035260693
|-
| -1303.730238||-1303.724178||-0.00606||-15907.50303||612.1550372||0.998369091
|-
| -1303.736813||-1303.727673||-0.00914||-23992.50457||15969.30616||0.999937384
|-
| -1303.738044||-1303.738503||0.000459||1204.87523||0.615057815||0.380827119
|-
|
|}

 
Stilbene
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''RR /hartree'''
| align="center" style="background:#f0f0f0;"|'''SS /hartree'''
| align="center" style="background:#f0f0f0;"|'''Difference /hartree'''
| align="center" style="background:#f0f0f0;"|'''Energy in j/mol'''
| align="center" style="background:#f0f0f0;"|'''K'''
| align="center" style="background:#f0f0f0;"|'''enantiomeric excess'''
|-
| -1534.687808||-1534.68344||-0.004368||-11466.00218||102.0346414||0.990294526
|-
| -1534.687252||-1534.685089||-0.002163||-5677.876081||9.879077234||0.908080439
|-
| -1534.700037||-1534.693818||-0.006219||-16324.87811||724.4060173||0.998621462
|-
| -1534.699901||-1534.691858||-0.008043||-21112.87902||4998.040213||0.999799962
|-
|
|}

 
Jacobsen catalyst
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''S,R /hartree'''
| align="center" style="background:#f0f0f0;"|'''R,S /hartree'''
| align="center" style="background:#f0f0f0;"|'''Difference /hartree'''
| align="center" style="background:#f0f0f0;"|'''energy in j/mol'''
| align="center" style="background:#f0f0f0;"|'''K'''
| align="center" style="background:#f0f0f0;"|'''enantiomeric excess'''
|-
| -3383.259559||-3383.25106||-0.008499||-22309.87925||8100.3572||0.999876564
|-
| -3383.253442||-3383.25027||-0.003172||-8326.501586||28.75632659||0.966393701
|-
| S,S /hartree||R,R /hartree||||||||
|-
| -3383.262481||-3383.253816||-0.008665||-22745.62933||9657.037968||0.999896459
|-
| -3383.257847||-3383.254344||-0.003503||-9195.376751||40.82752619||0.976092299
|-
|
|}

(K= exp(-ΔG/RT), enatiomeric excess= K/(1+K)<ref>Schneebeli et al. "Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations", ''J Am Chem Soc.'', '''2009''', ''131(11)'',3965–3973</ref>)

==References==
<references/>

Rep:Mod:orgyh3511

2013-11-21T13:51:36Z

Yh3511: /* Analysis of styrene and stilbene epoxides */

==Confirmational Analysis of Cyclopentadiene Dimer==
Cyclopentadiene dimerises to give product 1 and 2. Through further hydrogenation, derivatives 3 and 4 are produced. 
[[File:Capture_total.PNG]]
 
Whether the endo or the exo form dominate depends on whether the reaction is under kinetic or thermodynamic control. Therefore calculations are carried out to obtain values for total bond stretching, angle bending, torsional, van der Waals and electrostatic energies. MMFF94s method is used. The values are listed below in the table.

{| class="wikitable" border="1"
|+ Table 1: Energy values of dimers 1-4
! Property !! Dimer 1 (exo) !! Dimer 2 (endo)!! Dimer 3!! Dimer 4
|-
| Stretch kcal/mol || 3.54305 || 3.46741 || 3.31169 ||2.82305
|-
| Bend kcal/mol || 30.77271 || 33.19144 || 31.93522 || 24.68537
|-
| Torsion kcal/mol || -2.73105 ||-2.94939 || -1.46912 || -0.37837
|-
| van der Waals kcal/mol || 12.80155 || 12.35716 || 13.63750 ||10.63729
|-
| Electrostatic kcal/mol || 13.01372 || 14.18422 ||5.11952 ||5.14702
|-
| Total energy kcal/mol || 55.37344 || 58.19070 || 50.44568 || 41.25749
|-
| Structure ||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>Form 1 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>Form 2 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>3 JMOL.mol</uploadedFileContents>
</jmolApplet></jmol>||<jmol><jmolApplet><title>1</title><color>white</color>
<size>230</size><script>measure 6 5 1; measure 10 4 6</script>
<uploadedFileContents>4 JMOL.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
'''Analysis''' For molecules 1 and 2, it is evident that the exo form is lower in energy, it is the thermodynamic product. However the endo form is produced specifically. This means the kinetic product dominates. From the table above we can see that the angle bending energy contributes largely to the difference in total energy. This could be due to less strained angles in the endo form at sp2 and sp3 carbon centres (since typical angle values for sp2 carbon is 120o and for sp3 carbon is 109o) .
 For molecules 3 and 4, from the energy values we can see that dimer 4 should be the thermodynamic product. From the angles, it it obvious that dimer 3 should be the kinetic product.
 

==Atropisomerism in an Intermediate related to the Synthesis of Taxol==
The two intermediates (9 and 10) in the formation of taxol are optimised and analysed using MMFF94s method.
[[File:Capture_9_and_10.PNG]]
 
The energies of the two atropisomers are given in the table below.
{| class="wikitable" border="1"
|+ Table 2: Energy values of isomers 9-10
! Property !! Isomer 9 !! Isomer 10
|-
| Stretch kcal/mol || 7.65325 || 7.75545
|-
| Bend kcal/mol || 28.28188 || 18.98819
|-
| Torsion kcal/mol || 0.26912 ||3.79387
|-
| van der Waals kcal/mol || 33.14267 || 34.99601
|-
| Electrostatic kcal/mol || 0.30295 || -0.05982
|-
| Total energy kcal/mol || 70.54025 || 66.29283
|-
| Structure|| <jmol><jmolApplet><title>9</title><color>white</color>
<size>230</size><script>measure 6 4 24; measure 16 9 15</script>
<uploadedFileContents>9_JMOL3.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>10</title><color>white</color>
<size>230</size><script>measure 6 4 24; measure 16 9 15</script>
<uploadedFileContents>10_JMOL2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

 It is evident that isomer 10 (down) has the lower energy therefor it is the thermodynamic product. This is due to less contribution from the angle bending energy. From the angles labelled in structures we can see that isomer 10 has a less strained structure. Therefore it could be the kinetic product as well. 
'''Products after hydrogenation'''<ref>W. F. Maier, P. Von Rague Schleyer, ''J. Am. Chem. Soc.'', '''1981''', ''103'', 1891.</ref> 
The energies of the products from hydrogenation of isomers 9 and 10 are also analysed using the same method.
[[File:9 and 10 single.PNG]]
{| class="wikitable" border="1"
|+ Table 3: Energy values of saturated forms
! Property !! Isomer 9 (saturated) !! Isomer 10 (saturated)
|-
| Stretch kcal/mol || 7.22403 || 7.35327
|-
| Bend kcal/mol || 23.32429 || 30.23447
|-
| Torsion kcal/mol || 8.10832 ||6.51434
|-
| van der Waals kcal/mol || 33.55023 || 33.94051
|-
| Electrostatic kcal/mol || 0.00000 || 0.00000
|-
| Total energy kcal/mol || 72.32844 || 78.49372
|}
The saturated products have higher energies than the unsaturated one. This means for the hydrogenation of isomers 9 and 10, the products are less stable than the reactants. Therefore it is an unfavourable process.

==Spectroscopic Simulation using Quantum Mechanics ==
Molecules 17 and 18 are derivatives from molecules 9 and 10 above. For isomer 18, the structure is optimized, and 1H and 13C spectra are simulated using gaussian. [[File:Capture_17_and_18.PNG]]
 
{| class="wikitable" border="1"
|+ Table 4:Molecules 17 and 18
! !!Molecule 17 !!Molecule 18
|-
| Jmol image || <jmol><jmolApplet><title>18</title><color>white</color>
<size>230</size>
<uploadedFileContents>17jmol.mol</uploadedFileContents>
</jmolApplet></jmol> || <jmol><jmolApplet><title>18</title><color>white</color>
<size>230</size>
<uploadedFileContents>18 run 3 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
|-
| Bond stretching energy kcal/mol|| 15.89829|| 14.44122
|-
| Angle bending energy kcal/mol|| 35.38739 || 28.81334
|-
| Torsion kcal/mol|| 14.35822 || 13.37805
|-
| van der Waals kcal/mol|| 53.68261 || 50.45971
|-
| Electrostatic kcal/mol|| -7.12920|| -6.21523
|-
| Total energy kcal/mol|| 113.98747 || 102.38268
|}

{| class="wikitable" border="1"
|+ Table 5: Molecules 18 spectra
! !! Images
|-
| 1H NMR|| [[File:H nmr.PNG|800px]]
|-
| 13C NMR|| [[File:C nmr.PNG|800px]]

|}
 
{| class="wikitable" border="1"
|+ Table for 1H NMR
! Atom number!!Chemical shift!! Integration !!Reference values (300 MHz, C6D6 <ref>Spectroscopic data: L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, J. Am. ''Chem. Soc.'','''1990''', ''112'', 277-283</ref>)
|-
| 25-H || 5.3799000000 || 1 || rowspan="31"| 5.21 (m, 1 H), 3.00-2.70 (m, 6 H), 2.70-2.35(m, 4 H), 2.20-1.70 (m, 6 H), 1.58 (t, J = 5.4 Hz, 1 H), 1.50-1.20 (m, 3 H), 1.10 (s, 3 H), 1.07(s, 3 H), 1.03 (s, 3 H)
|-
| 53-H || 3.3549000000 || 1
|-
| 52-H || 3.1421000000 || 1
|-
| 50-H || 3.0461000000 || 1
|-
| 51-H || 2.9783000000 || 1
|-
| 39-H || 2.8347000000 || 1
|-
| 37-H || 2.5414000000 || 1
|-
| 29-H || 2.4458000000 || 1
|-
| 38-H || 2.4396000000 || 2
|-
| 41-H || 2.2127000000 || 1
|-
| 27-H || 2.1244000000 || 1
|-
| 19-H || 2.0957000000 || 2
|-
| 26-H || 1.9936000000 || 1
|-
| 42-H || 1.9921000000 || 2
|-
| 45-H || 1.9888000000 || 3
|-
| 30-H || 1.9628000000 || 4
|-
| 28-H || 1.8624000000 || 1
|-
| 43-H || 1.7942000000 || 1
|-
| 47-H || 1.7491000000 || 2
|-
| 44-H || 1.6772000000 || 1
|-
| 19-H || 2.0957000000 || 2
|-
| 31-H || 1.5435000000 || 1
|-
| 34-H || 1.5162000000 || 2
|-
| 40-H || 1.4073000000 || 1
|-
| 49-H || 1.3150000000 || 1
|-
| 35-H || 1.1656000000 || 1
|-
| 46-H || 1.1176000000 || 2
|-
| 48-H || 1.0804000000 || 3
|-
| 36-H || 1.0476000000 || 4
|-
| 33-H || 0.9840000000 || 1
|-
| 32-H || 0.9728000000 || 2
|}

{| class="wikitable" border="1"
|+ Table for 13C NMR
! Atom number!!Chemical shift!! Integration !!Reference values (75 MHz, C6D6 <ref>Spectroscopic data: L. Paquette, N. A. Pegg, D. Toops, G. D. Maynard, R. D. Rogers, J. Am. ''Chem. Soc.'','''1990''', ''112'', 277-283</ref>)
|-
| 12-C || 212.2430000000 || 1 || rowspan="20"|211.49, 148.72, 120.90, 74.61, 60.53, 51.30, 50.94, 45.53, 43.28, 40.82, 38.73, 36.78, 35.47, 30.84.30.00, 25.56, 25.35, 22.21, 21.39, 19.83
|-
| 2-C || 148.8953000000 || 1
|-
| 3-C || 118.5509000000 || 1
|-
| 14-C || 89.0565000000 || 1
|-
| 10-C || 67.5747000000 || 1
|-
| 11-C || 56.3146000000 || 1
|-
| 5-C || 55.5376000000 || 1
|-
| 6-C || 50.0936000000 || 1
|-
| 23-C || 46.8216000000 || 1
|-
| 22-C || 44.4718000000 || 1
|-
| 15-C || 41.2998000000 || 1
|-
| 13-C || 37.6775000000 || 1
|-
| 17-C || 36.2823000000 || 1
|-
| 9-C || 32.0825000000 || 1
|-
| 18-C || 29.0650000000 || 1
|-
| 1-C || 28.6982000000 || 1
|-
| 7-C || 25.8648000000 || 1
|-
| 4-C || 25.2119000000 || 1
|-
| 8-C || 23.2836000000 || 1
|-
| 16-C || 21.7432000000 || 1
|}

Comment on NMR spectra: the calculated values generally agree well with experimental data, with some differences in integration numbers. This could be caused by peaks merging together during measurements due to similar chemical shifts. Therefore each hydrogen or carbon cannot be read separately.

For 18: Sum of electronic and thermal free Energies (ΔG)= 1651.462785 Hartree 
 

==Analysis of the properties of the synthesised alkene epoxides==
===Molecule 21===
The pre-catalyst 21 is used in the Shi asymmetric Fructose catalysis. [[File:bond.PNG|200px|right]]It is searched in the Cambridge crystal database (CCDC) to obtain information about bond lengths in this molecule. Two molecules are found in Mercury.

<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>500</size><script>measure 44 52; measure 46 52; measure 40 51; measure 51 38;measure 47 48; measure 39 40; measure 48 39; measure 10 16; measure 8 16; measure 3 4; measure 3 12; measure 4 15; measure 2 15; measure 48 39 40 </script>
<uploadedFileContents>NELQEA01.xyz</uploadedFileContents>
</jmolApplet></jmol>
 
C-O bond lengths (with O-C-O substructures) are labelled. 
Typical C-O bond length is 1.43 Å <ref>CRC Handbook of Chemistry and Physics 65Th Ed.</ref>. Both bond a and bond b are slightly shorter than this value. This could be due to p orbital overlap of the two oxygen atoms.

 

===Molecule 23===
The stable pre-catalyst 23 is used in the Jacobsen asymmetric catalysis. Two molecules are found in Mercury. [[File:Capture23.PNG|200px|right]]
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>500</size><script>measure 139 186; measure 143 182; measure 46 92; measure 51 88</script>
<uploadedFileContents>TOVNIB01.xyz</uploadedFileContents>
</jmolApplet></jmol>
 Within the distance of 2.4 Å, molecules would have interactions. However repulsive interactions occur within 2.1 Å <ref>?</ref>.For molecule 23, from the labelled through space distances we can see that only 1 out of the 4 labelled bonds has disfavoured interactions. Therefore overall the molecule can be considered as stabilized.
 

==Analysis of styrene and stilbene epoxides==
==== Styrene epoxide (1) (R conformer) ====
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>Styrene jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Styrene C.PNG|700px]]

1H NMR
[[File:Styrene H.PNG|700px]] 

ECD spectra 
[[File:Styrene ECD.PNG|700px]] 

VCD spectra 
[[File:Styrene VCD.PNG|700px]]
 
[Alpha] (5890.0A)= 48.89 deg (lit. 44.8 deg <ref>Kuladip Sarma et al., "A novel method for the synthesis of chiral epoxides from
styrene derivatives using chiral acids in presence of Pseudomonas lipase G6 [PSL G6] and hydrogen peroxide", ''Tetrahedron'', '''2007''', ''63'',735–8741 </ref>)
 
'''NCI (non-covalent-interaction) analysis''' [[File:Labelled1.PNG]] Arrow 1 points to the attractive interaction between styrene and the catalyst 22. Arrow 2 points out the bond that is formed in the transition state between the two molecules.
 
'''Electronic topology (QTAIM)''' [[File:QTAIM.PNG]] The solid lines with a yellow dot in the middle indicates a BCP (bond critical point). The dashed line with a yellow dot in the middle indicates a non-covalent BCP.

==== Styrene epoxide (2) (S conformer) ====
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>styrene2 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Styrene2 C.PNG|700px]]

1H NMR
[[File:Styrene2 H.PNG|700px]] 

ECD spectra 
[[File:Styrene2 ECD.PNG|700px]] 

VCD spectra 
[[File:Styrene2 VCD.PNG|700px]] 

[Alpha](5890.0 A) = 30.39 deg (lit. 33.2 deg <ref>E. J. Corey et al, "An Efficient and Catalytically Enantioselective
Route to (S )- (-)-Phenyloxirane", ''J Org Chem'', '''1988''', ''53'',2861-2863 </ref>)

==== Trans-stilbene epoxide(RR) ====
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>stilbene nmr.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Stilbene_Cnmr.PNG|700px]]

1H NMR
[[File:Stilbene_Hnmr.PNG|700px]] 

ECD spectra 
[[File:Stilbene ECD.PNG|700px]] 

VCD spectra 
[[File:Stilbene VCD.PNG|700px]]
 
[Alpha](5890.0 A)= 298.01 deg (lit. 361.0 deg <ref>Philip C. Bulman Page et al, "Asymmetric organocatalysis of epoxidation by iminium salts under non-aqueous conditions", ''Tetrahedron'', '''2007''', ''63'',5386–5393</ref>)
 

===Trans-stilbene epoxide (SS)===
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>stilbene 2 jmol.mol</uploadedFileContents>
</jmolApplet></jmol>
13C NMR
[[File:Stilbene2_cnmr.PNG|700px]]

1H NMR
[[File:Stilbene2_hnmr.PNG|700px]] 

===Using the calculated properties of transition state for the reaction===
Styrene
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''R /hartree'''
| align="center" style="background:#f0f0f0;"|'''S /hartree'''
| align="center" style="background:#f0f0f0;"|'''Difference /hartree'''
| align="center" style="background:#f0f0f0;"|'''Energy in j/mol'''
| align="center" style="background:#f0f0f0;"|'''K'''
| align="center" style="background:#f0f0f0;"|'''enantiomeric excess'''
|-
| -1303.730703||-1303.733828||0.003125||8203.126562||0.036549452||0.035260693
|-
| -1303.730238||-1303.724178||-0.00606||-15907.50303||612.1550372||0.998369091
|-
| -1303.736813||-1303.727673||-0.00914||-23992.50457||15969.30616||0.999937384
|-
| -1303.738044||-1303.738503||0.000459||1204.87523||0.615057815||0.380827119
|-
|
|}

 
Stilbene
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''RR /hartree'''
| align="center" style="background:#f0f0f0;"|'''SS /hartree'''
| align="center" style="background:#f0f0f0;"|'''Difference /hartree'''
| align="center" style="background:#f0f0f0;"|'''Energy in j/mol'''
| align="center" style="background:#f0f0f0;"|'''K'''
| align="center" style="background:#f0f0f0;"|'''enantiomeric excess'''
|-
| -1534.687808||-1534.68344||-0.004368||-11466.00218||102.0346414||0.990294526
|-
| -1534.687252||-1534.685089||-0.002163||-5677.876081||9.879077234||0.908080439
|-
| -1534.700037||-1534.693818||-0.006219||-16324.87811||724.4060173||0.998621462
|-
| -1534.699901||-1534.691858||-0.008043||-21112.87902||4998.040213||0.999799962
|-
|
|}

 
Jacobsen catalyst
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''S,R /hartree'''
| align="center" style="background:#f0f0f0;"|'''R,S /hartree'''
| align="center" style="background:#f0f0f0;"|'''Difference /hartree'''
| align="center" style="background:#f0f0f0;"|'''energy in j/mol'''
| align="center" style="background:#f0f0f0;"|'''K'''
| align="center" style="background:#f0f0f0;"|'''enantiomeric excess'''
|-
| -3383.259559||-3383.25106||-0.008499||-22309.87925||8100.3572||0.999876564
|-
| -3383.253442||-3383.25027||-0.003172||-8326.501586||28.75632659||0.966393701
|-
| S,S /hartree||R,R /hartree||||||||
|-
| -3383.262481||-3383.253816||-0.008665||-22745.62933||9657.037968||0.999896459
|-
| -3383.257847||-3383.254344||-0.003503||-9195.376751||40.82752619||0.976092299
|-
|
|}

(K= exp(-ΔG/RT), enatiomeric excess= K/(1+K)<ref>Schneebeli et al. "Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations", ''J Am Chem Soc.'', '''2009''', ''131(11)'',3965–3973</ref>)

==References==
<references/>

File:Stilbene2 hnmr.PNG

2013-11-21T12:50:44Z

Yh3511:

File:Stilbene2 cnmr.PNG

2013-11-21T12:50:43Z

Yh3511:

File:Stilbene 2 jmol.mol

2013-11-21T12:50:42Z

Yh3511:

Rep:Mod:orgyh3511

2013-11-20T17:53:59Z

2013-11-20T17:16:31Z

Yh3511:

Rep:Mod:orgyh3511

2013-11-20T16:56:17Z

Yh3511: /* Molecule 23 */