= Organic Computational Labs Module =

=== Calculations for Cyclopentadiene Dimers and their Hydrogenated Products ===

This part of the report uses ChemBio 3D to optimize complexes and determine the total energy of the molecule. The method used to optimize the molecules was a MM2 forcefield. The first comparison of energies was done between the 2 dimers of cyclopentadiene, it is known that cyclopentadiene takes the form of the endo dimer specifically over the exo dimer. By looking at the energies and hence the thermodynamic stability of the dimers it is possible to gain an insight into there formation.

'''1) Exo Dimer'''

This first molecule is the exo dimer of cyclopentadiene where MM2 minimization was used in order to obtain an energy minima.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>DDDDDDDDD1.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The table below shows the energy data obtained for the exo dimer.

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 76: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2855
Bend: 20.5794
Stretch-Bend: -0.8381
Torsion: 7.6571
Non-1,4 VDW: -1.4171
1,4 VDW: 4.2322
Dipole/Dipole: 0.3776
Total Energy: 31.8766 kcal/mol
Calculation completed
------------------------------------

'''2) Endo Dimer'''

This second molecule is the endo dimer of cyclopentadiene, again MM2 minimization was carried out.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CCCCC.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The minimization yielded the following results for the endo dimer:

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 103: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2502
Bend: 20.8488
Stretch-Bend: -0.8357
Torsion: 9.5109
Non-1,4 VDW: -1.5455
1,4 VDW: 4.3210
Dipole/Dipole: 0.4477
Total Energy: 33.9975 kcal/mol
Calculation completed
------------------------------------

By comparing the total energy of the two dimers it can be seen that the exo dimer is more stable by 2.1209 kcal/mol compared to the endo dimer, this is a significant difference. The majority of the energy difference observed here is due to torsion in the molecules as seen tables that sum to the total energy. This means that the reaction that forms cyclopentadiene is not controlled by only thermodynamics. It is believed therefore the the product formation is due to steric or orbital effects as it is known the endo dimer is in actuality favoured, despite the fact that the exo dimer was calculated to be more energetically stable.

The endo dimer can be hydrogenated at either of the two double bonds, this would result in the two molecules seen below, the same method of optimization has been used here so that the total energies of each molecule can be compared.

'''3) Endo Hydrogenation (1)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CPEN_D3.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2782
Bend: 19.8555
Stretch-Bend: -0.8346
Torsion: 10.8110
Non-1,4 VDW: -1.2202
1,4 VDW: 5.6331
Dipole/Dipole: 0.1621
Total Energy: 35.6850 kcal/mol
Calculation completed
------------------------------------

'''4) Endo Hydrogenation (2)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>FFFF.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 153: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.0968
Bend: 14.5244
Stretch-Bend: -0.5493
Torsion: 12.4974
Non-1,4 VDW: -1.0692
1,4 VDW: 4.5112
Dipole/Dipole: 0.1406
Total Energy: 31.1520 kcal/mol
Calculation completed
------------------------------------

Again, it is possible to compare the difference between the two total energies. The second hydrogenated molecule is more stable that first one by 4.533 kcal/mol, this means that it is the thermodynamic product of the hydrogenation reaction. It is possible to understand the different energies better by comparing the components that make up each total energy. The major contribution the large total energy difference between the two molecules appears to be the bending energy which has a difference of 5.3311 kcal/mol.

=== Comparison of Energies from Cyclopentadiene Dimers and There Hydrogenated Products ===

{| class="COMP " border="1px" align="center" width="900px"
|+ Comparison of Energies for Cyclopentadiene Dimers and There Hydrogenated Products
! Type !! Cyclopentadiene Dimer 1 !! Cyclopentadiene Dimer 2 !! Hydrogenated Dimer 1 !! Hydrogenated Dimer 2
|-
| Image ||[[File:CPEN_D2.jpg|300px|center]]||[[File:CPEN_D1.jpg|300px|center]]||[[File:CPEN_D3.jpg|300px|center]]||[[File:CPEN_D4.jpg|300px|center]]
|-
|Stretch (kcal mol<sup>-1</sup>) || 1.2855 || 1.2502 || 1.2782 || 1.0964
|-
|Bend (kcal mol<sup>-1</sup>) || 20.5794 || 20.8488 || 19.8555|| 14.5246
|-
| Stretch-Bend (kcal mol<sup>-1</sup>) || -0.8381 || -0.8346 || -0.5488 || -0.5494
|-
|Torsion (kcal mol<sup>-1</sup>) || 7.6571 || 9.5109 || 10.8110 || 12.4971
|-
| Non 1-4 Van der Waal's (kcal mol<sup>-1</sup>) || -1.4171 || -1.5455 || -1.2202 || -1.0701
|-
| 1,4 Van der Waal's (kcal mol<sup>-1</sup>) || 4.2322 || 4.3210 || 5.6331 || 4.5129
|-
| Dipole, Dipole (kcal mol<sup>-1</sup>) || 0.3776 || 0.4477 || 0.1621 || 0.1406
|-
| Total energy (kcal mol<sup>-1</sup>) || 31.8766 || 33.9975 || 35.6850 || 31.1520
|-
|}

The table above has complicated the data from the above calculations so that the relative energy's of each component can be easily compared. It can be seen that between dimers or products most of the energy's are very similar and there are few differences between the two as would be expected.

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

This section of the report is looking at two isomers of an intermediate in the synthesis of taxol, the two isomers occur due to the possibility of rotation of the keytone group, it can either be orientated up or down on the ring. The first step at analyzing the two possible isomers was to construct them with the correct steriochemistry, these molecules where then optimized using a MM2 field and the energy was then calculated again using a MMFF94. The results of these calculations and the molecules constructed can be seen below.

[[File:TAX_D15.jpg|300px|center]]
[[File:Taxol_A.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_A.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(26)-H(27)
Separating coincident atoms: H(37)-H(39)
Warning: Some parameters are guessed (Quality = 1).
Iteration 228: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7863
Bend: 16.5503
Stretch-Bend: 0.4310
Torsion: 18.2501
Non-1,4 VDW: -1.5648
1,4 VDW: 13.1116
Dipole/Dipole: -1.7249
Total Energy: 47.8396 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 58: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 70.5359 kcal/mol
Calculation completed
------------------------------------

[[File:TAX_D16.jpg|300px|center]]

[[File:Taxol_B.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_B.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(31)-H(32)
Separating coincident atoms: H(35)-H(36)
Warning: Some parameters are guessed (Quality = 1).
Iteration 246: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6228
Bend: 11.3382
Stretch-Bend: 0.3439
Torsion: 19.6639
Non-1,4 VDW: -2.1524
1,4 VDW: 12.8688
Dipole/Dipole: -2.0018
Total Energy: 42.6834 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 37: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 60.5719 kcal/mol
Calculation completed
------------------------------------

By looking at the energy's obtained by both calculations it can be seen that the second isomer is more stable than the first, the energy difference as calculated using the MM2 method is 5.1562 kcal/mol and the difference using the MMFF94 is 9.964 kcal/mol. It can therefore be said that the the intermediate with the keytone pointing in the same orientation as the neighboring hydrogen atoms is the one formed during the reaction.
By looking at the composition of the energy's calculated using the MM2 method the largest difference between the two is again in the bending component of the total energy. The key structual difference observed between the two isomers (apart form the inversion of the keytone) is that the 6 membered ring flips conformation, this is shown in the image below.

Comparison image showing ring flip:

[[File:Taxol_RF.png|400px|center]]

=== Modelling Using Semi-empirical Molecular Orbital Theory. ===

This section of the report is looking at the diene shown below, the intial step where the same as above with the molecule being constructed in ChemBio 3D and then being optimized using the MM2 method, the results of which can be seen below:

[[File:Compound_12.jpg|300px|center]]

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 151: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.6183
Bend: 4.7355
Stretch-Bend: 0.0399
Torsion: 7.6600
Non-1,4 VDW: -1.0653
1,4 VDW: 5.7939
Dipole/Dipole: 0.1124
Total Energy: 17.8945 kcal/mol
Calculation completed
------------------------------------

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Idontknow.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The next step taken was to further optimize the molecule, this was done using the MOPAC method, this method takes into account any electronic effects that are not covered by the MM2 method. The result of the calculation can be seen below:

Mopac Job: AUX RM1 CHARGE=0 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09953 (< 0.10000) Heat of Formation = 22.82769 Kcal/Mol
-----------------------------------------

The MOPAC calculation also involves the optimization of the molecule by compring this structure to the MM2 optimized one it can be seen that they have different geometrys, this would be expected as the energies are different. The two different structures have been overlayed below to outline the key differences.

[[File:PICKYWIK.png|center|300px]]

From the overlapped molecules it can be seen that the chlorine atom distorts the ring more in the highlighted MOPAC optimization. This means that there are orbital interaction involved that force the ring on the left hand side to bend downwards. This increases the strain on the molecule as so increases it energy, it it not possible to compare the energys of the two optimizations howerve as they are calculated through different methods.

The next part of the analysis involves modeling the molecular orbitals of the molecule, a 2D representation of the HOMO and LUMO can be seen below, the files for this calculation can be found here: {{DOI|10042/24374}}

One molecular orbital below the HOMO

[[File:12HOMO1.jpg|center|300px]]

The HOMO molecular orbital

[[File:12HOMO.jpg|center|300px]]

The LUMO molecular orbital
[[File:12LUMO.jpg|center|300px]]

One above the LUMO molecular orbital
[[File:12LUMO1.jpg|center|300px]]

It can be seen that as expected these orbitals have a pane of symmetry along the molecule the chlorine atom has a large effect on the orbitals as the HOMO seems to center around it. The HOMO and LUMO are often looked at as they often give a lot of information about the bonding character of the molecule.

The image below shows the electrostactic potential surface for the molecule, it is symetrical and has most of the negative charge based around the alkene bonds and the chlorine atom as would be expected.
[[File:Diene_estat.jpg|center|300px]]

The final part of the analysis of this molecule was a vibrational analysis, this was run in Gaussian on the previously optimized molecule. The resulting vibrations can be seen on the molecule below, to view the differnt vibration right click on the image and place the curser over "model", you can then select which vibration you wish to view, it also displays in that selection the frequency of the vibration.

<div align="center">
<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>Diene_FREQ_LOG.log</uploadedFileContents>
</jmolApplet>
</jmol>
</div>

=== Monosaccharide chemistry and the mechanism of glycosidation ===

The computational methods we have looked at before have been shown to provide a good understanding of intermediates in a reaction, this section will be looking at part of a glycosidation reaction which can be seen below:

[[File:GLY.png|center]]

The first intermediate has 4 possible isomers, the optimizations for which can be seen below, the structres of each of isomer have been tabulated below for better comparison with there relevant energies.

Energy calculations for isomer 1

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4507
Bend: 11.5140
Stretch-Bend: 0.8750
Torsion: 1.4349
Non-1,4 VDW: 0.2620
1,4 VDW: 19.4581
Charge/Dipole: -28.6982
Dipole/Dipole: 5.2444
Total Energy: 12.5409 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09168 (< 0.10000) Heat of Formation = -70.04084 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 2

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4313
Bend: 11.7850
Stretch-Bend: 0.9826
Torsion: 1.4209
Non-1,4 VDW: 0.7701
1,4 VDW: 18.8357
Charge/Dipole: -27.0491
Dipole/Dipole: 5.9906
Total Energy: 15.1670 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09431 (< 0.10000) Heat of Formation = -79.27099 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 3

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 447: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2173
Bend: 10.6642
Stretch-Bend: 0.8233
Torsion: 0.6467
Non-1,4 VDW: -1.5632
1,4 VDW: 19.2644
Charge/Dipole: -15.9514
Dipole/Dipole: 3.8992
Total Energy: 20.0004 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07357 (< 0.10000) Heat of Formation = -65.36964 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 4

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2532
Bend: 11.1534
Stretch-Bend: 0.8510
Torsion: 1.1097
Non-1,4 VDW: -2.1220
1,4 VDW: 19.3508
Charge/Dipole: -11.5317
Dipole/Dipole: 3.8657
Total Energy: 24.9301 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08961 (< 0.10000) Heat of Formation = -62.83046 Kcal/Mol
-----------------------------------------

{| class="Isomers" border="1px" align="center" width="1000px"
|+ Table for comparison on first intermediate
! Isomer description !! Visual of MM2 optimized isomer !! Total energy of MM2 obtimzed isomer (Kcal/mol) !! Visual of MOPAC optimized isomer !! Heat of formation from MOPAC Kcal/mol !! Distance between carbonyl oxygen and acyl carbon
|-
| Axial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1.cml</uploadedFileContents>
</jmolApplet></jmol> || 12.5409 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -70.04084 || 2.00
|-
| Axial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2.cml</uploadedFileContents>
</jmolApplet></jmol> || 15.1670 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -79.27099 || 1.457
|-
| Equatorial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3.5.cml</uploadedFileContents>
</jmolApplet></jmol> || 20.0004 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -65.36964 || 2.869
|-
| Equatorial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4.1.cml</uploadedFileContents>
</jmolApplet></jmol> || 24.9301 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -62.83046 || 2.869
|-|}

This table shows that the isomer which have an axial carbonyl group are more stable than with an equitorial one, both MM2 and MOPAC agree with this. This means that under thermodynamic control either isomer 1 or 2 will be dominant. The total energies generated form MM2 indicate that the first isomer "Axial and above the ring" would be favored as it is 2.6261 Kcal/mol lower than isomer 2. This does not take into account electrostactis though which, considering the high charge density present, does not give a complete picture and so looking at the heats of formation from the MOPAC analysis it can be said that in reality isomer 2 is more stable. This is due to the added stability of an additional bond which cannot be seen in the representation but by looking at the distance between the carbonyl oxygen and acyl carbon can be understood to exist. This bond helps balance out the charges present and infact converts the molecule to the next step in the reaction drawn above. On the next page we will generate an energy for each isomer but with the new bond formed, the next page can be found [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]].

= This wiki page continues from the following link: [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]] =

Rep:Mod:AlexanderGray

2013-03-15T15:54:58Z

Ag3210: /* Modelling Using Semi-empirical Molecular Orbital Theory. */

= Organic Computational Labs Module =

=== Calculations for Cyclopentadiene Dimers and their Hydrogenated Products ===

This part of the report uses ChemBio 3D to optimize complexes and determine the total energy of the molecule. The method used to optimize the molecules was a MM2 forcefield. The first comparison of energies was done between the 2 dimers of cyclopentadiene, it is known that cyclopentadiene takes the form of the endo dimer specifically over the exo dimer. By looking at the energies and hence the thermodynamic stability of the dimers it is possible to gain an insight into there formation.

'''1) Exo Dimer'''

This first molecule is the exo dimer of cyclopentadiene where MM2 minimization was used in order to obtain an energy minima.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>DDDDDDDDD1.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The table below shows the energy data obtained for the exo dimer.

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 76: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2855
Bend: 20.5794
Stretch-Bend: -0.8381
Torsion: 7.6571
Non-1,4 VDW: -1.4171
1,4 VDW: 4.2322
Dipole/Dipole: 0.3776
Total Energy: 31.8766 kcal/mol
Calculation completed
------------------------------------

'''2) Endo Dimer'''

This second molecule is the endo dimer of cyclopentadiene, again MM2 minimization was carried out.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CCCCC.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The minimization yielded the following results for the endo dimer:

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 103: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2502
Bend: 20.8488
Stretch-Bend: -0.8357
Torsion: 9.5109
Non-1,4 VDW: -1.5455
1,4 VDW: 4.3210
Dipole/Dipole: 0.4477
Total Energy: 33.9975 kcal/mol
Calculation completed
------------------------------------

By comparing the total energy of the two dimers it can be seen that the exo dimer is more stable by 2.1209 kcal/mol compared to the endo dimer, this is a significant difference. The majority of the energy difference observed here is due to torsion in the molecules as seen tables that sum to the total energy. This means that the reaction that forms cyclopentadiene is not controlled by only thermodynamics. It is believed therefore the the product formation is due to steric or orbital effects as it is known the endo dimer is in actuality favoured, despite the fact that the exo dimer was calculated to be more energetically stable.

The endo dimer can be hydrogenated at either of the two double bonds, this would result in the two molecules seen below, the same method of optimization has been used here so that the total energies of each molecule can be compared.

'''3) Endo Hydrogenation (1)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CPEN_D3.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2782
Bend: 19.8555
Stretch-Bend: -0.8346
Torsion: 10.8110
Non-1,4 VDW: -1.2202
1,4 VDW: 5.6331
Dipole/Dipole: 0.1621
Total Energy: 35.6850 kcal/mol
Calculation completed
------------------------------------

'''4) Endo Hydrogenation (2)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>FFFF.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 153: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.0968
Bend: 14.5244
Stretch-Bend: -0.5493
Torsion: 12.4974
Non-1,4 VDW: -1.0692
1,4 VDW: 4.5112
Dipole/Dipole: 0.1406
Total Energy: 31.1520 kcal/mol
Calculation completed
------------------------------------

Again, it is possible to compare the difference between the two total energies. The second hydrogenated molecule is more stable that first one by 4.533 kcal/mol, this means that it is the thermodynamic product of the hydrogenation reaction. It is possible to understand the different energies better by comparing the components that make up each total energy. The major contribution the large total energy difference between the two molecules appears to be the bending energy which has a difference of 5.3311 kcal/mol.

=== Comparison of Energies from Cyclopentadiene Dimers and There Hydrogenated Products ===

{| class="COMP " border="1px" align="center" width="900px"
|+ Comparison of Energies for Cyclopentadiene Dimers and There Hydrogenated Products
! Type !! Cyclopentadiene Dimer 1 !! Cyclopentadiene Dimer 2 !! Hydrogenated Dimer 1 !! Hydrogenated Dimer 2
|-
| Image ||[[File:CPEN_D2.jpg|300px|center]]||[[File:CPEN_D1.jpg|300px|center]]||[[File:CPEN_D3.jpg|300px|center]]||[[File:CPEN_D4.jpg|300px|center]]
|-
|Stretch (kcal mol<sup>-1</sup>) || 1.2855 || 1.2502 || 1.2782 || 1.0964
|-
|Bend (kcal mol<sup>-1</sup>) || 20.5794 || 20.8488 || 19.8555|| 14.5246
|-
| Stretch-Bend (kcal mol<sup>-1</sup>) || -0.8381 || -0.8346 || -0.5488 || -0.5494
|-
|Torsion (kcal mol<sup>-1</sup>) || 7.6571 || 9.5109 || 10.8110 || 12.4971
|-
| Non 1-4 Van der Waal's (kcal mol<sup>-1</sup>) || -1.4171 || -1.5455 || -1.2202 || -1.0701
|-
| 1,4 Van der Waal's (kcal mol<sup>-1</sup>) || 4.2322 || 4.3210 || 5.6331 || 4.5129
|-
| Dipole, Dipole (kcal mol<sup>-1</sup>) || 0.3776 || 0.4477 || 0.1621 || 0.1406
|-
| Total energy (kcal mol<sup>-1</sup>) || 31.8766 || 33.9975 || 35.6850 || 31.1520
|-
|}

The table above has complicated the data from the above calculations so that the relative energy's of each component can be easily compared. It can be seen that between dimers or products most of the energy's are very similar and there are few differences between the two as would be expected.

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

This section of the report is looking at two isomers of an intermediate in the synthesis of taxol, the two isomers occur due to the possibility of rotation of the keytone group, it can either be orientated up or down on the ring. The first step at analyzing the two possible isomers was to construct them with the correct steriochemistry, these molecules where then optimized using a MM2 field and the energy was then calculated again using a MMFF94. The results of these calculations and the molecules constructed can be seen below.

[[File:TAX_D15.jpg|300px|center]]
[[File:Taxol_A.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_A.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(26)-H(27)
Separating coincident atoms: H(37)-H(39)
Warning: Some parameters are guessed (Quality = 1).
Iteration 228: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7863
Bend: 16.5503
Stretch-Bend: 0.4310
Torsion: 18.2501
Non-1,4 VDW: -1.5648
1,4 VDW: 13.1116
Dipole/Dipole: -1.7249
Total Energy: 47.8396 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 58: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 70.5359 kcal/mol
Calculation completed
------------------------------------

[[File:TAX_D16.jpg|300px|center]]

[[File:Taxol_B.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_B.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(31)-H(32)
Separating coincident atoms: H(35)-H(36)
Warning: Some parameters are guessed (Quality = 1).
Iteration 246: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6228
Bend: 11.3382
Stretch-Bend: 0.3439
Torsion: 19.6639
Non-1,4 VDW: -2.1524
1,4 VDW: 12.8688
Dipole/Dipole: -2.0018
Total Energy: 42.6834 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 37: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 60.5719 kcal/mol
Calculation completed
------------------------------------

By looking at the energy's obtained by both calculations it can be seen that the second isomer is more stable than the first, the energy difference as calculated using the MM2 method is 5.1562 kcal/mol and the difference using the MMFF94 is 9.964 kcal/mol. It can therefore be said that the the intermediate with the keytone pointing in the same orientation as the neighboring hydrogen atoms is the one formed during the reaction.
By looking at the composition of the energy's calculated using the MM2 method the largest difference between the two is again in the bending component of the total energy. The key structual difference observed between the two isomers (apart form the inversion of the keytone) is that the 6 membered ring flips conformation, this is shown in the image below.

Comparison image showing ring flip:

[[File:Taxol_RF.png|400px|center]]

=== Modelling Using Semi-empirical Molecular Orbital Theory. ===

This section of the report is looking at the diene shown below, the intial step where the same as above with the molecule being constructed in ChemBio 3D and then being optimized using the MM2 method, the results of which can be seen below:

[[File:Compound_12.jpg|300px|center]]

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 151: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.6183
Bend: 4.7355
Stretch-Bend: 0.0399
Torsion: 7.6600
Non-1,4 VDW: -1.0653
1,4 VDW: 5.7939
Dipole/Dipole: 0.1124
Total Energy: 17.8945 kcal/mol
Calculation completed
------------------------------------

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Idontknow.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The next step taken was to further optimize the molecule, this was done using the MOPAC method, this method takes into account any electronic effects that are not covered by the MM2 method. The result of the calculation can be seen below:

Mopac Job: AUX RM1 CHARGE=0 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09953 (< 0.10000) Heat of Formation = 22.82769 Kcal/Mol
-----------------------------------------

The MOPAC calculation also involves the optimization of the molecule by compring this structure to the MM2 optimized one it can be seen that they have different geometrys, this would be expected as the energies are different. The two different structures have been overlayed below to outline the key differences.

[[File:PICKYWIK.png|center|300px]]

From the overlapped molecules it can be seen that the chlorine atom distorts the ring more in the highlighted MOPAC optimization. This means that there are orbital interaction involved that force the ring on the left hand side to bend downwards. This increases the strain on the molecule as so increases it energy, it it not possible to compare the energys of the two optimizations howerve as they are calculated through different methods.

The next part of the analysis involves modeling the molecular orbitals of the molecule, a 2D representation of the HOMO and LUMO can be seen below, the files for this calculation can be found here: {{DOI|10042/24374}}

One molecular orbital below the HOMO

[[File:12HOMO1.jpg|center|300px]]

The HOMO molecular orbital

[[File:12HOMO.jpg|center|300px]]

The LUMO molecular orbital
[[File:12LUMO.jpg|center|300px]]

One above the LUMO molecular orbital
[[File:12LUMO1.jpg|center|300px]]

It can be seen that as expected these orbitals have a pane of symmetry along the molecule the chlorine atom has a large effect on the orbitalsas the HOMO seems to center around it.

The image below shows the electrostactic potential surface for the molecule, it is symetrical and has most of the negative charge based around the alkene bonds and the chlorine atom as would be expected.
[[File:Diene_estat.jpg|center|300px]]

The final part of the analysis of this molecule was a vibrational analysis, this was run in Gaussian on the previously optimized molecule. The resulting vibrations can be seen on the molecule below, to view the differnt vibration right click on the image and place the curser over "model", you can then select which vibration you wish to view, it also displays in that selection the frequency of the vibration.

<div align="center">
<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>Diene_FREQ_LOG.log</uploadedFileContents>
</jmolApplet>
</jmol>
</div>

=== Monosaccharide chemistry and the mechanism of glycosidation ===

The computational methods we have looked at before have been shown to provide a good understanding of intermediates in a reaction, this section will be looking at part of a glycosidation reaction which can be seen below:

[[File:GLY.png|center]]

The first intermediate has 4 possible isomers, the optimizations for which can be seen below, the structres of each of isomer have been tabulated below for better comparison with there relevant energies.

Energy calculations for isomer 1

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4507
Bend: 11.5140
Stretch-Bend: 0.8750
Torsion: 1.4349
Non-1,4 VDW: 0.2620
1,4 VDW: 19.4581
Charge/Dipole: -28.6982
Dipole/Dipole: 5.2444
Total Energy: 12.5409 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09168 (< 0.10000) Heat of Formation = -70.04084 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 2

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4313
Bend: 11.7850
Stretch-Bend: 0.9826
Torsion: 1.4209
Non-1,4 VDW: 0.7701
1,4 VDW: 18.8357
Charge/Dipole: -27.0491
Dipole/Dipole: 5.9906
Total Energy: 15.1670 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09431 (< 0.10000) Heat of Formation = -79.27099 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 3

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 447: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2173
Bend: 10.6642
Stretch-Bend: 0.8233
Torsion: 0.6467
Non-1,4 VDW: -1.5632
1,4 VDW: 19.2644
Charge/Dipole: -15.9514
Dipole/Dipole: 3.8992
Total Energy: 20.0004 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07357 (< 0.10000) Heat of Formation = -65.36964 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 4

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2532
Bend: 11.1534
Stretch-Bend: 0.8510
Torsion: 1.1097
Non-1,4 VDW: -2.1220
1,4 VDW: 19.3508
Charge/Dipole: -11.5317
Dipole/Dipole: 3.8657
Total Energy: 24.9301 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08961 (< 0.10000) Heat of Formation = -62.83046 Kcal/Mol
-----------------------------------------

{| class="Isomers" border="1px" align="center" width="1000px"
|+ Table for comparison on first intermediate
! Isomer description !! Visual of MM2 optimized isomer !! Total energy of MM2 obtimzed isomer (Kcal/mol) !! Visual of MOPAC optimized isomer !! Heat of formation from MOPAC Kcal/mol !! Distance between carbonyl oxygen and acyl carbon
|-
| Axial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1.cml</uploadedFileContents>
</jmolApplet></jmol> || 12.5409 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -70.04084 || 2.00
|-
| Axial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2.cml</uploadedFileContents>
</jmolApplet></jmol> || 15.1670 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -79.27099 || 1.457
|-
| Equatorial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3.5.cml</uploadedFileContents>
</jmolApplet></jmol> || 20.0004 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -65.36964 || 2.869
|-
| Equatorial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4.1.cml</uploadedFileContents>
</jmolApplet></jmol> || 24.9301 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -62.83046 || 2.869
|-|}

This table shows that the isomer which have an axial carbonyl group are more stable than with an equitorial one, both MM2 and MOPAC agree with this. This means that under thermodynamic control either isomer 1 or 2 will be dominant. The total energies generated form MM2 indicate that the first isomer "Axial and above the ring" would be favored as it is 2.6261 Kcal/mol lower than isomer 2. This does not take into account electrostactis though which, considering the high charge density present, does not give a complete picture and so looking at the heats of formation from the MOPAC analysis it can be said that in reality isomer 2 is more stable. This is due to the added stability of an additional bond which cannot be seen in the representation but by looking at the distance between the carbonyl oxygen and acyl carbon can be understood to exist. This bond helps balance out the charges present and infact converts the molecule to the next step in the reaction drawn above. On the next page we will generate an energy for each isomer but with the new bond formed, the next page can be found [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]].

= This wiki page continues from the following link: [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]] =

File:12LUMO1.jpg

2013-03-15T15:50:33Z

Ag3210:

File:12HOMO1.jpg

2013-03-15T15:50:32Z

Ag3210:

File:12LUMO.jpg

2013-03-15T15:50:32Z

Ag3210: uploaded a new version of "File:12LUMO.jpg"

File:12HOMO.jpg

2013-03-15T15:50:31Z

Ag3210: uploaded a new version of "File:12HOMO.jpg"

File:HOMO.tif

2013-03-15T15:48:41Z

Ag3210: uploaded a new version of "File:HOMO.tif"

Rep:Mod:AlexanderGray

2013-03-15T15:25:07Z

Ag3210: /* Modelling Using Semi-empirical Molecular Orbital Theory. */

= Organic Computational Labs Module =

=== Calculations for Cyclopentadiene Dimers and their Hydrogenated Products ===

This part of the report uses ChemBio 3D to optimize complexes and determine the total energy of the molecule. The method used to optimize the molecules was a MM2 forcefield. The first comparison of energies was done between the 2 dimers of cyclopentadiene, it is known that cyclopentadiene takes the form of the endo dimer specifically over the exo dimer. By looking at the energies and hence the thermodynamic stability of the dimers it is possible to gain an insight into there formation.

'''1) Exo Dimer'''

This first molecule is the exo dimer of cyclopentadiene where MM2 minimization was used in order to obtain an energy minima.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>DDDDDDDDD1.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The table below shows the energy data obtained for the exo dimer.

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 76: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2855
Bend: 20.5794
Stretch-Bend: -0.8381
Torsion: 7.6571
Non-1,4 VDW: -1.4171
1,4 VDW: 4.2322
Dipole/Dipole: 0.3776
Total Energy: 31.8766 kcal/mol
Calculation completed
------------------------------------

'''2) Endo Dimer'''

This second molecule is the endo dimer of cyclopentadiene, again MM2 minimization was carried out.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CCCCC.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The minimization yielded the following results for the endo dimer:

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 103: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2502
Bend: 20.8488
Stretch-Bend: -0.8357
Torsion: 9.5109
Non-1,4 VDW: -1.5455
1,4 VDW: 4.3210
Dipole/Dipole: 0.4477
Total Energy: 33.9975 kcal/mol
Calculation completed
------------------------------------

By comparing the total energy of the two dimers it can be seen that the exo dimer is more stable by 2.1209 kcal/mol compared to the endo dimer, this is a significant difference. The majority of the energy difference observed here is due to torsion in the molecules as seen tables that sum to the total energy. This means that the reaction that forms cyclopentadiene is not controlled by only thermodynamics. It is believed therefore the the product formation is due to steric or orbital effects as it is known the endo dimer is in actuality favoured, despite the fact that the exo dimer was calculated to be more energetically stable.

The endo dimer can be hydrogenated at either of the two double bonds, this would result in the two molecules seen below, the same method of optimization has been used here so that the total energies of each molecule can be compared.

'''3) Endo Hydrogenation (1)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CPEN_D3.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2782
Bend: 19.8555
Stretch-Bend: -0.8346
Torsion: 10.8110
Non-1,4 VDW: -1.2202
1,4 VDW: 5.6331
Dipole/Dipole: 0.1621
Total Energy: 35.6850 kcal/mol
Calculation completed
------------------------------------

'''4) Endo Hydrogenation (2)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>FFFF.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 153: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.0968
Bend: 14.5244
Stretch-Bend: -0.5493
Torsion: 12.4974
Non-1,4 VDW: -1.0692
1,4 VDW: 4.5112
Dipole/Dipole: 0.1406
Total Energy: 31.1520 kcal/mol
Calculation completed
------------------------------------

Again, it is possible to compare the difference between the two total energies. The second hydrogenated molecule is more stable that first one by 4.533 kcal/mol, this means that it is the thermodynamic product of the hydrogenation reaction. It is possible to understand the different energies better by comparing the components that make up each total energy. The major contribution the large total energy difference between the two molecules appears to be the bending energy which has a difference of 5.3311 kcal/mol.

=== Comparison of Energies from Cyclopentadiene Dimers and There Hydrogenated Products ===

{| class="COMP " border="1px" align="center" width="900px"
|+ Comparison of Energies for Cyclopentadiene Dimers and There Hydrogenated Products
! Type !! Cyclopentadiene Dimer 1 !! Cyclopentadiene Dimer 2 !! Hydrogenated Dimer 1 !! Hydrogenated Dimer 2
|-
| Image ||[[File:CPEN_D2.jpg|300px|center]]||[[File:CPEN_D1.jpg|300px|center]]||[[File:CPEN_D3.jpg|300px|center]]||[[File:CPEN_D4.jpg|300px|center]]
|-
|Stretch (kcal mol<sup>-1</sup>) || 1.2855 || 1.2502 || 1.2782 || 1.0964
|-
|Bend (kcal mol<sup>-1</sup>) || 20.5794 || 20.8488 || 19.8555|| 14.5246
|-
| Stretch-Bend (kcal mol<sup>-1</sup>) || -0.8381 || -0.8346 || -0.5488 || -0.5494
|-
|Torsion (kcal mol<sup>-1</sup>) || 7.6571 || 9.5109 || 10.8110 || 12.4971
|-
| Non 1-4 Van der Waal's (kcal mol<sup>-1</sup>) || -1.4171 || -1.5455 || -1.2202 || -1.0701
|-
| 1,4 Van der Waal's (kcal mol<sup>-1</sup>) || 4.2322 || 4.3210 || 5.6331 || 4.5129
|-
| Dipole, Dipole (kcal mol<sup>-1</sup>) || 0.3776 || 0.4477 || 0.1621 || 0.1406
|-
| Total energy (kcal mol<sup>-1</sup>) || 31.8766 || 33.9975 || 35.6850 || 31.1520
|-
|}

The table above has complicated the data from the above calculations so that the relative energy's of each component can be easily compared. It can be seen that between dimers or products most of the energy's are very similar and there are few differences between the two as would be expected.

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

This section of the report is looking at two isomers of an intermediate in the synthesis of taxol, the two isomers occur due to the possibility of rotation of the keytone group, it can either be orientated up or down on the ring. The first step at analyzing the two possible isomers was to construct them with the correct steriochemistry, these molecules where then optimized using a MM2 field and the energy was then calculated again using a MMFF94. The results of these calculations and the molecules constructed can be seen below.

[[File:TAX_D15.jpg|300px|center]]
[[File:Taxol_A.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_A.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(26)-H(27)
Separating coincident atoms: H(37)-H(39)
Warning: Some parameters are guessed (Quality = 1).
Iteration 228: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7863
Bend: 16.5503
Stretch-Bend: 0.4310
Torsion: 18.2501
Non-1,4 VDW: -1.5648
1,4 VDW: 13.1116
Dipole/Dipole: -1.7249
Total Energy: 47.8396 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 58: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 70.5359 kcal/mol
Calculation completed
------------------------------------

[[File:TAX_D16.jpg|300px|center]]

[[File:Taxol_B.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_B.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(31)-H(32)
Separating coincident atoms: H(35)-H(36)
Warning: Some parameters are guessed (Quality = 1).
Iteration 246: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6228
Bend: 11.3382
Stretch-Bend: 0.3439
Torsion: 19.6639
Non-1,4 VDW: -2.1524
1,4 VDW: 12.8688
Dipole/Dipole: -2.0018
Total Energy: 42.6834 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 37: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 60.5719 kcal/mol
Calculation completed
------------------------------------

By looking at the energy's obtained by both calculations it can be seen that the second isomer is more stable than the first, the energy difference as calculated using the MM2 method is 5.1562 kcal/mol and the difference using the MMFF94 is 9.964 kcal/mol. It can therefore be said that the the intermediate with the keytone pointing in the same orientation as the neighboring hydrogen atoms is the one formed during the reaction.
By looking at the composition of the energy's calculated using the MM2 method the largest difference between the two is again in the bending component of the total energy. The key structual difference observed between the two isomers (apart form the inversion of the keytone) is that the 6 membered ring flips conformation, this is shown in the image below.

Comparison image showing ring flip:

[[File:Taxol_RF.png|400px|center]]

=== Modelling Using Semi-empirical Molecular Orbital Theory. ===

This section of the report is looking at the diene shown below, the intial step where the same as above with the molecule being constructed in ChemBio 3D and then being optimized using the MM2 method, the results of which can be seen below:

[[File:Compound_12.jpg|300px|center]]

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 151: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.6183
Bend: 4.7355
Stretch-Bend: 0.0399
Torsion: 7.6600
Non-1,4 VDW: -1.0653
1,4 VDW: 5.7939
Dipole/Dipole: 0.1124
Total Energy: 17.8945 kcal/mol
Calculation completed
------------------------------------

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Idontknow.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The next step taken was to further optimize the molecule, this was done using the MOPAC method, this method takes into account any electronic effects that are not covered by the MM2 method. The result of the calculation can be seen below:

Mopac Job: AUX RM1 CHARGE=0 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09953 (< 0.10000) Heat of Formation = 22.82769 Kcal/Mol
-----------------------------------------

The MOPAC calculation also involves the optimization of the molecule by compring this structure to the MM2 optimized one it can be seen that they have different geometrys, this would be expected as the energies are different. The two different structures have been overlayed below to outline the key differences.

[[File:PICKYWIK.png|center|300px]]

From the overlapped molecules it can be seen that the chlorine atom distorts the ring more in the highlighted MOPAC optimization. This means that there are orbital interaction involved that force the ring on the left hand side to bend downwards. This increases the strain on the molecule as so increases it energy, it it not possible to compare the energys of the two optimizations howerve as they are calculated through different methods.

The next part of the analysis involes modeling the molecular orbitals of the molecule, a 2D representation of this can be seen here:
[[File:Diene_estat.jpg|center|300px]]

The final part of the analysis of this molecule was a vibrational analysis, this was run in Gaussian on the previously optimized molecule. The resulting vibrations can be seen on the molecule below, to view the differnt vibration right click on the image and place the curser over "model", you can then select which vibration you wish to view, it also displays in that selection the frequency of the vibration.

<div align="center">
<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>Diene_FREQ_LOG.log</uploadedFileContents>
</jmolApplet>
</jmol>
</div>

=== Monosaccharide chemistry and the mechanism of glycosidation ===

The computational methods we have looked at before have been shown to provide a good understanding of intermediates in a reaction, this section will be looking at part of a glycosidation reaction which can be seen below:

[[File:GLY.png|center]]

The first intermediate has 4 possible isomers, the optimizations for which can be seen below, the structres of each of isomer have been tabulated below for better comparison with there relevant energies.

Energy calculations for isomer 1

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4507
Bend: 11.5140
Stretch-Bend: 0.8750
Torsion: 1.4349
Non-1,4 VDW: 0.2620
1,4 VDW: 19.4581
Charge/Dipole: -28.6982
Dipole/Dipole: 5.2444
Total Energy: 12.5409 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09168 (< 0.10000) Heat of Formation = -70.04084 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 2

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4313
Bend: 11.7850
Stretch-Bend: 0.9826
Torsion: 1.4209
Non-1,4 VDW: 0.7701
1,4 VDW: 18.8357
Charge/Dipole: -27.0491
Dipole/Dipole: 5.9906
Total Energy: 15.1670 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09431 (< 0.10000) Heat of Formation = -79.27099 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 3

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 447: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2173
Bend: 10.6642
Stretch-Bend: 0.8233
Torsion: 0.6467
Non-1,4 VDW: -1.5632
1,4 VDW: 19.2644
Charge/Dipole: -15.9514
Dipole/Dipole: 3.8992
Total Energy: 20.0004 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07357 (< 0.10000) Heat of Formation = -65.36964 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 4

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2532
Bend: 11.1534
Stretch-Bend: 0.8510
Torsion: 1.1097
Non-1,4 VDW: -2.1220
1,4 VDW: 19.3508
Charge/Dipole: -11.5317
Dipole/Dipole: 3.8657
Total Energy: 24.9301 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08961 (< 0.10000) Heat of Formation = -62.83046 Kcal/Mol
-----------------------------------------

{| class="Isomers" border="1px" align="center" width="1000px"
|+ Table for comparison on first intermediate
! Isomer description !! Visual of MM2 optimized isomer !! Total energy of MM2 obtimzed isomer (Kcal/mol) !! Visual of MOPAC optimized isomer !! Heat of formation from MOPAC Kcal/mol !! Distance between carbonyl oxygen and acyl carbon
|-
| Axial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1.cml</uploadedFileContents>
</jmolApplet></jmol> || 12.5409 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -70.04084 || 2.00
|-
| Axial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2.cml</uploadedFileContents>
</jmolApplet></jmol> || 15.1670 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -79.27099 || 1.457
|-
| Equatorial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3.5.cml</uploadedFileContents>
</jmolApplet></jmol> || 20.0004 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -65.36964 || 2.869
|-
| Equatorial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4.1.cml</uploadedFileContents>
</jmolApplet></jmol> || 24.9301 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -62.83046 || 2.869
|-|}

This table shows that the isomer which have an axial carbonyl group are more stable than with an equitorial one, both MM2 and MOPAC agree with this. This means that under thermodynamic control either isomer 1 or 2 will be dominant. The total energies generated form MM2 indicate that the first isomer "Axial and above the ring" would be favored as it is 2.6261 Kcal/mol lower than isomer 2. This does not take into account electrostactis though which, considering the high charge density present, does not give a complete picture and so looking at the heats of formation from the MOPAC analysis it can be said that in reality isomer 2 is more stable. This is due to the added stability of an additional bond which cannot be seen in the representation but by looking at the distance between the carbonyl oxygen and acyl carbon can be understood to exist. This bond helps balance out the charges present and infact converts the molecule to the next step in the reaction drawn above. On the next page we will generate an energy for each isomer but with the new bond formed, the next page can be found [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]].

= This wiki page continues from the following link: [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]] =

Rep:Mod:AlexanderGrayCont

2013-03-15T15:16:58Z

Ag3210: /* Vibrational Analysis */

= Organic Computaional Labs Continued, Part1 =

==== The Second Reaction Intermediate of a Glycosidation Reaction ====

As stated previously the results for the MM2 and MOPAC calculations of each isomer of the second reaction intermediate are shown below (These calculations where run on a new version of the software):

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly1is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.1410
Bend: 15.2130
Stretch-Bend: 0.7546
Torsion: 9.4948
Non-1,4 VDW: -3.7163
1,4 VDW: 17.7977
Charge/Dipole: -4.6530
Dipole/Dipole: -0.7804
Total Energy: 36.2514 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09967 (< 0.10000) Heat of Formation = -76.27765 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly2is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.0053
Bend: 13.4884
Stretch-Bend: 0.7191
Torsion: 9.9562
Non-1,4 VDW: -2.8698
1,4 VDW: 18.0192
Charge/Dipole: -7.7771
Dipole/Dipole: -2.4245
Total Energy: 31.1168 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08015 (< 0.10000) Heat of Formation = -79.45545 Kcal/Mol
-----------------------------------------

The MOPAC calculations result for the Heat of Formation here is the same as the isomer from the other part, this shows that they are in fact the same molecule and that the bond does indeed exist in the previous part even though it is not visible.

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly3is.cml</uploadedFileContents>
</jmolApplet></jmol>

MM2 Calculation completed successfully
------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6633
Bend: 19.5290
Stretch-Bend: 0.7749
Torsion: 9.1167
Non-1,4 VDW: -3.2021
1,4 VDW: 19.0162
Charge/Dipole: 3.3946
Dipole/Dipole: -1.5909
Total Energy: 49.7016 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX AM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08886 (< 0.10000) Heat of Formation = -62.63771 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly4is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7503
Bend: 18.0616
Stretch-Bend: 0.8380
Torsion: 9.9783
Non-1,4 VDW: -2.6260
1,4 VDW: 19.5983
Charge/Dipole: 2.3600
Dipole/Dipole: -1.6307
Total Energy: 49.3298 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09213 (< 0.10000) Heat of Formation = -54.08588 Kcal/Mol
-----------------------------------------

For isomers 1,3 and 4 the additional bond adds strain to the molecule and so raises the total energy of the molecule and lowers the heat of formation.

== Part 2, Module 1 ==

=== Taxol ===

To test the NMR prediction capability's of the software a molecule of Taxol was generated, optimized and then run though an NMR analysis, this is shown below:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>New_Taxol.cml</uploadedFileContents>
</jmolApplet></jmol>

The optimization log file can be found here: [[File:Log_for_new_taxol.log]]

[[File:Taxol_OPTED.gjf]]

The NMR analysis for taxol using a Basis set of mpw1pw91/6-31G(d,p) can be found here {{DOI|10042/24302}}

The H<sup>1</sup> NMR spectrum for the Taxol Complex can be seen below:
[[File:TAXOL.png]]

The C13 NMR spectrum for the Taxol complex can be seen below:

[[File:Taxol_NMR_C.png]]

The literature NMR data has been tabulated below with the corrisponding calculated NMR data for comparison:

{| class="wikitable"
|+ Table comparing C<sup>13</sup> NMR data
|-
| Liturature NMR (ppm) || Calculated NMR (ppm)
|-
| 218.8 || 213.6
|-
| 144.6 || 150.3
|-
| 125.3 || 120.7
|-
| 72.9 || 87.0
|-
| 56.2 || 65.8
|-
| 52.5 || 56.5
|-
| 48.5 || 55.0
|-
| 46.8 || 50.4
|-
| 45.8 || 50.4
|-
| 39.8 || 38.3
|-
| 38.8 || 42.9
|-
| 35.9 || 41.5
|-
| 32.7 || 35.9
|-
| 28.8 || 34.9
|-
| 28.3 || 31.9
|-
| 26.9 || 28.5
|-
| 25.7 || 29.1
|-
| 23.9 || 26.3
|-
| 21.0 || 23.9
|-
| 18.7 || 21.0
|-
|}

As can be seen from the table there is generally good agreement between the calculated and literature results for the C13 NMR spectrum. In general the calculated results are a few ppm higher than the literature values, this is most likely due to a too smaller basis set being used or the reference conditions being used are not exactly the same as the literature. As the basis set is improved then the accuracy of the computed NMR will increase and this should account for the difference.

=== Mini Project ===

For this mini project the molecule shown below was chosen from literature so that its reported NMR could be checked to confirm that the different isomers had been assigned correctly. The first set was to construct the molecule with the different possible isomer and then generate predicted NMRs this is shown below:

[[File:Mini.png]]
The reaction scheme for the formation of the products being looked at in this project

This is a Jmol of one of the isomers present:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>2_CML.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 105: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.4999
Bend: 5.6308
Stretch-Bend: -0.1001
Torsion: 0.6953
Non-1,4 VDW: -0.2984
1,4 VDW: 1.7252
Dipole/Dipole: 3.6138
Total Energy: 11.7665 kcal/mol
Calculation completed
------------------------------------

The same molecule was optimized on Gaussview the following log file was generated from this: [[File:OPT_1.LOG]]
The optimized molecule was then further optimzed using the 6-31G(d,p) basis set the file ca be found here: [[File:OPT_2.LOG]]

For each of the isomers the molecule was optimized using gaussian after being modified from the perviously opimized molecule, the files from each optimization can be found with the corresponding DOI links.

Optimization of isomer 2 {{DOI|10042/24282}}

Optimization of isomer 3 {{DOI|10042/24284}}

Optimization of isomer 4 {{DOI|10042/24285}}

On these optimized molecules an NMR analysis was run using the B3LYP - 6-31G(d,p) basis set, the NMR spectra obtained are displayed below and the files for these calculations can be found at the followin links:

NMR analysis for isomer 1 {{DOI|10042/24286}}

NMR analysis for isomer 2 {{DOI|10042/24287}}

NMR analysis for isomer 3 {{DOI|10042/24288}}

NMR analysis for isomer 4 {{DOI|10042/24289}}

A second NMR analysis was then run this time using a much larger basis set (cc-pVTZ) to investigate if the predicted NMR could be improved, the results have been tabulated below and the files for the calculations can be found here:

Larger basis set NMR analysis for isomer 1 {{DOI|10042/24290}}

Larger basis set NMR analysis for isomer 2 {{DOI|10042/24291}}

Larger basis set NMR analysis for isomer 3 {{DOI|10042/24292}}

Larger basis set NMR analysis for isomer 4 {{DOI|10042/24293}}

For all of the spectra in this table the relavent reference molecule has been used apart from in the case of the F<sup>19</sup> NMR where there was no references in Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V1_F.png]] || [[File:V1_C.png]] || [[File:V1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V2_F.png]] || [[File:V2_C.png]] || [[File:V2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V3_F.png]] || [[File:V3_C.png]] || [[File:V3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V4_F.png]] || [[File:V4_C.png]] || [[File:V4_H.png]]
|}

The table below contains the same NMR spectra as above but they have been calculated using a higher basis set. The spectra here have been shown to correlate better to the recorded NMR found in literature. To allow analysis of the F<sup>19</sup> NMR a reference molecule was made and the shielding constant (168.5547) was manually entered into Gaussian, the molecule was one of CFCl<sub>3</sub> chosen as it is the same one used in the literature. The output files for the [[Media:CFCL3.LOG|optimization]] and [[Media:CFCL3_NMR.LOG|NMR analysis]] for CFCl<sub>3</sub> can be found at there respective links. The ppm values obtained from Gaussian have been found to be slightly too low, this could be down to the reference calculated or some other area of Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides calculated using the cc-pVTZ basis set
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV1_F.png]] || [[File:2HV1_C.png]] || [[File:2HV1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV2_F.png]] || [[File:2HV2_C.png]] || [[File:2HV2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV3_F.png]] || [[File:2HV3_C.png]] || [[File:2HV3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV4_F.png]] || [[File:2HV4_C.png]] || [[File:2HV4_H.png]]
|}

The NMR data from Liturate has been tabulated below:

{| class="wikitable" border="1"
|+ H<sup>1</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| 2.00-3.30 (m, 2H); || 2.00-2.90 (m, 2H) || 2.06 (tdt, 1H) || 2.35 (tt, 2H)
|-
| 5.22 (ddd, 1H); || 5.68 (ddm, 1H) || 2.40-3.10 (m, 1H) || 5.78 (ddm, 2H)
|-
| 5.6 (ddm, 1H); || 6.00-6.80 (m, 3H) || 4.90-5.90 (m, 2H) || 5.80-6.40 (m, 2H)
|-
| 5.85 (dm, 1H); || || 6.18-6.40 (m, 2H) ||
|-
| 6.80 (m, 1H); || || ||
|-
|}

By comparing the chemical shift recorded to the predicted shifts above it can be seen that there is some agreement in the order and approximate number of chemical shifts present, taking into account that some peaks recorded as multiplets of a relative number of hydrogens more than one correlate to multiple predicted peaks. For example if we look at isomer 1 it can be seen for the predicted NMR graph that there should be 6H's present, this is the case, and that there are expected to be 2 H's between 2-3ppm, again the case. The peaks seen in liturature at 5.2, 5.6 and 5.8 have also been correctly predicted by the NMR prediction software, however the peak with chemical shift of 6.8 has been predicted at 6.2 ppm, a significatly lower value, this implies that the software has not correctly predicted the chemical shift of the hydrogen attached to an alkene and with a flourine on a neibouring carbon atom. Howvere the general good agreement shows that isomer one has been correctly predicted by the software and assigned correctly by the literature.

Unfortunately the other isomers do not show as close a similarity to the literature, it is stated that the purity of isomer 2 (compound 3 in literature) is not of complete purity, this can be seen from the wide ranges in ppm recorded and the number of multiplets. The predicted spectra shows 2 H's at rougly 2.5 ppm, this can be correlated to the liturature values between 2.0-2.9ppm the rest of the spectra does not however corrilate to the predicted spectra any more than any other isomer and so the NMR data, stated unreliable in the literature should not been be for further analysis.

The remaining two isomer can be seen to relate to the predicted NMR spectra but there is still a reasonably large margin of error as far as the chemical shifts are concerned but it can be said that the H1 NMR spectra of compounds have been assigned correctly.

{| class="wikitable" border="1"
|+ F<sup>19</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| -176 (ddm, 1F); || -159 (m, 1F) || -161 (m) || -171 (m)
|-
| -187 (m, 1F); || -167 (m, 1F) || ||
|-
|}

The literature values for the F<sup>19</sup> NMR, seen above, can be seen to have a higher (less negative) chemical shift than the predicted NMR values despite the corrections made. looking at the distribution of the peaks however it is possible to see that the for isomer 1 and 2 both methods show 2 distinguishable peaks with the spacing between peaks being larger for isomer 1 than 2. For isomer 2 only 1 peak is expected as the molecule is symmetric and so both flourines are in the same environment, only one peak is seen in the actual NMR, this is a multiplet probably due to coupling with the hydrogen atoms. Isomer 4 has been predicted to show 2 peaks that should be differentiable, this however is not the case, the chemical shift of isomer 3 is predicted to be higher (less negative) than that of isomer 4, although the values are not the same the relationship is and so it can be said that the correct assignment has been made.

=== J coupling ===

To look at the spin coupling for each molecule the following data was extracted from the log files of each of the diflorinated molecules, the original log files for each can be found above. The data below shows the couplings between each atom, the labeling system relates the the molecule above the data, the light blue atoms are fluorine atoms, the white hydrogen and the grey carbon.

Unfortunately as the literature does not provide many coupling constants there is very little comparative analysis possible here. Values of interest have been tabulated below each set of data.

[[File:V1.jpg|300px]]

Isomer 1

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.342866D+02 0.000000D+00
3 0.895875D+01 0.387721D+02 0.000000D+00
4 0.432962D+01 0.357276D+01 0.814371D+02 0.000000D+00
5 0.286622D+02 0.761418D+01 0.168366D+00 0.277392D+02 0.000000D+00
6 0.620195D+01 0.250870D+01 0.154230D+03 0.241025D+01 0.890794D+01
7 0.641252D+01 0.975844D+01 0.233016D+01 0.151755D+03 0.453581D+01
8 -0.356953D+01 0.490619D+01 0.420895D+01 -0.373378D+01 0.118209D+03
9 -0.562801D+01 -0.180511D+01 0.340892D+01 -0.614534D+01 0.112126D+03
10 0.131662D+03 -0.504874D+01 -0.296543D+00 0.105109D+01 -0.136180D+01
11 -0.228247D+03 0.199291D+02 0.648570D+01 0.435993D+01 0.161753D+02
12 0.158580D+02 -0.221931D+03 0.181425D+02 0.275804D+01 0.247006D+01
13 -0.387550D+01 0.133542D+03 -0.281012D+01 0.386991D+01 -0.136352D+01
6 7 8 9 10
6 0.000000D+00
7 0.570798D+01 0.000000D+00
8 -0.239625D+01 0.333843D+01 0.000000D+00
9 -0.377890D+01 0.273722D+01 -0.164174D+02 0.000000D+00
10 0.152419D+00 -0.118905D+00 0.752471D+01 0.513857D+01 0.000000D+00
11 0.114526D+01 0.180493D+01 0.496252D+00 0.209070D+02 0.485841D+02
12 0.243819D+01 -0.284005D+01 0.609967D+00 0.104561D+02 0.227008D+02
13 0.225434D+01 -0.251199D+01 0.230756D+01 0.300313D+01 0.361997D+01
11 12 13
11 0.000000D+00
12 -0.656033D+01 0.000000D+00
13 0.173949D+02 0.493934D+02 0.000000D+00

From this data the most significant couplings have been tabulated below:

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 22
|-
| F-F coupling / Literature || 18
|}

The same file for isomer 2 is below:

[[File:V2.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.298057D+02 0.000000D+00
3 0.360005D+01 0.383120D+02 0.000000D+00
4 0.140841D+01 0.568185D+01 0.847547D+02 0.000000D+00
5 0.272228D+02 0.661319D+01 0.146319D+01 0.276719D+02 0.000000D+00
6 0.531289D+01 0.294077D+01 0.154554D+03 0.326074D+01 0.956471D+01
7 0.552333D+01 0.112712D+02 0.331786D+01 0.151972D+03 0.495994D+01
8 -0.540504D+01 0.397276D+01 0.386070D+01 -0.396731D+01 0.116736D+03
9 0.381514D+01 -0.113783D+01 0.287703D+01 -0.488835D+01 0.111760D+03
10 0.884900D+01 -0.227663D+03 0.174540D+02 0.474589D+01 -0.173807D+01
11 0.548960D+01 0.132178D+03 -0.215125D+01 0.257544D+01 -0.786536D+00
12 -0.224697D+03 0.112122D+02 -0.314235D+00 -0.149288D+01 0.150435D+02
13 0.145676D+03 0.312450D+00 0.540799D+01 0.585986D+01 0.177718D+01
6 7 8 9 10
6 0.000000D+00
7 0.541089D+01 0.000000D+00
8 -0.230815D+01 0.333160D+01 0.000000D+00
9 -0.411266D+01 0.255795D+01 -0.176851D+02 0.000000D+00
10 0.241296D+01 -0.149280D+01 0.181811D+00 0.359811D+01 0.000000D+00
11 0.215383D+01 -0.323173D+01 0.133489D+01 0.274682D+01 0.442501D+02
12 -0.119884D-01 -0.683563D-02 0.213811D+02 0.256981D+02 -0.570540D+01
13 0.288938D+00 0.320102D+00 0.497912D-01 0.396887D+01 -0.132042D+01
11 12 13
11 0.000000D+00
12 0.122457D+02 0.000000D+00
13 0.410809D+01 0.492388D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 5.7
|-
| F-F coupling / Literature || None reported
|}

For isomer 3:

[[File:V31.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.273345D+02 0.000000D+00
3 0.351869D+01 0.357805D+02 0.000000D+00
4 0.351678D+01 0.356759D+01 0.851369D+02 0.000000D+00
5 0.273508D+02 0.784544D+01 0.356356D+01 0.357942D+02 0.000000D+00
6 0.415912D+01 0.232123D+01 0.153275D+03 0.317256D+01 0.115299D+02
7 0.415929D+01 0.115328D+02 0.317046D+01 0.153272D+03 0.232109D+01
8 0.126697D+01 0.766162D+00 0.282143D+01 -0.214675D+01 0.135968D+03
9 0.110154D+02 -0.221170D+03 0.175499D+02 0.268770D+01 -0.224820D+01
10 0.126219D+01 0.135964D+03 -0.214746D+01 0.281796D+01 0.765104D+00
11 0.120768D+03 -0.126794D+01 0.546578D+01 0.546538D+01 -0.126249D+01
12 0.108735D+03 -0.707120D+01 -0.156287D+00 -0.156513D+00 -0.707035D+01
13 0.110113D+02 -0.226057D+01 0.268852D+01 0.175542D+02 -0.221062D+03
6 7 8 9 10
6 0.000000D+00
7 0.509273D+01 0.000000D+00
8 -0.209240D+01 0.221891D+01 0.000000D+00
9 0.250491D+01 -0.292515D+01 0.110507D+02 0.000000D+00
10 0.221853D+01 -0.209470D+01 0.188537D+01 0.483661D+02 0.000000D+00
11 -0.246804D+00 -0.246888D+00 0.628814D+01 0.404899D+00 0.628769D+01
12 -0.122410D+00 -0.120443D+00 0.486518D+01 0.246650D+02 0.486525D+01
13 -0.293299D+01 0.250911D+01 0.483593D+02 0.121202D+02 0.110678D+02
11 12 13
11 0.000000D+00
12 -0.122699D+02 0.000000D+00
13 0.410527D+00 0.246816D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 12.1
|-
| F-F coupling / Literature || None reported
|}

Isomer 4:

[[File:V4.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.291101D+02 0.000000D+00
3 0.376865D+01 0.360903D+02 0.000000D+00
4 0.327801D+01 0.501414D+01 0.846316D+02 0.000000D+00
5 0.293380D+02 0.528212D+01 0.261876D+01 0.337271D+02 0.000000D+00
6 0.452981D+01 0.290011D+01 0.152690D+03 0.334557D+01 0.114129D+02
7 0.428822D+01 0.108793D+02 0.372204D+01 0.153433D+03 0.387792D+01
8 0.126708D+02 -0.215381D+03 0.149397D+02 0.209481D+01 0.934862D+01
9 -0.600859D-01 0.134584D+03 -0.146461D+01 0.311426D+01 -0.920073D+00
10 0.117780D+03 -0.161334D+01 0.628257D+01 0.319068D+01 -0.485410D+01
11 0.109076D+03 -0.669288D+01 -0.176798D+00 0.856155D+00 -0.822490D+00
12 0.180918D+02 -0.366872D+01 0.296262D+01 0.774594D+01 -0.211300D+03
13 -0.195171D+00 0.546568D+01 0.457133D+01 -0.927065D+00 0.141349D+03
6 7 8 9 10
6 0.000000D+00
7 0.515899D+01 0.000000D+00
8 0.306287D+01 -0.256222D+01 0.000000D+00
9 0.222974D+01 -0.258174D+01 0.477343D+02 0.000000D+00
10 -0.172590D+00 0.135473D+00 0.311884D+00 0.566856D+01 0.000000D+00
11 -0.605838D+00 -0.518467D+00 0.236849D+02 0.415039D+01 -0.140235D+02
12 -0.434430D+01 0.255227D+01 0.190874D+02 0.799236D+01 0.176430D+02
13 -0.876659D+00 0.260831D+01 0.140782D+00 0.175197D+01 0.551757D-01
11 12 13
11 0.000000D+00
12 0.246213D+02 0.000000D+00
13 0.565082D+01 0.497731D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 19.1
|-
| F-F coupling / Literature || None reported
|}

=== Vibrational Analysis ===

The optimized molecules for above where then run through vibrational analysis to produce IR spectra, the literature did not run IR spectra which these can be compared to, but it is a helpful technique to check that the compound is has been optimized and to compare any differences that arise (the IR spectra should contain the same peaks).

{| class="wikitable" border="1"
|+ Table of IR spectra
! Isomer Number !! Calculated IR Spectrum
|-
| Isomer 1 || [[File:IR1.png]]
|-
| Isomer 2 || [[File:IR2.png]]
|-
| Isomer 3 || [[File:IR3.png]]
|-
| Isomer 4 || [[File:IR4.png]]
|-
|}

Comparison of the spectra shows that they are not all the same, however it is mainly the intensity of the peaks rather that there existence that changes. All the the molecuels contain the expected peaks, Isomer 3 has additional peaks and much larger peaks compared to the other isomers, this is due to its high level of symmetry.

=== Conclusions ===

The data provided by the literature source has been proven to be of a poor quality and that computational analysis has provided more detailed evidence for the identification of each of the isomers produced. The liturature did however get the assingment correct and so has been supported not disproved by this analysis.

=== References ===

http://ac.els-cdn.com/002211399403190B/1-s2.0-002211399403190B-main.pdf?_tid=930742b8-8a51-11e2-a537-00000aacb362&acdnat=1363009553_0579d0d0ad7eb0ece5d46549b57556e0
Mini project
http://www.sciencedirect.com/science/article/pii/002211399403190B#

Taxol
http://pubs.acs.org/doi/abs/10.1021/ja00157a043

Rep:Mod:AlexanderGray

2013-03-15T15:09:23Z

Ag3210: /* Calculations for Cyclopentadiene Dimers and their Hydrogenated Products */

= Organic Computational Labs Module =

=== Calculations for Cyclopentadiene Dimers and their Hydrogenated Products ===

This part of the report uses ChemBio 3D to optimize complexes and determine the total energy of the molecule. The method used to optimize the molecules was a MM2 forcefield. The first comparison of energies was done between the 2 dimers of cyclopentadiene, it is known that cyclopentadiene takes the form of the endo dimer specifically over the exo dimer. By looking at the energies and hence the thermodynamic stability of the dimers it is possible to gain an insight into there formation.

'''1) Exo Dimer'''

This first molecule is the exo dimer of cyclopentadiene where MM2 minimization was used in order to obtain an energy minima.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>DDDDDDDDD1.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The table below shows the energy data obtained for the exo dimer.

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 76: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2855
Bend: 20.5794
Stretch-Bend: -0.8381
Torsion: 7.6571
Non-1,4 VDW: -1.4171
1,4 VDW: 4.2322
Dipole/Dipole: 0.3776
Total Energy: 31.8766 kcal/mol
Calculation completed
------------------------------------

'''2) Endo Dimer'''

This second molecule is the endo dimer of cyclopentadiene, again MM2 minimization was carried out.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CCCCC.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The minimization yielded the following results for the endo dimer:

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 103: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2502
Bend: 20.8488
Stretch-Bend: -0.8357
Torsion: 9.5109
Non-1,4 VDW: -1.5455
1,4 VDW: 4.3210
Dipole/Dipole: 0.4477
Total Energy: 33.9975 kcal/mol
Calculation completed
------------------------------------

By comparing the total energy of the two dimers it can be seen that the exo dimer is more stable by 2.1209 kcal/mol compared to the endo dimer, this is a significant difference. The majority of the energy difference observed here is due to torsion in the molecules as seen tables that sum to the total energy. This means that the reaction that forms cyclopentadiene is not controlled by only thermodynamics. It is believed therefore the the product formation is due to steric or orbital effects as it is known the endo dimer is in actuality favoured, despite the fact that the exo dimer was calculated to be more energetically stable.

The endo dimer can be hydrogenated at either of the two double bonds, this would result in the two molecules seen below, the same method of optimization has been used here so that the total energies of each molecule can be compared.

'''3) Endo Hydrogenation (1)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CPEN_D3.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2782
Bend: 19.8555
Stretch-Bend: -0.8346
Torsion: 10.8110
Non-1,4 VDW: -1.2202
1,4 VDW: 5.6331
Dipole/Dipole: 0.1621
Total Energy: 35.6850 kcal/mol
Calculation completed
------------------------------------

'''4) Endo Hydrogenation (2)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>FFFF.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 153: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.0968
Bend: 14.5244
Stretch-Bend: -0.5493
Torsion: 12.4974
Non-1,4 VDW: -1.0692
1,4 VDW: 4.5112
Dipole/Dipole: 0.1406
Total Energy: 31.1520 kcal/mol
Calculation completed
------------------------------------

Again, it is possible to compare the difference between the two total energies. The second hydrogenated molecule is more stable that first one by 4.533 kcal/mol, this means that it is the thermodynamic product of the hydrogenation reaction. It is possible to understand the different energies better by comparing the components that make up each total energy. The major contribution the large total energy difference between the two molecules appears to be the bending energy which has a difference of 5.3311 kcal/mol.

=== Comparison of Energies from Cyclopentadiene Dimers and There Hydrogenated Products ===

{| class="COMP " border="1px" align="center" width="900px"
|+ Comparison of Energies for Cyclopentadiene Dimers and There Hydrogenated Products
! Type !! Cyclopentadiene Dimer 1 !! Cyclopentadiene Dimer 2 !! Hydrogenated Dimer 1 !! Hydrogenated Dimer 2
|-
| Image ||[[File:CPEN_D2.jpg|300px|center]]||[[File:CPEN_D1.jpg|300px|center]]||[[File:CPEN_D3.jpg|300px|center]]||[[File:CPEN_D4.jpg|300px|center]]
|-
|Stretch (kcal mol<sup>-1</sup>) || 1.2855 || 1.2502 || 1.2782 || 1.0964
|-
|Bend (kcal mol<sup>-1</sup>) || 20.5794 || 20.8488 || 19.8555|| 14.5246
|-
| Stretch-Bend (kcal mol<sup>-1</sup>) || -0.8381 || -0.8346 || -0.5488 || -0.5494
|-
|Torsion (kcal mol<sup>-1</sup>) || 7.6571 || 9.5109 || 10.8110 || 12.4971
|-
| Non 1-4 Van der Waal's (kcal mol<sup>-1</sup>) || -1.4171 || -1.5455 || -1.2202 || -1.0701
|-
| 1,4 Van der Waal's (kcal mol<sup>-1</sup>) || 4.2322 || 4.3210 || 5.6331 || 4.5129
|-
| Dipole, Dipole (kcal mol<sup>-1</sup>) || 0.3776 || 0.4477 || 0.1621 || 0.1406
|-
| Total energy (kcal mol<sup>-1</sup>) || 31.8766 || 33.9975 || 35.6850 || 31.1520
|-
|}

The table above has complicated the data from the above calculations so that the relative energy's of each component can be easily compared. It can be seen that between dimers or products most of the energy's are very similar and there are few differences between the two as would be expected.

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

This section of the report is looking at two isomers of an intermediate in the synthesis of taxol, the two isomers occur due to the possibility of rotation of the keytone group, it can either be orientated up or down on the ring. The first step at analyzing the two possible isomers was to construct them with the correct steriochemistry, these molecules where then optimized using a MM2 field and the energy was then calculated again using a MMFF94. The results of these calculations and the molecules constructed can be seen below.

[[File:TAX_D15.jpg|300px|center]]
[[File:Taxol_A.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_A.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(26)-H(27)
Separating coincident atoms: H(37)-H(39)
Warning: Some parameters are guessed (Quality = 1).
Iteration 228: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7863
Bend: 16.5503
Stretch-Bend: 0.4310
Torsion: 18.2501
Non-1,4 VDW: -1.5648
1,4 VDW: 13.1116
Dipole/Dipole: -1.7249
Total Energy: 47.8396 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 58: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 70.5359 kcal/mol
Calculation completed
------------------------------------

[[File:TAX_D16.jpg|300px|center]]

[[File:Taxol_B.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_B.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(31)-H(32)
Separating coincident atoms: H(35)-H(36)
Warning: Some parameters are guessed (Quality = 1).
Iteration 246: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6228
Bend: 11.3382
Stretch-Bend: 0.3439
Torsion: 19.6639
Non-1,4 VDW: -2.1524
1,4 VDW: 12.8688
Dipole/Dipole: -2.0018
Total Energy: 42.6834 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 37: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 60.5719 kcal/mol
Calculation completed
------------------------------------

By looking at the energy's obtained by both calculations it can be seen that the second isomer is more stable than the first, the energy difference as calculated using the MM2 method is 5.1562 kcal/mol and the difference using the MMFF94 is 9.964 kcal/mol. It can therefore be said that the the intermediate with the keytone pointing in the same orientation as the neighboring hydrogen atoms is the one formed during the reaction.
By looking at the composition of the energy's calculated using the MM2 method the largest difference between the two is again in the bending component of the total energy. The key structual difference observed between the two isomers (apart form the inversion of the keytone) is that the 6 membered ring flips conformation, this is shown in the image below.

Comparison image showing ring flip:

[[File:Taxol_RF.png|400px|center]]

=== Modelling Using Semi-empirical Molecular Orbital Theory. ===

This section of the report is looking at the diene shown below, the intial step where the same as above with the molecule being constructed in ChemBio 3D and then being optimized using the MM2 method, the results of which can be seen below:

[[File:Compound_12.jpg|300px|center]]

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 151: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.6183
Bend: 4.7355
Stretch-Bend: 0.0399
Torsion: 7.6600
Non-1,4 VDW: -1.0653
1,4 VDW: 5.7939
Dipole/Dipole: 0.1124
Total Energy: 17.8945 kcal/mol
Calculation completed
------------------------------------

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Idontknow.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The next step taken was to further optimize the molecule, this was done using the MOPAC method, this method takes into account any electronic effects that are not covered by the MM2 method. The result of the calculation can be seen below:

Mopac Job: AUX RM1 CHARGE=0 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09953 (< 0.10000) Heat of Formation = 22.82769 Kcal/Mol
-----------------------------------------

The MOPAC calculation also involves the optimization of the molecule by compring this structure to the MM2 optimized one it can be seen that they have different geometrys, this would be expected as the energies are different. The two different structures have been overlayed below to outline the key differences.

[[File:Diene_estat.jpg|center|300px]]

The final part of the analysis of this molecule was a vibrational analysis, this was run in Gaussian on the previously optimized molecule. The resulting vibrations can be seen on the molecule below, to view the differnt vibration right click on the image and place the curser over "model", you can then select which vibration you wish to view, it also displays in that selection the frequency of the vibration.

<div align="center">
<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>Diene_FREQ_LOG.log</uploadedFileContents>
</jmolApplet>
</jmol>
</div>

=== Monosaccharide chemistry and the mechanism of glycosidation ===

The computational methods we have looked at before have been shown to provide a good understanding of intermediates in a reaction, this section will be looking at part of a glycosidation reaction which can be seen below:

[[File:GLY.png|center]]

The first intermediate has 4 possible isomers, the optimizations for which can be seen below, the structres of each of isomer have been tabulated below for better comparison with there relevant energies.

Energy calculations for isomer 1

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4507
Bend: 11.5140
Stretch-Bend: 0.8750
Torsion: 1.4349
Non-1,4 VDW: 0.2620
1,4 VDW: 19.4581
Charge/Dipole: -28.6982
Dipole/Dipole: 5.2444
Total Energy: 12.5409 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09168 (< 0.10000) Heat of Formation = -70.04084 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 2

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4313
Bend: 11.7850
Stretch-Bend: 0.9826
Torsion: 1.4209
Non-1,4 VDW: 0.7701
1,4 VDW: 18.8357
Charge/Dipole: -27.0491
Dipole/Dipole: 5.9906
Total Energy: 15.1670 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09431 (< 0.10000) Heat of Formation = -79.27099 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 3

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 447: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2173
Bend: 10.6642
Stretch-Bend: 0.8233
Torsion: 0.6467
Non-1,4 VDW: -1.5632
1,4 VDW: 19.2644
Charge/Dipole: -15.9514
Dipole/Dipole: 3.8992
Total Energy: 20.0004 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07357 (< 0.10000) Heat of Formation = -65.36964 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 4

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2532
Bend: 11.1534
Stretch-Bend: 0.8510
Torsion: 1.1097
Non-1,4 VDW: -2.1220
1,4 VDW: 19.3508
Charge/Dipole: -11.5317
Dipole/Dipole: 3.8657
Total Energy: 24.9301 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08961 (< 0.10000) Heat of Formation = -62.83046 Kcal/Mol
-----------------------------------------

{| class="Isomers" border="1px" align="center" width="1000px"
|+ Table for comparison on first intermediate
! Isomer description !! Visual of MM2 optimized isomer !! Total energy of MM2 obtimzed isomer (Kcal/mol) !! Visual of MOPAC optimized isomer !! Heat of formation from MOPAC Kcal/mol !! Distance between carbonyl oxygen and acyl carbon
|-
| Axial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1.cml</uploadedFileContents>
</jmolApplet></jmol> || 12.5409 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -70.04084 || 2.00
|-
| Axial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2.cml</uploadedFileContents>
</jmolApplet></jmol> || 15.1670 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -79.27099 || 1.457
|-
| Equatorial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3.5.cml</uploadedFileContents>
</jmolApplet></jmol> || 20.0004 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -65.36964 || 2.869
|-
| Equatorial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4.1.cml</uploadedFileContents>
</jmolApplet></jmol> || 24.9301 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -62.83046 || 2.869
|-|}

This table shows that the isomer which have an axial carbonyl group are more stable than with an equitorial one, both MM2 and MOPAC agree with this. This means that under thermodynamic control either isomer 1 or 2 will be dominant. The total energies generated form MM2 indicate that the first isomer "Axial and above the ring" would be favored as it is 2.6261 Kcal/mol lower than isomer 2. This does not take into account electrostactis though which, considering the high charge density present, does not give a complete picture and so looking at the heats of formation from the MOPAC analysis it can be said that in reality isomer 2 is more stable. This is due to the added stability of an additional bond which cannot be seen in the representation but by looking at the distance between the carbonyl oxygen and acyl carbon can be understood to exist. This bond helps balance out the charges present and infact converts the molecule to the next step in the reaction drawn above. On the next page we will generate an energy for each isomer but with the new bond formed, the next page can be found [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]].

= This wiki page continues from the following link: [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]] =

Rep:Mod:AlexanderGray

2013-03-15T15:08:56Z

Ag3210: /* Calculations for Cyclopentadiene Dimers and their Hydrogenated Products */

= Organic Computational Labs Module =

=== Calculations for Cyclopentadiene Dimers and their Hydrogenated Products ===

This part of the report uses ChemBio 3D to optimize complexes and determine the total energy of the molecule. The method used to optimize the molecules was a MM2 forcefield. The first comparison of energies was done between the 2 dimers of cyclopentadiene, it is known that cyclopentadiene takes the form of the endo dimer specifically over the exo dimer. By looking at the energies and hence the thermodynamic stability of the dimers it is possible to gain an insight into there formation.

'''1) Exo Dimer'''

This first molecule is the exo dimer of cyclopentadiene where MM2 minimization was used in order to obtain an energy minima.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>DDDDDDDDD1.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The table below shows the energy data obtained for the exo dimer.

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 76: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2855
Bend: 20.5794
Stretch-Bend: -0.8381
Torsion: 7.6571
Non-1,4 VDW: -1.4171
1,4 VDW: 4.2322
Dipole/Dipole: 0.3776
Total Energy: 31.8766 kcal/mol
Calculation completed
------------------------------------

'''2) Endo Dimer'''

This second molecule is the endo dimer of cyclopentadiene, again MM2 minimization was carried out.

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CCCCC.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The minimization yielded the following results for the endo dimer:

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 103: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2502
Bend: 20.8488
Stretch-Bend: -0.8357
Torsion: 9.5109
Non-1,4 VDW: -1.5455
1,4 VDW: 4.3210
Dipole/Dipole: 0.4477
Total Energy: 33.9975 kcal/mol
Calculation completed
------------------------------------

By comparing the total energy of the two dimers it can be seen that the exo dimer is more stable by 2.1209 kcal/mol compared to the endo dimer, this is a significant difference. The majority of the energy difference observed here is due to torsion in the molecules as seen tables that sum to the total energy. This means that the reaction that forms cyclopentadiene is not controlled by only thermodynamics. It is believed therefore the the product formation is due to steric or orbital effects as it is known the endo dimer is in actuality favoured, despite the fact that the exo dimer was calculated to be more energetically stable.

The endo dimer can be hydrogenated at either of the two double bonds, this would result in the two molecules seen below, the same method of optimization has been used here so that the total energies of each molecule can be compared.

'''3) Endo Hydrogenation (1)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>CPEN_D3.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.2782
Bend: 19.8555
Stretch-Bend: -0.8346
Torsion: 10.8110
Non-1,4 VDW: -1.2202
1,4 VDW: 5.6331
Dipole/Dipole: 0.1621
Total Energy: 35.6850 kcal/mol
Calculation completed
------------------------------------

'''4) Endo Hydrogenation (2)'''

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>FFFF.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Note: All parameters used are finalized (Quality = 4).
Iteration 153: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.0968
Bend: 14.5244
Stretch-Bend: -0.5493
Torsion: 12.4974
Non-1,4 VDW: -1.0692
1,4 VDW: 4.5112
Dipole/Dipole: 0.1406
Total Energy: 31.1520 kcal/mol
Calculation completed
------------------------------------

Again, it is possible to compare the difference between the two total energies. The second hydrogenated molecule is more stable that first one by 4.533 kcal/mol, this means that it is the thermodynamic product of the hydrogenation reaction. It is possible to understand the different energies better by comparing the components that make up each total energy. The major contribution the large total energy difference between the two molecules appears to be the bending energy which has a difference of 5.3311 kcal/mol.

=== Comparison of Energies from Cyclopentadiene Dimers and There Hydrogenated Products ===

{| class="COMP " border="1px" align="center" width="900px"
|+ Comparison of Energies for Cyclopentadiene Dimers and There Hydrogenated Products
! Type !! Cyclopentadiene Dimer 1 !! Cyclopentadiene Dimer 2 !! Hydrogenated Dimer 1 !! Hydrogenated Dimer 2
|-
| Image ||[[File:CPEN_D2.jpg|300px|center]]||[[File:CPEN_D1.jpg|300px|center]]||[[File:CPEN_D3.jpg|300px|center]]||[[File:CPEN_D4.jpg|300px|center]]
|-
|Stretch (kcal mol<sup>-1</sup>) || 1.2855 || 1.2502 || 1.2782 || 1.0964
|-
|Bend (kcal mol<sup>-1</sup>) || 20.5794 || 20.8488 || 19.8555|| 14.5246
|-
| Stretch-Bend (kcal mol<sup>-1</sup>) || -0.8381 || -0.8346 || -0.5488 || -0.5494
|-
|Torsion (kcal mol<sup>-1</sup>) || 7.6571 || 9.5109 || 10.8110 || 12.4971
|-
| Non 1-4 Van der Waal's (kcal mol<sup>-1</sup>) || -1.4171 || -1.5455 || -1.2202 || -1.0701
|-
| 1,4 Van der Waal's (kcal mol<sup>-1</sup>) || 4.2322 || 4.3210 || 5.6331 || 4.5129
|-
| Dipole, Dipole (kcal mol<sup>-1</sup>) || 0.3776 || 0.4477 || 0.1621 || 0.1406
|-
| Total energy (kcal mol<sup>-1</sup>) || 31.8766 || 33.9975 || 35.6850 || 31.1520
|-
|}

The table above has complicated the data from the above calculations so that the relative energy's of each component can be easily compared. It can be seen that between dimers or products most of the energy's are very similar and there are few differences between the two as would be expected.

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

This section of the report is looking at two isomers of an intermediate in the synthesis of taxol, the two isomers occur due to the possibility of rotation of the keytone group, it can either be orientated up or down on the ring. The first step at analyzing the two possible isomers was to construct them with the correct steriochemistry, these molecules where then optimized using a MM2 field and the energy was then calculated again using a MMFF94. The results of these calculations and the molecules constructed can be seen below.

[[File:TAX_D15.jpg|300px|center]]
[[File:Taxol_A.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_A.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(26)-H(27)
Separating coincident atoms: H(37)-H(39)
Warning: Some parameters are guessed (Quality = 1).
Iteration 228: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7863
Bend: 16.5503
Stretch-Bend: 0.4310
Torsion: 18.2501
Non-1,4 VDW: -1.5648
1,4 VDW: 13.1116
Dipole/Dipole: -1.7249
Total Energy: 47.8396 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 58: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 70.5359 kcal/mol
Calculation completed
------------------------------------

[[File:TAX_D16.jpg|300px|center]]

[[File:Taxol_B.5.mol|300px|center]]

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Taxol_B.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

------------MM2 Minimization------------
Separating coincident atoms: H(31)-H(32)
Separating coincident atoms: H(35)-H(36)
Warning: Some parameters are guessed (Quality = 1).
Iteration 246: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6228
Bend: 11.3382
Stretch-Bend: 0.3439
Torsion: 19.6639
Non-1,4 VDW: -2.1524
1,4 VDW: 12.8688
Dipole/Dipole: -2.0018
Total Energy: 42.6834 kcal/mol
Calculation completed
------------------------------------

------------MMFF94 Minimization------------
Iteration 37: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Final Energy: 60.5719 kcal/mol
Calculation completed
------------------------------------

By looking at the energy's obtained by both calculations it can be seen that the second isomer is more stable than the first, the energy difference as calculated using the MM2 method is 5.1562 kcal/mol and the difference using the MMFF94 is 9.964 kcal/mol. It can therefore be said that the the intermediate with the keytone pointing in the same orientation as the neighboring hydrogen atoms is the one formed during the reaction.
By looking at the composition of the energy's calculated using the MM2 method the largest difference between the two is again in the bending component of the total energy. The key structual difference observed between the two isomers (apart form the inversion of the keytone) is that the 6 membered ring flips conformation, this is shown in the image below.

Comparison image showing ring flip:

[[File:Taxol_RF.png|400px|center]]

=== Modelling Using Semi-empirical Molecular Orbital Theory. ===

This section of the report is looking at the diene shown below, the intial step where the same as above with the molecule being constructed in ChemBio 3D and then being optimized using the MM2 method, the results of which can be seen below:

[[File:Compound_12.jpg|300px|center]]

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 151: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.6183
Bend: 4.7355
Stretch-Bend: 0.0399
Torsion: 7.6600
Non-1,4 VDW: -1.0653
1,4 VDW: 5.7939
Dipole/Dipole: 0.1124
Total Energy: 17.8945 kcal/mol
Calculation completed
------------------------------------

<div align="center">
<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Idontknow.cml</uploadedFileContents>
</jmolApplet></jmol>
</div>

The next step taken was to further optimize the molecule, this was done using the MOPAC method, this method takes into account any electronic effects that are not covered by the MM2 method. The result of the calculation can be seen below:

Mopac Job: AUX RM1 CHARGE=0 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09953 (< 0.10000) Heat of Formation = 22.82769 Kcal/Mol
-----------------------------------------

The MOPAC calculation also involves the optimization of the molecule by compring this structure to the MM2 optimized one it can be seen that they have different geometrys, this would be expected as the energies are different. The two different structures have been overlayed below to outline the key differences.

[[File:Diene_estat.jpg|center|300px]]

The final part of the analysis of this molecule was a vibrational analysis, this was run in Gaussian on the previously optimized molecule. The resulting vibrations can be seen on the molecule below, to view the differnt vibration right click on the image and place the curser over "model", you can then select which vibration you wish to view, it also displays in that selection the frequency of the vibration.

<div align="center">
<jmol>
<jmolApplet>
<title>Vibration</title><color>white</color><size>200</size>
<script>frame 8;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script><uploadedFileContents>Diene_FREQ_LOG.log</uploadedFileContents>
</jmolApplet>
</jmol>
</div>

=== Monosaccharide chemistry and the mechanism of glycosidation ===

The computational methods we have looked at before have been shown to provide a good understanding of intermediates in a reaction, this section will be looking at part of a glycosidation reaction which can be seen below:

[[File:GLY.png|center]]

The first intermediate has 4 possible isomers, the optimizations for which can be seen below, the structres of each of isomer have been tabulated below for better comparison with there relevant energies.

Energy calculations for isomer 1

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4507
Bend: 11.5140
Stretch-Bend: 0.8750
Torsion: 1.4349
Non-1,4 VDW: 0.2620
1,4 VDW: 19.4581
Charge/Dipole: -28.6982
Dipole/Dipole: 5.2444
Total Energy: 12.5409 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09168 (< 0.10000) Heat of Formation = -70.04084 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 2

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.4313
Bend: 11.7850
Stretch-Bend: 0.9826
Torsion: 1.4209
Non-1,4 VDW: 0.7701
1,4 VDW: 18.8357
Charge/Dipole: -27.0491
Dipole/Dipole: 5.9906
Total Energy: 15.1670 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09431 (< 0.10000) Heat of Formation = -79.27099 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 3

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 447: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2173
Bend: 10.6642
Stretch-Bend: 0.8233
Torsion: 0.6467
Non-1,4 VDW: -1.5632
1,4 VDW: 19.2644
Charge/Dipole: -15.9514
Dipole/Dipole: 3.8992
Total Energy: 20.0004 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07357 (< 0.10000) Heat of Formation = -65.36964 Kcal/Mol
-----------------------------------------

Energy calculations for isomer 4

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.2532
Bend: 11.1534
Stretch-Bend: 0.8510
Torsion: 1.1097
Non-1,4 VDW: -2.1220
1,4 VDW: 19.3508
Charge/Dipole: -11.5317
Dipole/Dipole: 3.8657
Total Energy: 24.9301 kcal/mol
Calculation completed
------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08961 (< 0.10000) Heat of Formation = -62.83046 Kcal/Mol
-----------------------------------------

{| class="Isomers" border="1px" align="center" width="1000px"
|+ Table for comparison on first intermediate
! Isomer description !! Visual of MM2 optimized isomer !! Total energy of MM2 obtimzed isomer (Kcal/mol) !! Visual of MOPAC optimized isomer !! Heat of formation from MOPAC Kcal/mol !! Distance between carbonyl oxygen and acyl carbon
|-
| Axial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1.cml</uploadedFileContents>
</jmolApplet></jmol> || 12.5409 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_1_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -70.04084 || 2.00
|-
| Axial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2.cml</uploadedFileContents>
</jmolApplet></jmol> || 15.1670 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_2_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -79.27099 || 1.457
|-
| Equatorial and above the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3.5.cml</uploadedFileContents>
</jmolApplet></jmol> || 20.0004 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_3_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -65.36964 || 2.869
|-
| Equatorial and below the ring || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4.1.cml</uploadedFileContents>
</jmolApplet></jmol> || 24.9301 || <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Glu_4_MOPAC.cml</uploadedFileContents>
</jmolApplet></jmol> || -62.83046 || 2.869
|-|}

This table shows that the isomer which have an axial carbonyl group are more stable than with an equitorial one, both MM2 and MOPAC agree with this. This means that under thermodynamic control either isomer 1 or 2 will be dominant. The total energies generated form MM2 indicate that the first isomer "Axial and above the ring" would be favored as it is 2.6261 Kcal/mol lower than isomer 2. This does not take into account electrostactis though which, considering the high charge density present, does not give a complete picture and so looking at the heats of formation from the MOPAC analysis it can be said that in reality isomer 2 is more stable. This is due to the added stability of an additional bond which cannot be seen in the representation but by looking at the distance between the carbonyl oxygen and acyl carbon can be understood to exist. This bond helps balance out the charges present and infact converts the molecule to the next step in the reaction drawn above. On the next page we will generate an energy for each isomer but with the new bond formed, the next page can be found [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]].

= This wiki page continues from the following link: [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AlexanderGrayCont here]] =

File:PICKYWIK.png

2013-03-15T15:08:24Z

Ag3210:

2013-03-15T13:42:34Z

Ag3210:

Rep:Mod:AlexanderGrayCont

2013-03-15T13:37:13Z

Ag3210: /* References */

= Organic Computaional Labs Continued, Part1 =

==== The Second Reaction Intermediate of a Glycosidation Reaction ====

As stated previously the results for the MM2 and MOPAC calculations of each isomer of the second reaction intermediate are shown below:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly1is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.1410
Bend: 15.2130
Stretch-Bend: 0.7546
Torsion: 9.4948
Non-1,4 VDW: -3.7163
1,4 VDW: 17.7977
Charge/Dipole: -4.6530
Dipole/Dipole: -0.7804
Total Energy: 36.2514 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09886 (< 0.10000) Heat of Formation = -46.61530 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly2is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.0053
Bend: 13.4884
Stretch-Bend: 0.7191
Torsion: 9.9562
Non-1,4 VDW: -2.8698
1,4 VDW: 18.0192
Charge/Dipole: -7.7771
Dipole/Dipole: -2.4245
Total Energy: 31.1168 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07455 (< 0.10000) Heat of Formation = -45.78147 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly3is.cml</uploadedFileContents>
</jmolApplet></jmol>

MM2 Calculation completed successfully
------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6633
Bend: 19.5290
Stretch-Bend: 0.7749
Torsion: 9.1167
Non-1,4 VDW: -3.2021
1,4 VDW: 19.0162
Charge/Dipole: 3.3946
Dipole/Dipole: -1.5909
Total Energy: 49.7016 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08973 (< 0.10000) Heat of Formation = -46.61374 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly4is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7503
Bend: 18.0616
Stretch-Bend: 0.8380
Torsion: 9.9783
Non-1,4 VDW: -2.6260
1,4 VDW: 19.5983
Charge/Dipole: 2.3600
Dipole/Dipole: -1.6307
Total Energy: 49.3298 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08822 (< 0.10000) Heat of Formation = -45.78368 Kcal/Mol
-----------------------------------------

== Part 2, Module 1 ==

=== Taxol ===

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>New_Taxol.cml</uploadedFileContents>
</jmolApplet></jmol>

The optimization log file can be found here: [[File:Log_for_new_taxol.log]]

[[File:Taxol_OPTED.gjf]]

The NMR analysis for taxol using a Basis set of mpw1pw91/6-31G(d,p) can be found here {{DOI|10042/24302}}

The H<sup>1</sup> NMR spectrum for the Taxol Complex can be seen below:
[[File:TAXOL.png]]

The literature NMR data has been tabulated below with the corrisponding calculated NMR data for comparison:

{| class="wikitable"
|+ Comparing the NMR data for calculation and experiment
|-
| Liturature NMR (ppm) || Calculated NMR (ppm)
|-
| 218.8 || 217.7
|-
| 144.6 || 146.6
|-
| 125.3 || 125.5
|-
| 72.9 || 88.7
|-
| 56.2 || 60.1
|-
| 52.5 || 57.2
|-
| 48.5 || 52.0
|-
| 46.8 || 51.3
|-
| 45.8 || 47.6
|-
| 39.8 || 43.6
|-
| 38.8 || 41.6
|-
| 35.9 || 41.5
|-
| 32.7 || 35.9
|-
| 28.8 || 31.3
|-
| 28.3 || 28.7
|-
| 26.9 || 28.5
|-
| 25.7 || 27.4
|-
| 23.9 || 26.3
|-
| 21.0 || 24.5
|-
| 18.7 || 20.3
|-
|}

=== Mini Project ===

For this mini project the molecule shown below was chosen from literature so that its reported NMR could be checked to confirm that the different isomers had been assigned correctly. The first set was to construct the molecule with the different possible isomer and then generate predicted NMRs this is shown below:

[[File:Mini.png]]
The reaction scheme for the formation of the products being looked at in this project

This is a Jmol of one of the isomers present:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>2_CML.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 105: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.4999
Bend: 5.6308
Stretch-Bend: -0.1001
Torsion: 0.6953
Non-1,4 VDW: -0.2984
1,4 VDW: 1.7252
Dipole/Dipole: 3.6138
Total Energy: 11.7665 kcal/mol
Calculation completed
------------------------------------

The same molecule was optimized on Gaussview the following log file was generated from this: [[File:OPT_1.LOG]]
The optimized molecule was then further optimzed using the 6-31G(d,p) basis set the file ca be found here: [[File:OPT_2.LOG]]

For each of the isomers the molecule was optimized using gaussian after being modified from the perviously opimized molecule, the files from each optimization can be found with the corresponding DOI links.

Optimization of isomer 2 {{DOI|10042/24282}}

Optimization of isomer 3 {{DOI|10042/24284}}

Optimization of isomer 4 {{DOI|10042/24285}}

On these optimized molecules an NMR analysis was run using the B3LYP - 6-31G(d,p) basis set, the NMR spectra obtained are displayed below and the files for these calculations can be found at the followin links:

NMR analysis for isomer 1 {{DOI|10042/24286}}

NMR analysis for isomer 2 {{DOI|10042/24287}}

NMR analysis for isomer 3 {{DOI|10042/24288}}

NMR analysis for isomer 4 {{DOI|10042/24289}}

A second NMR analysis was then run this time using a much larger basis set (cc-pVTZ) to investigate if the predicted NMR could be improved, the results have been tabulated below and the files for the calculations can be found here:

Larger basis set NMR analysis for isomer 1 {{DOI|10042/24290}}

Larger basis set NMR analysis for isomer 2 {{DOI|10042/24291}}

Larger basis set NMR analysis for isomer 3 {{DOI|10042/24292}}

Larger basis set NMR analysis for isomer 4 {{DOI|10042/24293}}

For all of the spectra in this table the relavent reference molecule has been used apart from in the case of the F<sup>19</sup> NMR where there was no references in Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V1_F.png]] || [[File:V1_C.png]] || [[File:V1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V2_F.png]] || [[File:V2_C.png]] || [[File:V2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V3_F.png]] || [[File:V3_C.png]] || [[File:V3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V4_F.png]] || [[File:V4_C.png]] || [[File:V4_H.png]]
|}

The table below contains the same NMR spectra as above but they have been calculated using a higher basis set. The spectra here have been shown to correlate better to the recorded NMR found in literature. To allow analysis of the F<sup>19</sup> NMR a reference molecule was made and the shielding constant (168.5547) was manually entered into Gaussian, the molecule was one of CFCl<sub>3</sub> chosen as it is the same one used in the literature. The output files for the [[Media:CFCL3.LOG|optimization]] and [[Media:CFCL3_NMR.LOG|NMR analysis]] for CFCl<sub>3</sub> can be found at there respective links. The ppm values obtained from Gaussian have been found to be slightly too low, this could be down to the reference calculated or some other area of Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides calculated using the cc-pVTZ basis set
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV1_F.png]] || [[File:2HV1_C.png]] || [[File:2HV1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV2_F.png]] || [[File:2HV2_C.png]] || [[File:2HV2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV3_F.png]] || [[File:2HV3_C.png]] || [[File:2HV3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV4_F.png]] || [[File:2HV4_C.png]] || [[File:2HV4_H.png]]
|}

The NMR data from Liturate has been tabulated below:

{| class="wikitable" border="1"
|+ H<sup>1</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| 2.00-3.30 (m, 2H); || 2.00-2.90 (m, 2H) || 2.06 (tdt, 1H) || 2.35 (tt, 2H)
|-
| 5.22 (ddd, 1H); || 5.68 (ddm, 1H) || 2.40-3.10 (m, 1H) || 5.78 (ddm, 2H)
|-
| 5.6 (ddm, 1H); || 6.00-6.80 (m, 3H) || 4.90-5.90 (m, 2H) || 5.80-6.40 (m, 2H)
|-
| 5.85 (dm, 1H); || || 6.18-6.40 (m, 2H) ||
|-
| 6.80 (m, 1H); || || ||
|-
|}

By comparing the chemical shift recorded to the predicted shifts above it can be seen that there is some agreement in the order and approximate number of chemical shifts present, taking into account that some peaks recorded as multiplets of a relative number of hydrogens more than one correlate to multiple predicted peaks. For example if we look at isomer 1 it can be seen for the predicted NMR graph that there should be 6H's present, this is the case, and that there are expected to be 2 H's between 2-3ppm, again the case. The peaks seen in liturature at 5.2, 5.6 and 5.8 have also been correctly predicted by the NMR prediction software, however the peak with chemical shift of 6.8 has been predicted at 6.2 ppm, a significatly lower value, this implies that the software has not correctly predicted the chemical shift of the hydrogen attached to an alkene and with a flourine on a neibouring carbon atom. Howvere the general good agreement shows that isomer one has been correctly predicted by the software and assigned correctly by the literature.

Unfortunately the other isomers do not show as close a similarity to the literature, it is stated that the purity of isomer 2 (compound 3 in literature) is not of complete purity, this can be seen from the wide ranges in ppm recorded and the number of multiplets. The predicted spectra shows 2 H's at rougly 2.5 ppm, this can be correlated to the liturature values between 2.0-2.9ppm the rest of the spectra does not however corrilate to the predicted spectra any more than any other isomer and so the NMR data, stated unreliable in the literature should not been be for further analysis.

The remaining two isomer can be seen to relate to the predicted NMR spectra but there is still a reasonably large margin of error as far as the chemical shifts are concerned but it can be said that the H1 NMR spectra of compounds have been assigned correctly.

{| class="wikitable" border="1"
|+ F<sup>19</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| -176 (ddm, 1F); || -159 (m, 1F) || -161 (m) || -171 (m)
|-
| -187 (m, 1F); || -167 (m, 1F) || ||
|-
|}

The literature values for the F<sup>19</sup> NMR, seen above, can be seen to have a higher (less negative) chemical shift than the predicted NMR values despite the corrections made. looking at the distribution of the peaks however it is possible to see that the for isomer 1 and 2 both methods show 2 distinguishable peaks with the spacing between peaks being larger for isomer 1 than 2. For isomer 2 only 1 peak is expected as the molecule is symmetric and so both flourines are in the same environment, only one peak is seen in the actual NMR, this is a multiplet probably due to coupling with the hydrogen atoms. Isomer 4 has been predicted to show 2 peaks that should be differentiable, this however is not the case, the chemical shift of isomer 3 is predicted to be higher (less negative) than that of isomer 4, although the values are not the same the relationship is and so it can be said that the correct assignment has been made.

=== J coupling ===

To look at the spin coupling for each molecule the following data was extracted from the log files of each of the diflorinated molecules, the original log files for each can be found above. The data below shows the couplings between each atom, the labeling system relates the the molecule above the data, the light blue atoms are fluorine atoms, the white hydrogen and the grey carbon.

Unfortunately as the literature does not provide many coupling constants there is very little comparative analysis possible here. Values of interest have been tabulated below each set of data.

[[File:V1.jpg|300px]]

Isomer 1

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.342866D+02 0.000000D+00
3 0.895875D+01 0.387721D+02 0.000000D+00
4 0.432962D+01 0.357276D+01 0.814371D+02 0.000000D+00
5 0.286622D+02 0.761418D+01 0.168366D+00 0.277392D+02 0.000000D+00
6 0.620195D+01 0.250870D+01 0.154230D+03 0.241025D+01 0.890794D+01
7 0.641252D+01 0.975844D+01 0.233016D+01 0.151755D+03 0.453581D+01
8 -0.356953D+01 0.490619D+01 0.420895D+01 -0.373378D+01 0.118209D+03
9 -0.562801D+01 -0.180511D+01 0.340892D+01 -0.614534D+01 0.112126D+03
10 0.131662D+03 -0.504874D+01 -0.296543D+00 0.105109D+01 -0.136180D+01
11 -0.228247D+03 0.199291D+02 0.648570D+01 0.435993D+01 0.161753D+02
12 0.158580D+02 -0.221931D+03 0.181425D+02 0.275804D+01 0.247006D+01
13 -0.387550D+01 0.133542D+03 -0.281012D+01 0.386991D+01 -0.136352D+01
6 7 8 9 10
6 0.000000D+00
7 0.570798D+01 0.000000D+00
8 -0.239625D+01 0.333843D+01 0.000000D+00
9 -0.377890D+01 0.273722D+01 -0.164174D+02 0.000000D+00
10 0.152419D+00 -0.118905D+00 0.752471D+01 0.513857D+01 0.000000D+00
11 0.114526D+01 0.180493D+01 0.496252D+00 0.209070D+02 0.485841D+02
12 0.243819D+01 -0.284005D+01 0.609967D+00 0.104561D+02 0.227008D+02
13 0.225434D+01 -0.251199D+01 0.230756D+01 0.300313D+01 0.361997D+01
11 12 13
11 0.000000D+00
12 -0.656033D+01 0.000000D+00
13 0.173949D+02 0.493934D+02 0.000000D+00

From this data the most significant couplings have been tabulated below:

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 22
|-
| F-F coupling / Literature || 18
|}

The same file for isomer 2 is below:

[[File:V2.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.298057D+02 0.000000D+00
3 0.360005D+01 0.383120D+02 0.000000D+00
4 0.140841D+01 0.568185D+01 0.847547D+02 0.000000D+00
5 0.272228D+02 0.661319D+01 0.146319D+01 0.276719D+02 0.000000D+00
6 0.531289D+01 0.294077D+01 0.154554D+03 0.326074D+01 0.956471D+01
7 0.552333D+01 0.112712D+02 0.331786D+01 0.151972D+03 0.495994D+01
8 -0.540504D+01 0.397276D+01 0.386070D+01 -0.396731D+01 0.116736D+03
9 0.381514D+01 -0.113783D+01 0.287703D+01 -0.488835D+01 0.111760D+03
10 0.884900D+01 -0.227663D+03 0.174540D+02 0.474589D+01 -0.173807D+01
11 0.548960D+01 0.132178D+03 -0.215125D+01 0.257544D+01 -0.786536D+00
12 -0.224697D+03 0.112122D+02 -0.314235D+00 -0.149288D+01 0.150435D+02
13 0.145676D+03 0.312450D+00 0.540799D+01 0.585986D+01 0.177718D+01
6 7 8 9 10
6 0.000000D+00
7 0.541089D+01 0.000000D+00
8 -0.230815D+01 0.333160D+01 0.000000D+00
9 -0.411266D+01 0.255795D+01 -0.176851D+02 0.000000D+00
10 0.241296D+01 -0.149280D+01 0.181811D+00 0.359811D+01 0.000000D+00
11 0.215383D+01 -0.323173D+01 0.133489D+01 0.274682D+01 0.442501D+02
12 -0.119884D-01 -0.683563D-02 0.213811D+02 0.256981D+02 -0.570540D+01
13 0.288938D+00 0.320102D+00 0.497912D-01 0.396887D+01 -0.132042D+01
11 12 13
11 0.000000D+00
12 0.122457D+02 0.000000D+00
13 0.410809D+01 0.492388D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 5.7
|-
| F-F coupling / Literature || None reported
|}

For isomer 3:

[[File:V31.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.273345D+02 0.000000D+00
3 0.351869D+01 0.357805D+02 0.000000D+00
4 0.351678D+01 0.356759D+01 0.851369D+02 0.000000D+00
5 0.273508D+02 0.784544D+01 0.356356D+01 0.357942D+02 0.000000D+00
6 0.415912D+01 0.232123D+01 0.153275D+03 0.317256D+01 0.115299D+02
7 0.415929D+01 0.115328D+02 0.317046D+01 0.153272D+03 0.232109D+01
8 0.126697D+01 0.766162D+00 0.282143D+01 -0.214675D+01 0.135968D+03
9 0.110154D+02 -0.221170D+03 0.175499D+02 0.268770D+01 -0.224820D+01
10 0.126219D+01 0.135964D+03 -0.214746D+01 0.281796D+01 0.765104D+00
11 0.120768D+03 -0.126794D+01 0.546578D+01 0.546538D+01 -0.126249D+01
12 0.108735D+03 -0.707120D+01 -0.156287D+00 -0.156513D+00 -0.707035D+01
13 0.110113D+02 -0.226057D+01 0.268852D+01 0.175542D+02 -0.221062D+03
6 7 8 9 10
6 0.000000D+00
7 0.509273D+01 0.000000D+00
8 -0.209240D+01 0.221891D+01 0.000000D+00
9 0.250491D+01 -0.292515D+01 0.110507D+02 0.000000D+00
10 0.221853D+01 -0.209470D+01 0.188537D+01 0.483661D+02 0.000000D+00
11 -0.246804D+00 -0.246888D+00 0.628814D+01 0.404899D+00 0.628769D+01
12 -0.122410D+00 -0.120443D+00 0.486518D+01 0.246650D+02 0.486525D+01
13 -0.293299D+01 0.250911D+01 0.483593D+02 0.121202D+02 0.110678D+02
11 12 13
11 0.000000D+00
12 -0.122699D+02 0.000000D+00
13 0.410527D+00 0.246816D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 12.1
|-
| F-F coupling / Literature || None reported
|}

Isomer 4:

[[File:V4.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.291101D+02 0.000000D+00
3 0.376865D+01 0.360903D+02 0.000000D+00
4 0.327801D+01 0.501414D+01 0.846316D+02 0.000000D+00
5 0.293380D+02 0.528212D+01 0.261876D+01 0.337271D+02 0.000000D+00
6 0.452981D+01 0.290011D+01 0.152690D+03 0.334557D+01 0.114129D+02
7 0.428822D+01 0.108793D+02 0.372204D+01 0.153433D+03 0.387792D+01
8 0.126708D+02 -0.215381D+03 0.149397D+02 0.209481D+01 0.934862D+01
9 -0.600859D-01 0.134584D+03 -0.146461D+01 0.311426D+01 -0.920073D+00
10 0.117780D+03 -0.161334D+01 0.628257D+01 0.319068D+01 -0.485410D+01
11 0.109076D+03 -0.669288D+01 -0.176798D+00 0.856155D+00 -0.822490D+00
12 0.180918D+02 -0.366872D+01 0.296262D+01 0.774594D+01 -0.211300D+03
13 -0.195171D+00 0.546568D+01 0.457133D+01 -0.927065D+00 0.141349D+03
6 7 8 9 10
6 0.000000D+00
7 0.515899D+01 0.000000D+00
8 0.306287D+01 -0.256222D+01 0.000000D+00
9 0.222974D+01 -0.258174D+01 0.477343D+02 0.000000D+00
10 -0.172590D+00 0.135473D+00 0.311884D+00 0.566856D+01 0.000000D+00
11 -0.605838D+00 -0.518467D+00 0.236849D+02 0.415039D+01 -0.140235D+02
12 -0.434430D+01 0.255227D+01 0.190874D+02 0.799236D+01 0.176430D+02
13 -0.876659D+00 0.260831D+01 0.140782D+00 0.175197D+01 0.551757D-01
11 12 13
11 0.000000D+00
12 0.246213D+02 0.000000D+00
13 0.565082D+01 0.497731D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 19.1
|-
| F-F coupling / Literature || None reported
|}

=== Vibrational Analysis ===

The optimized molecules for above where then run through vibrational analysis to produce IR spectra, the literature did not run IR spectra which these can be compared to, but it is a helpful technique to check that the compound is has been optimized and to compare any differences that arise (the IR spectra should contain the same peaks).

{| class="wikitable" border="1"
|+ Table of IR spectra
! Isomer Number !! Calculated IR Spectrum
|-
| Isomer 1 || [[File:IR1.png]]
|-
| Isomer 2 || [[File:IR2.png]]
|-
| Isomer 3 || [[File:IR3.png]]
|-
| Isomer 4 || [[File:IR4.png]]
|-
|}

Comparison of the spectra shows that they are not all the same, however it is mainly the intensity of the peaks rather that there existence that changes. All the the molecuels contain the expected peaks, Isomer 3 has additional peaks and much larger peaks compared to the other isomers, this is due to its high level of symmetry.

=== References ===

http://ac.els-cdn.com/002211399403190B/1-s2.0-002211399403190B-main.pdf?_tid=930742b8-8a51-11e2-a537-00000aacb362&acdnat=1363009553_0579d0d0ad7eb0ece5d46549b57556e0
Mini project
http://www.sciencedirect.com/science/article/pii/002211399403190B#

Taxol
http://pubs.acs.org/doi/abs/10.1021/ja00157a043

Rep:Mod:AlexanderGrayCont

2013-03-15T13:36:09Z

Ag3210: /* Taxol */

= Organic Computaional Labs Continued, Part1 =

==== The Second Reaction Intermediate of a Glycosidation Reaction ====

As stated previously the results for the MM2 and MOPAC calculations of each isomer of the second reaction intermediate are shown below:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly1is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.1410
Bend: 15.2130
Stretch-Bend: 0.7546
Torsion: 9.4948
Non-1,4 VDW: -3.7163
1,4 VDW: 17.7977
Charge/Dipole: -4.6530
Dipole/Dipole: -0.7804
Total Energy: 36.2514 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09886 (< 0.10000) Heat of Formation = -46.61530 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly2is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.0053
Bend: 13.4884
Stretch-Bend: 0.7191
Torsion: 9.9562
Non-1,4 VDW: -2.8698
1,4 VDW: 18.0192
Charge/Dipole: -7.7771
Dipole/Dipole: -2.4245
Total Energy: 31.1168 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07455 (< 0.10000) Heat of Formation = -45.78147 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly3is.cml</uploadedFileContents>
</jmolApplet></jmol>

MM2 Calculation completed successfully
------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6633
Bend: 19.5290
Stretch-Bend: 0.7749
Torsion: 9.1167
Non-1,4 VDW: -3.2021
1,4 VDW: 19.0162
Charge/Dipole: 3.3946
Dipole/Dipole: -1.5909
Total Energy: 49.7016 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08973 (< 0.10000) Heat of Formation = -46.61374 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly4is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7503
Bend: 18.0616
Stretch-Bend: 0.8380
Torsion: 9.9783
Non-1,4 VDW: -2.6260
1,4 VDW: 19.5983
Charge/Dipole: 2.3600
Dipole/Dipole: -1.6307
Total Energy: 49.3298 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08822 (< 0.10000) Heat of Formation = -45.78368 Kcal/Mol
-----------------------------------------

== Part 2, Module 1 ==

=== Taxol ===

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>New_Taxol.cml</uploadedFileContents>
</jmolApplet></jmol>

The optimization log file can be found here: [[File:Log_for_new_taxol.log]]

[[File:Taxol_OPTED.gjf]]

The NMR analysis for taxol using a Basis set of mpw1pw91/6-31G(d,p) can be found here {{DOI|10042/24302}}

The H<sup>1</sup> NMR spectrum for the Taxol Complex can be seen below:
[[File:TAXOL.png]]

The literature NMR data has been tabulated below with the corrisponding calculated NMR data for comparison:

{| class="wikitable"
|+ Comparing the NMR data for calculation and experiment
|-
| Liturature NMR (ppm) || Calculated NMR (ppm)
|-
| 218.8 || 217.7
|-
| 144.6 || 146.6
|-
| 125.3 || 125.5
|-
| 72.9 || 88.7
|-
| 56.2 || 60.1
|-
| 52.5 || 57.2
|-
| 48.5 || 52.0
|-
| 46.8 || 51.3
|-
| 45.8 || 47.6
|-
| 39.8 || 43.6
|-
| 38.8 || 41.6
|-
| 35.9 || 41.5
|-
| 32.7 || 35.9
|-
| 28.8 || 31.3
|-
| 28.3 || 28.7
|-
| 26.9 || 28.5
|-
| 25.7 || 27.4
|-
| 23.9 || 26.3
|-
| 21.0 || 24.5
|-
| 18.7 || 20.3
|-
|}

=== Mini Project ===

For this mini project the molecule shown below was chosen from literature so that its reported NMR could be checked to confirm that the different isomers had been assigned correctly. The first set was to construct the molecule with the different possible isomer and then generate predicted NMRs this is shown below:

[[File:Mini.png]]
The reaction scheme for the formation of the products being looked at in this project

This is a Jmol of one of the isomers present:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>2_CML.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 105: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.4999
Bend: 5.6308
Stretch-Bend: -0.1001
Torsion: 0.6953
Non-1,4 VDW: -0.2984
1,4 VDW: 1.7252
Dipole/Dipole: 3.6138
Total Energy: 11.7665 kcal/mol
Calculation completed
------------------------------------

The same molecule was optimized on Gaussview the following log file was generated from this: [[File:OPT_1.LOG]]
The optimized molecule was then further optimzed using the 6-31G(d,p) basis set the file ca be found here: [[File:OPT_2.LOG]]

For each of the isomers the molecule was optimized using gaussian after being modified from the perviously opimized molecule, the files from each optimization can be found with the corresponding DOI links.

Optimization of isomer 2 {{DOI|10042/24282}}

Optimization of isomer 3 {{DOI|10042/24284}}

Optimization of isomer 4 {{DOI|10042/24285}}

On these optimized molecules an NMR analysis was run using the B3LYP - 6-31G(d,p) basis set, the NMR spectra obtained are displayed below and the files for these calculations can be found at the followin links:

NMR analysis for isomer 1 {{DOI|10042/24286}}

NMR analysis for isomer 2 {{DOI|10042/24287}}

NMR analysis for isomer 3 {{DOI|10042/24288}}

NMR analysis for isomer 4 {{DOI|10042/24289}}

A second NMR analysis was then run this time using a much larger basis set (cc-pVTZ) to investigate if the predicted NMR could be improved, the results have been tabulated below and the files for the calculations can be found here:

Larger basis set NMR analysis for isomer 1 {{DOI|10042/24290}}

Larger basis set NMR analysis for isomer 2 {{DOI|10042/24291}}

Larger basis set NMR analysis for isomer 3 {{DOI|10042/24292}}

Larger basis set NMR analysis for isomer 4 {{DOI|10042/24293}}

For all of the spectra in this table the relavent reference molecule has been used apart from in the case of the F<sup>19</sup> NMR where there was no references in Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V1_F.png]] || [[File:V1_C.png]] || [[File:V1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V2_F.png]] || [[File:V2_C.png]] || [[File:V2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V3_F.png]] || [[File:V3_C.png]] || [[File:V3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V4_F.png]] || [[File:V4_C.png]] || [[File:V4_H.png]]
|}

The table below contains the same NMR spectra as above but they have been calculated using a higher basis set. The spectra here have been shown to correlate better to the recorded NMR found in literature. To allow analysis of the F<sup>19</sup> NMR a reference molecule was made and the shielding constant (168.5547) was manually entered into Gaussian, the molecule was one of CFCl<sub>3</sub> chosen as it is the same one used in the literature. The output files for the [[Media:CFCL3.LOG|optimization]] and [[Media:CFCL3_NMR.LOG|NMR analysis]] for CFCl<sub>3</sub> can be found at there respective links. The ppm values obtained from Gaussian have been found to be slightly too low, this could be down to the reference calculated or some other area of Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides calculated using the cc-pVTZ basis set
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV1_F.png]] || [[File:2HV1_C.png]] || [[File:2HV1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV2_F.png]] || [[File:2HV2_C.png]] || [[File:2HV2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV3_F.png]] || [[File:2HV3_C.png]] || [[File:2HV3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV4_F.png]] || [[File:2HV4_C.png]] || [[File:2HV4_H.png]]
|}

The NMR data from Liturate has been tabulated below:

{| class="wikitable" border="1"
|+ H<sup>1</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| 2.00-3.30 (m, 2H); || 2.00-2.90 (m, 2H) || 2.06 (tdt, 1H) || 2.35 (tt, 2H)
|-
| 5.22 (ddd, 1H); || 5.68 (ddm, 1H) || 2.40-3.10 (m, 1H) || 5.78 (ddm, 2H)
|-
| 5.6 (ddm, 1H); || 6.00-6.80 (m, 3H) || 4.90-5.90 (m, 2H) || 5.80-6.40 (m, 2H)
|-
| 5.85 (dm, 1H); || || 6.18-6.40 (m, 2H) ||
|-
| 6.80 (m, 1H); || || ||
|-
|}

By comparing the chemical shift recorded to the predicted shifts above it can be seen that there is some agreement in the order and approximate number of chemical shifts present, taking into account that some peaks recorded as multiplets of a relative number of hydrogens more than one correlate to multiple predicted peaks. For example if we look at isomer 1 it can be seen for the predicted NMR graph that there should be 6H's present, this is the case, and that there are expected to be 2 H's between 2-3ppm, again the case. The peaks seen in liturature at 5.2, 5.6 and 5.8 have also been correctly predicted by the NMR prediction software, however the peak with chemical shift of 6.8 has been predicted at 6.2 ppm, a significatly lower value, this implies that the software has not correctly predicted the chemical shift of the hydrogen attached to an alkene and with a flourine on a neibouring carbon atom. Howvere the general good agreement shows that isomer one has been correctly predicted by the software and assigned correctly by the literature.

Unfortunately the other isomers do not show as close a similarity to the literature, it is stated that the purity of isomer 2 (compound 3 in literature) is not of complete purity, this can be seen from the wide ranges in ppm recorded and the number of multiplets. The predicted spectra shows 2 H's at rougly 2.5 ppm, this can be correlated to the liturature values between 2.0-2.9ppm the rest of the spectra does not however corrilate to the predicted spectra any more than any other isomer and so the NMR data, stated unreliable in the literature should not been be for further analysis.

The remaining two isomer can be seen to relate to the predicted NMR spectra but there is still a reasonably large margin of error as far as the chemical shifts are concerned but it can be said that the H1 NMR spectra of compounds have been assigned correctly.

{| class="wikitable" border="1"
|+ F<sup>19</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| -176 (ddm, 1F); || -159 (m, 1F) || -161 (m) || -171 (m)
|-
| -187 (m, 1F); || -167 (m, 1F) || ||
|-
|}

The literature values for the F<sup>19</sup> NMR, seen above, can be seen to have a higher (less negative) chemical shift than the predicted NMR values despite the corrections made. looking at the distribution of the peaks however it is possible to see that the for isomer 1 and 2 both methods show 2 distinguishable peaks with the spacing between peaks being larger for isomer 1 than 2. For isomer 2 only 1 peak is expected as the molecule is symmetric and so both flourines are in the same environment, only one peak is seen in the actual NMR, this is a multiplet probably due to coupling with the hydrogen atoms. Isomer 4 has been predicted to show 2 peaks that should be differentiable, this however is not the case, the chemical shift of isomer 3 is predicted to be higher (less negative) than that of isomer 4, although the values are not the same the relationship is and so it can be said that the correct assignment has been made.

=== J coupling ===

To look at the spin coupling for each molecule the following data was extracted from the log files of each of the diflorinated molecules, the original log files for each can be found above. The data below shows the couplings between each atom, the labeling system relates the the molecule above the data, the light blue atoms are fluorine atoms, the white hydrogen and the grey carbon.

Unfortunately as the literature does not provide many coupling constants there is very little comparative analysis possible here. Values of interest have been tabulated below each set of data.

[[File:V1.jpg|300px]]

Isomer 1

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.342866D+02 0.000000D+00
3 0.895875D+01 0.387721D+02 0.000000D+00
4 0.432962D+01 0.357276D+01 0.814371D+02 0.000000D+00
5 0.286622D+02 0.761418D+01 0.168366D+00 0.277392D+02 0.000000D+00
6 0.620195D+01 0.250870D+01 0.154230D+03 0.241025D+01 0.890794D+01
7 0.641252D+01 0.975844D+01 0.233016D+01 0.151755D+03 0.453581D+01
8 -0.356953D+01 0.490619D+01 0.420895D+01 -0.373378D+01 0.118209D+03
9 -0.562801D+01 -0.180511D+01 0.340892D+01 -0.614534D+01 0.112126D+03
10 0.131662D+03 -0.504874D+01 -0.296543D+00 0.105109D+01 -0.136180D+01
11 -0.228247D+03 0.199291D+02 0.648570D+01 0.435993D+01 0.161753D+02
12 0.158580D+02 -0.221931D+03 0.181425D+02 0.275804D+01 0.247006D+01
13 -0.387550D+01 0.133542D+03 -0.281012D+01 0.386991D+01 -0.136352D+01
6 7 8 9 10
6 0.000000D+00
7 0.570798D+01 0.000000D+00
8 -0.239625D+01 0.333843D+01 0.000000D+00
9 -0.377890D+01 0.273722D+01 -0.164174D+02 0.000000D+00
10 0.152419D+00 -0.118905D+00 0.752471D+01 0.513857D+01 0.000000D+00
11 0.114526D+01 0.180493D+01 0.496252D+00 0.209070D+02 0.485841D+02
12 0.243819D+01 -0.284005D+01 0.609967D+00 0.104561D+02 0.227008D+02
13 0.225434D+01 -0.251199D+01 0.230756D+01 0.300313D+01 0.361997D+01
11 12 13
11 0.000000D+00
12 -0.656033D+01 0.000000D+00
13 0.173949D+02 0.493934D+02 0.000000D+00

From this data the most significant couplings have been tabulated below:

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 22
|-
| F-F coupling / Literature || 18
|}

The same file for isomer 2 is below:

[[File:V2.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.298057D+02 0.000000D+00
3 0.360005D+01 0.383120D+02 0.000000D+00
4 0.140841D+01 0.568185D+01 0.847547D+02 0.000000D+00
5 0.272228D+02 0.661319D+01 0.146319D+01 0.276719D+02 0.000000D+00
6 0.531289D+01 0.294077D+01 0.154554D+03 0.326074D+01 0.956471D+01
7 0.552333D+01 0.112712D+02 0.331786D+01 0.151972D+03 0.495994D+01
8 -0.540504D+01 0.397276D+01 0.386070D+01 -0.396731D+01 0.116736D+03
9 0.381514D+01 -0.113783D+01 0.287703D+01 -0.488835D+01 0.111760D+03
10 0.884900D+01 -0.227663D+03 0.174540D+02 0.474589D+01 -0.173807D+01
11 0.548960D+01 0.132178D+03 -0.215125D+01 0.257544D+01 -0.786536D+00
12 -0.224697D+03 0.112122D+02 -0.314235D+00 -0.149288D+01 0.150435D+02
13 0.145676D+03 0.312450D+00 0.540799D+01 0.585986D+01 0.177718D+01
6 7 8 9 10
6 0.000000D+00
7 0.541089D+01 0.000000D+00
8 -0.230815D+01 0.333160D+01 0.000000D+00
9 -0.411266D+01 0.255795D+01 -0.176851D+02 0.000000D+00
10 0.241296D+01 -0.149280D+01 0.181811D+00 0.359811D+01 0.000000D+00
11 0.215383D+01 -0.323173D+01 0.133489D+01 0.274682D+01 0.442501D+02
12 -0.119884D-01 -0.683563D-02 0.213811D+02 0.256981D+02 -0.570540D+01
13 0.288938D+00 0.320102D+00 0.497912D-01 0.396887D+01 -0.132042D+01
11 12 13
11 0.000000D+00
12 0.122457D+02 0.000000D+00
13 0.410809D+01 0.492388D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 5.7
|-
| F-F coupling / Literature || None reported
|}

For isomer 3:

[[File:V31.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.273345D+02 0.000000D+00
3 0.351869D+01 0.357805D+02 0.000000D+00
4 0.351678D+01 0.356759D+01 0.851369D+02 0.000000D+00
5 0.273508D+02 0.784544D+01 0.356356D+01 0.357942D+02 0.000000D+00
6 0.415912D+01 0.232123D+01 0.153275D+03 0.317256D+01 0.115299D+02
7 0.415929D+01 0.115328D+02 0.317046D+01 0.153272D+03 0.232109D+01
8 0.126697D+01 0.766162D+00 0.282143D+01 -0.214675D+01 0.135968D+03
9 0.110154D+02 -0.221170D+03 0.175499D+02 0.268770D+01 -0.224820D+01
10 0.126219D+01 0.135964D+03 -0.214746D+01 0.281796D+01 0.765104D+00
11 0.120768D+03 -0.126794D+01 0.546578D+01 0.546538D+01 -0.126249D+01
12 0.108735D+03 -0.707120D+01 -0.156287D+00 -0.156513D+00 -0.707035D+01
13 0.110113D+02 -0.226057D+01 0.268852D+01 0.175542D+02 -0.221062D+03
6 7 8 9 10
6 0.000000D+00
7 0.509273D+01 0.000000D+00
8 -0.209240D+01 0.221891D+01 0.000000D+00
9 0.250491D+01 -0.292515D+01 0.110507D+02 0.000000D+00
10 0.221853D+01 -0.209470D+01 0.188537D+01 0.483661D+02 0.000000D+00
11 -0.246804D+00 -0.246888D+00 0.628814D+01 0.404899D+00 0.628769D+01
12 -0.122410D+00 -0.120443D+00 0.486518D+01 0.246650D+02 0.486525D+01
13 -0.293299D+01 0.250911D+01 0.483593D+02 0.121202D+02 0.110678D+02
11 12 13
11 0.000000D+00
12 -0.122699D+02 0.000000D+00
13 0.410527D+00 0.246816D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 12.1
|-
| F-F coupling / Literature || None reported
|}

Isomer 4:

[[File:V4.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.291101D+02 0.000000D+00
3 0.376865D+01 0.360903D+02 0.000000D+00
4 0.327801D+01 0.501414D+01 0.846316D+02 0.000000D+00
5 0.293380D+02 0.528212D+01 0.261876D+01 0.337271D+02 0.000000D+00
6 0.452981D+01 0.290011D+01 0.152690D+03 0.334557D+01 0.114129D+02
7 0.428822D+01 0.108793D+02 0.372204D+01 0.153433D+03 0.387792D+01
8 0.126708D+02 -0.215381D+03 0.149397D+02 0.209481D+01 0.934862D+01
9 -0.600859D-01 0.134584D+03 -0.146461D+01 0.311426D+01 -0.920073D+00
10 0.117780D+03 -0.161334D+01 0.628257D+01 0.319068D+01 -0.485410D+01
11 0.109076D+03 -0.669288D+01 -0.176798D+00 0.856155D+00 -0.822490D+00
12 0.180918D+02 -0.366872D+01 0.296262D+01 0.774594D+01 -0.211300D+03
13 -0.195171D+00 0.546568D+01 0.457133D+01 -0.927065D+00 0.141349D+03
6 7 8 9 10
6 0.000000D+00
7 0.515899D+01 0.000000D+00
8 0.306287D+01 -0.256222D+01 0.000000D+00
9 0.222974D+01 -0.258174D+01 0.477343D+02 0.000000D+00
10 -0.172590D+00 0.135473D+00 0.311884D+00 0.566856D+01 0.000000D+00
11 -0.605838D+00 -0.518467D+00 0.236849D+02 0.415039D+01 -0.140235D+02
12 -0.434430D+01 0.255227D+01 0.190874D+02 0.799236D+01 0.176430D+02
13 -0.876659D+00 0.260831D+01 0.140782D+00 0.175197D+01 0.551757D-01
11 12 13
11 0.000000D+00
12 0.246213D+02 0.000000D+00
13 0.565082D+01 0.497731D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 19.1
|-
| F-F coupling / Literature || None reported
|}

=== Vibrational Analysis ===

The optimized molecules for above where then run through vibrational analysis to produce IR spectra, the literature did not run IR spectra which these can be compared to, but it is a helpful technique to check that the compound is has been optimized and to compare any differences that arise (the IR spectra should contain the same peaks).

{| class="wikitable" border="1"
|+ Table of IR spectra
! Isomer Number !! Calculated IR Spectrum
|-
| Isomer 1 || [[File:IR1.png]]
|-
| Isomer 2 || [[File:IR2.png]]
|-
| Isomer 3 || [[File:IR3.png]]
|-
| Isomer 4 || [[File:IR4.png]]
|-
|}

Comparison of the spectra shows that they are not all the same, however it is mainly the intensity of the peaks rather that there existence that changes. All the the molecuels contain the expected peaks, Isomer 3 has additional peaks and much larger peaks compared to the other isomers, this is due to its high level of symmetry.

=== References ===
http://ac.els-cdn.com/002211399403190B/1-s2.0-002211399403190B-main.pdf?_tid=930742b8-8a51-11e2-a537-00000aacb362&acdnat=1363009553_0579d0d0ad7eb0ece5d46549b57556e0
http://www.sciencedirect.com/science/article/pii/002211399403190B#

Rep:Mod:AlexanderGrayCont

2013-03-15T13:24:25Z

Ag3210: /* Vibrational Analysis */

= Organic Computaional Labs Continued, Part1 =

==== The Second Reaction Intermediate of a Glycosidation Reaction ====

As stated previously the results for the MM2 and MOPAC calculations of each isomer of the second reaction intermediate are shown below:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly1is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.1410
Bend: 15.2130
Stretch-Bend: 0.7546
Torsion: 9.4948
Non-1,4 VDW: -3.7163
1,4 VDW: 17.7977
Charge/Dipole: -4.6530
Dipole/Dipole: -0.7804
Total Energy: 36.2514 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09886 (< 0.10000) Heat of Formation = -46.61530 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly2is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.0053
Bend: 13.4884
Stretch-Bend: 0.7191
Torsion: 9.9562
Non-1,4 VDW: -2.8698
1,4 VDW: 18.0192
Charge/Dipole: -7.7771
Dipole/Dipole: -2.4245
Total Energy: 31.1168 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07455 (< 0.10000) Heat of Formation = -45.78147 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly3is.cml</uploadedFileContents>
</jmolApplet></jmol>

MM2 Calculation completed successfully
------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6633
Bend: 19.5290
Stretch-Bend: 0.7749
Torsion: 9.1167
Non-1,4 VDW: -3.2021
1,4 VDW: 19.0162
Charge/Dipole: 3.3946
Dipole/Dipole: -1.5909
Total Energy: 49.7016 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08973 (< 0.10000) Heat of Formation = -46.61374 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly4is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7503
Bend: 18.0616
Stretch-Bend: 0.8380
Torsion: 9.9783
Non-1,4 VDW: -2.6260
1,4 VDW: 19.5983
Charge/Dipole: 2.3600
Dipole/Dipole: -1.6307
Total Energy: 49.3298 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08822 (< 0.10000) Heat of Formation = -45.78368 Kcal/Mol
-----------------------------------------

== Part 2, Module 1 ==

=== Taxol ===

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>New_Taxol.cml</uploadedFileContents>
</jmolApplet></jmol>

The optimization log file can be found here: [[File:Log_for_new_taxol.log]]

[[File:Taxol_OPTED.gjf]]

The NMR analysis for taxol using a Basis set of mpw1pw91/6-31G(d,p) can be found here {{DOI|10042/24302}}

The H<sup>1</sup> NMR spectrum for the Taxol Complex can be seen below:
[[File:TAXOL.png]]

=== Mini Project ===

For this mini project the molecule shown below was chosen from literature so that its reported NMR could be checked to confirm that the different isomers had been assigned correctly. The first set was to construct the molecule with the different possible isomer and then generate predicted NMRs this is shown below:

[[File:Mini.png]]
The reaction scheme for the formation of the products being looked at in this project

This is a Jmol of one of the isomers present:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>2_CML.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 105: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.4999
Bend: 5.6308
Stretch-Bend: -0.1001
Torsion: 0.6953
Non-1,4 VDW: -0.2984
1,4 VDW: 1.7252
Dipole/Dipole: 3.6138
Total Energy: 11.7665 kcal/mol
Calculation completed
------------------------------------

The same molecule was optimized on Gaussview the following log file was generated from this: [[File:OPT_1.LOG]]
The optimized molecule was then further optimzed using the 6-31G(d,p) basis set the file ca be found here: [[File:OPT_2.LOG]]

For each of the isomers the molecule was optimized using gaussian after being modified from the perviously opimized molecule, the files from each optimization can be found with the corresponding DOI links.

Optimization of isomer 2 {{DOI|10042/24282}}

Optimization of isomer 3 {{DOI|10042/24284}}

Optimization of isomer 4 {{DOI|10042/24285}}

On these optimized molecules an NMR analysis was run using the B3LYP - 6-31G(d,p) basis set, the NMR spectra obtained are displayed below and the files for these calculations can be found at the followin links:

NMR analysis for isomer 1 {{DOI|10042/24286}}

NMR analysis for isomer 2 {{DOI|10042/24287}}

NMR analysis for isomer 3 {{DOI|10042/24288}}

NMR analysis for isomer 4 {{DOI|10042/24289}}

A second NMR analysis was then run this time using a much larger basis set (cc-pVTZ) to investigate if the predicted NMR could be improved, the results have been tabulated below and the files for the calculations can be found here:

Larger basis set NMR analysis for isomer 1 {{DOI|10042/24290}}

Larger basis set NMR analysis for isomer 2 {{DOI|10042/24291}}

Larger basis set NMR analysis for isomer 3 {{DOI|10042/24292}}

Larger basis set NMR analysis for isomer 4 {{DOI|10042/24293}}

For all of the spectra in this table the relavent reference molecule has been used apart from in the case of the F<sup>19</sup> NMR where there was no references in Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V1_F.png]] || [[File:V1_C.png]] || [[File:V1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V2_F.png]] || [[File:V2_C.png]] || [[File:V2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V3_F.png]] || [[File:V3_C.png]] || [[File:V3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V4_F.png]] || [[File:V4_C.png]] || [[File:V4_H.png]]
|}

The table below contains the same NMR spectra as above but they have been calculated using a higher basis set. The spectra here have been shown to correlate better to the recorded NMR found in literature. To allow analysis of the F<sup>19</sup> NMR a reference molecule was made and the shielding constant (168.5547) was manually entered into Gaussian, the molecule was one of CFCl<sub>3</sub> chosen as it is the same one used in the literature. The output files for the [[Media:CFCL3.LOG|optimization]] and [[Media:CFCL3_NMR.LOG|NMR analysis]] for CFCl<sub>3</sub> can be found at there respective links. The ppm values obtained from Gaussian have been found to be slightly too low, this could be down to the reference calculated or some other area of Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides calculated using the cc-pVTZ basis set
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV1_F.png]] || [[File:2HV1_C.png]] || [[File:2HV1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV2_F.png]] || [[File:2HV2_C.png]] || [[File:2HV2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV3_F.png]] || [[File:2HV3_C.png]] || [[File:2HV3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV4_F.png]] || [[File:2HV4_C.png]] || [[File:2HV4_H.png]]
|}

The NMR data from Liturate has been tabulated below:

{| class="wikitable" border="1"
|+ H<sup>1</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| 2.00-3.30 (m, 2H); || 2.00-2.90 (m, 2H) || 2.06 (tdt, 1H) || 2.35 (tt, 2H)
|-
| 5.22 (ddd, 1H); || 5.68 (ddm, 1H) || 2.40-3.10 (m, 1H) || 5.78 (ddm, 2H)
|-
| 5.6 (ddm, 1H); || 6.00-6.80 (m, 3H) || 4.90-5.90 (m, 2H) || 5.80-6.40 (m, 2H)
|-
| 5.85 (dm, 1H); || || 6.18-6.40 (m, 2H) ||
|-
| 6.80 (m, 1H); || || ||
|-
|}

By comparing the chemical shift recorded to the predicted shifts above it can be seen that there is some agreement in the order and approximate number of chemical shifts present, taking into account that some peaks recorded as multiplets of a relative number of hydrogens more than one correlate to multiple predicted peaks. For example if we look at isomer 1 it can be seen for the predicted NMR graph that there should be 6H's present, this is the case, and that there are expected to be 2 H's between 2-3ppm, again the case. The peaks seen in liturature at 5.2, 5.6 and 5.8 have also been correctly predicted by the NMR prediction software, however the peak with chemical shift of 6.8 has been predicted at 6.2 ppm, a significatly lower value, this implies that the software has not correctly predicted the chemical shift of the hydrogen attached to an alkene and with a flourine on a neibouring carbon atom. Howvere the general good agreement shows that isomer one has been correctly predicted by the software and assigned correctly by the literature.

Unfortunately the other isomers do not show as close a similarity to the literature, it is stated that the purity of isomer 2 (compound 3 in literature) is not of complete purity, this can be seen from the wide ranges in ppm recorded and the number of multiplets. The predicted spectra shows 2 H's at rougly 2.5 ppm, this can be correlated to the liturature values between 2.0-2.9ppm the rest of the spectra does not however corrilate to the predicted spectra any more than any other isomer and so the NMR data, stated unreliable in the literature should not been be for further analysis.

The remaining two isomer can be seen to relate to the predicted NMR spectra but there is still a reasonably large margin of error as far as the chemical shifts are concerned but it can be said that the H1 NMR spectra of compounds have been assigned correctly.

{| class="wikitable" border="1"
|+ F<sup>19</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| -176 (ddm, 1F); || -159 (m, 1F) || -161 (m) || -171 (m)
|-
| -187 (m, 1F); || -167 (m, 1F) || ||
|-
|}

The literature values for the F<sup>19</sup> NMR, seen above, can be seen to have a higher (less negative) chemical shift than the predicted NMR values despite the corrections made. looking at the distribution of the peaks however it is possible to see that the for isomer 1 and 2 both methods show 2 distinguishable peaks with the spacing between peaks being larger for isomer 1 than 2. For isomer 2 only 1 peak is expected as the molecule is symmetric and so both flourines are in the same environment, only one peak is seen in the actual NMR, this is a multiplet probably due to coupling with the hydrogen atoms. Isomer 4 has been predicted to show 2 peaks that should be differentiable, this however is not the case, the chemical shift of isomer 3 is predicted to be higher (less negative) than that of isomer 4, although the values are not the same the relationship is and so it can be said that the correct assignment has been made.

=== J coupling ===

To look at the spin coupling for each molecule the following data was extracted from the log files of each of the diflorinated molecules, the original log files for each can be found above. The data below shows the couplings between each atom, the labeling system relates the the molecule above the data, the light blue atoms are fluorine atoms, the white hydrogen and the grey carbon.

Unfortunately as the literature does not provide many coupling constants there is very little comparative analysis possible here. Values of interest have been tabulated below each set of data.

[[File:V1.jpg|300px]]

Isomer 1

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.342866D+02 0.000000D+00
3 0.895875D+01 0.387721D+02 0.000000D+00
4 0.432962D+01 0.357276D+01 0.814371D+02 0.000000D+00
5 0.286622D+02 0.761418D+01 0.168366D+00 0.277392D+02 0.000000D+00
6 0.620195D+01 0.250870D+01 0.154230D+03 0.241025D+01 0.890794D+01
7 0.641252D+01 0.975844D+01 0.233016D+01 0.151755D+03 0.453581D+01
8 -0.356953D+01 0.490619D+01 0.420895D+01 -0.373378D+01 0.118209D+03
9 -0.562801D+01 -0.180511D+01 0.340892D+01 -0.614534D+01 0.112126D+03
10 0.131662D+03 -0.504874D+01 -0.296543D+00 0.105109D+01 -0.136180D+01
11 -0.228247D+03 0.199291D+02 0.648570D+01 0.435993D+01 0.161753D+02
12 0.158580D+02 -0.221931D+03 0.181425D+02 0.275804D+01 0.247006D+01
13 -0.387550D+01 0.133542D+03 -0.281012D+01 0.386991D+01 -0.136352D+01
6 7 8 9 10
6 0.000000D+00
7 0.570798D+01 0.000000D+00
8 -0.239625D+01 0.333843D+01 0.000000D+00
9 -0.377890D+01 0.273722D+01 -0.164174D+02 0.000000D+00
10 0.152419D+00 -0.118905D+00 0.752471D+01 0.513857D+01 0.000000D+00
11 0.114526D+01 0.180493D+01 0.496252D+00 0.209070D+02 0.485841D+02
12 0.243819D+01 -0.284005D+01 0.609967D+00 0.104561D+02 0.227008D+02
13 0.225434D+01 -0.251199D+01 0.230756D+01 0.300313D+01 0.361997D+01
11 12 13
11 0.000000D+00
12 -0.656033D+01 0.000000D+00
13 0.173949D+02 0.493934D+02 0.000000D+00

From this data the most significant couplings have been tabulated below:

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 22
|-
| F-F coupling / Literature || 18
|}

The same file for isomer 2 is below:

[[File:V2.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.298057D+02 0.000000D+00
3 0.360005D+01 0.383120D+02 0.000000D+00
4 0.140841D+01 0.568185D+01 0.847547D+02 0.000000D+00
5 0.272228D+02 0.661319D+01 0.146319D+01 0.276719D+02 0.000000D+00
6 0.531289D+01 0.294077D+01 0.154554D+03 0.326074D+01 0.956471D+01
7 0.552333D+01 0.112712D+02 0.331786D+01 0.151972D+03 0.495994D+01
8 -0.540504D+01 0.397276D+01 0.386070D+01 -0.396731D+01 0.116736D+03
9 0.381514D+01 -0.113783D+01 0.287703D+01 -0.488835D+01 0.111760D+03
10 0.884900D+01 -0.227663D+03 0.174540D+02 0.474589D+01 -0.173807D+01
11 0.548960D+01 0.132178D+03 -0.215125D+01 0.257544D+01 -0.786536D+00
12 -0.224697D+03 0.112122D+02 -0.314235D+00 -0.149288D+01 0.150435D+02
13 0.145676D+03 0.312450D+00 0.540799D+01 0.585986D+01 0.177718D+01
6 7 8 9 10
6 0.000000D+00
7 0.541089D+01 0.000000D+00
8 -0.230815D+01 0.333160D+01 0.000000D+00
9 -0.411266D+01 0.255795D+01 -0.176851D+02 0.000000D+00
10 0.241296D+01 -0.149280D+01 0.181811D+00 0.359811D+01 0.000000D+00
11 0.215383D+01 -0.323173D+01 0.133489D+01 0.274682D+01 0.442501D+02
12 -0.119884D-01 -0.683563D-02 0.213811D+02 0.256981D+02 -0.570540D+01
13 0.288938D+00 0.320102D+00 0.497912D-01 0.396887D+01 -0.132042D+01
11 12 13
11 0.000000D+00
12 0.122457D+02 0.000000D+00
13 0.410809D+01 0.492388D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 5.7
|-
| F-F coupling / Literature || None reported
|}

For isomer 3:

[[File:V31.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.273345D+02 0.000000D+00
3 0.351869D+01 0.357805D+02 0.000000D+00
4 0.351678D+01 0.356759D+01 0.851369D+02 0.000000D+00
5 0.273508D+02 0.784544D+01 0.356356D+01 0.357942D+02 0.000000D+00
6 0.415912D+01 0.232123D+01 0.153275D+03 0.317256D+01 0.115299D+02
7 0.415929D+01 0.115328D+02 0.317046D+01 0.153272D+03 0.232109D+01
8 0.126697D+01 0.766162D+00 0.282143D+01 -0.214675D+01 0.135968D+03
9 0.110154D+02 -0.221170D+03 0.175499D+02 0.268770D+01 -0.224820D+01
10 0.126219D+01 0.135964D+03 -0.214746D+01 0.281796D+01 0.765104D+00
11 0.120768D+03 -0.126794D+01 0.546578D+01 0.546538D+01 -0.126249D+01
12 0.108735D+03 -0.707120D+01 -0.156287D+00 -0.156513D+00 -0.707035D+01
13 0.110113D+02 -0.226057D+01 0.268852D+01 0.175542D+02 -0.221062D+03
6 7 8 9 10
6 0.000000D+00
7 0.509273D+01 0.000000D+00
8 -0.209240D+01 0.221891D+01 0.000000D+00
9 0.250491D+01 -0.292515D+01 0.110507D+02 0.000000D+00
10 0.221853D+01 -0.209470D+01 0.188537D+01 0.483661D+02 0.000000D+00
11 -0.246804D+00 -0.246888D+00 0.628814D+01 0.404899D+00 0.628769D+01
12 -0.122410D+00 -0.120443D+00 0.486518D+01 0.246650D+02 0.486525D+01
13 -0.293299D+01 0.250911D+01 0.483593D+02 0.121202D+02 0.110678D+02
11 12 13
11 0.000000D+00
12 -0.122699D+02 0.000000D+00
13 0.410527D+00 0.246816D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 12.1
|-
| F-F coupling / Literature || None reported
|}

Isomer 4:

[[File:V4.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.291101D+02 0.000000D+00
3 0.376865D+01 0.360903D+02 0.000000D+00
4 0.327801D+01 0.501414D+01 0.846316D+02 0.000000D+00
5 0.293380D+02 0.528212D+01 0.261876D+01 0.337271D+02 0.000000D+00
6 0.452981D+01 0.290011D+01 0.152690D+03 0.334557D+01 0.114129D+02
7 0.428822D+01 0.108793D+02 0.372204D+01 0.153433D+03 0.387792D+01
8 0.126708D+02 -0.215381D+03 0.149397D+02 0.209481D+01 0.934862D+01
9 -0.600859D-01 0.134584D+03 -0.146461D+01 0.311426D+01 -0.920073D+00
10 0.117780D+03 -0.161334D+01 0.628257D+01 0.319068D+01 -0.485410D+01
11 0.109076D+03 -0.669288D+01 -0.176798D+00 0.856155D+00 -0.822490D+00
12 0.180918D+02 -0.366872D+01 0.296262D+01 0.774594D+01 -0.211300D+03
13 -0.195171D+00 0.546568D+01 0.457133D+01 -0.927065D+00 0.141349D+03
6 7 8 9 10
6 0.000000D+00
7 0.515899D+01 0.000000D+00
8 0.306287D+01 -0.256222D+01 0.000000D+00
9 0.222974D+01 -0.258174D+01 0.477343D+02 0.000000D+00
10 -0.172590D+00 0.135473D+00 0.311884D+00 0.566856D+01 0.000000D+00
11 -0.605838D+00 -0.518467D+00 0.236849D+02 0.415039D+01 -0.140235D+02
12 -0.434430D+01 0.255227D+01 0.190874D+02 0.799236D+01 0.176430D+02
13 -0.876659D+00 0.260831D+01 0.140782D+00 0.175197D+01 0.551757D-01
11 12 13
11 0.000000D+00
12 0.246213D+02 0.000000D+00
13 0.565082D+01 0.497731D+02 0.000000D+00

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms / source !! Coupling (Hz)
|-
| F-F coupling / Computed || 19.1
|-
| F-F coupling / Literature || None reported
|}

=== Vibrational Analysis ===

The optimized molecules for above where then run through vibrational analysis to produce IR spectra, the literature did not run IR spectra which these can be compared to, but it is a helpful technique to check that the compound is has been optimized and to compare any differences that arise (the IR spectra should contain the same peaks).

{| class="wikitable" border="1"
|+ Table of IR spectra
! Isomer Number !! Calculated IR Spectrum
|-
| Isomer 1 || [[File:IR1.png]]
|-
| Isomer 2 || [[File:IR2.png]]
|-
| Isomer 3 || [[File:IR3.png]]
|-
| Isomer 4 || [[File:IR4.png]]
|-
|}

Comparison of the spectra shows that they are not all the same, however it is mainly the intensity of the peaks rather that there existence that changes. All the the molecuels contain the expected peaks, Isomer 3 has additional peaks and much larger peaks compared to the other isomers, this is due to its high level of symmetry.

=== References ===
http://ac.els-cdn.com/002211399403190B/1-s2.0-002211399403190B-main.pdf?_tid=930742b8-8a51-11e2-a537-00000aacb362&acdnat=1363009553_0579d0d0ad7eb0ece5d46549b57556e0
http://www.sciencedirect.com/science/article/pii/002211399403190B#

File:IR4.png

2013-03-15T13:13:12Z

Ag3210: uploaded a new version of "File:IR4.png"

File:IR3.png

2013-03-15T13:13:12Z

Ag3210: uploaded a new version of "File:IR3.png"

File:IR2.png

2013-03-15T13:13:11Z

Ag3210: uploaded a new version of "File:IR2.png"

2013-03-15T09:50:16Z

Ag3210: /* Mini Project */

= Organic Computaional Labs Continued, Part1 =

==== The Second Reaction Intermediate of a Glycosidation Reaction ====

As stated previously the results for the MM2 and MOPAC calculations of each isomer of the second reaction intermediate are shown below:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly1is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.1410
Bend: 15.2130
Stretch-Bend: 0.7546
Torsion: 9.4948
Non-1,4 VDW: -3.7163
1,4 VDW: 17.7977
Charge/Dipole: -4.6530
Dipole/Dipole: -0.7804
Total Energy: 36.2514 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.09886 (< 0.10000) Heat of Formation = -46.61530 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly2is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.0053
Bend: 13.4884
Stretch-Bend: 0.7191
Torsion: 9.9562
Non-1,4 VDW: -2.8698
1,4 VDW: 18.0192
Charge/Dipole: -7.7771
Dipole/Dipole: -2.4245
Total Energy: 31.1168 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07455 (< 0.10000) Heat of Formation = -45.78147 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly3is.cml</uploadedFileContents>
</jmolApplet></jmol>

MM2 Calculation completed successfully
------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.6633
Bend: 19.5290
Stretch-Bend: 0.7749
Torsion: 9.1167
Non-1,4 VDW: -3.2021
1,4 VDW: 19.0162
Charge/Dipole: 3.3946
Dipole/Dipole: -1.5909
Total Energy: 49.7016 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08973 (< 0.10000) Heat of Formation = -46.61374 Kcal/Mol
-----------------------------------------

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>Gly4is.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 2.7503
Bend: 18.0616
Stretch-Bend: 0.8380
Torsion: 9.9783
Non-1,4 VDW: -2.6260
1,4 VDW: 19.5983
Charge/Dipole: 2.3600
Dipole/Dipole: -1.6307
Total Energy: 49.3298 kcal/mol
Calculation ended
-------------------------------------------

Mopac Job: AUX RM1 CHARGE=1 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08822 (< 0.10000) Heat of Formation = -45.78368 Kcal/Mol
-----------------------------------------

== Part 2, Module 1 ==

=== Taxol ===

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>New_Taxol.cml</uploadedFileContents>
</jmolApplet></jmol>

The optimization log file can be found here: [[File:Log_for_new_taxol.log]]

[[File:Taxol_OPTED.gjf]]

The NMR analysis for taxol using a Basis set of mpw1pw91/6-31G(d,p) can be found here {{DOI|10042/24302}}

The H<sup>1</sup> NMR spectrum for the Taxol Complex can be seen below:
[[File:TAXOL.png]]

=== Mini Project ===

For this mini project the molecule shown below was chosen from literature so that its reported NMR could be checked to confirm that the different isomers had been assigned correctly. The first set was to construct the molecule with the different possible isomer and then generate predicted NMRs this is shown below:

[[File:Mini.png]]
The reaction scheme for the formation of the products being looked at in this project

This is a Jmol of one of the isomers present:

<jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>2_CML.cml</uploadedFileContents>
</jmolApplet></jmol>

------------MM2 Minimization------------
Warning: Some parameters are guessed (Quality = 1).
Iteration 105: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 0.4999
Bend: 5.6308
Stretch-Bend: -0.1001
Torsion: 0.6953
Non-1,4 VDW: -0.2984
1,4 VDW: 1.7252
Dipole/Dipole: 3.6138
Total Energy: 11.7665 kcal/mol
Calculation completed
------------------------------------

The same molecule was optimized on Gaussview the following log file was generated from this: [[File:OPT_1.LOG]]
The optimized molecule was then further optimzed using the 6-31G(d,p) basis set the file ca be found here: [[File:OPT_2.LOG]]

For each of the isomers the molecule was optimized using gaussian after being modified from the perviously opimized molecule, the files from each optimization can be found with the corresponding DOI links.

Optimization of isomer 2 {{DOI|10042/24282}}

Optimization of isomer 3 {{DOI|10042/24284}}

Optimization of isomer 4 {{DOI|10042/24285}}

On these optimized molecules an NMR analysis was run using the B3LYP - 6-31G(d,p) basis set, the NMR spectra obtained are displayed below and the files for these calculations can be found at the followin links:

NMR analysis for isomer 1 {{DOI|10042/24286}}

NMR analysis for isomer 2 {{DOI|10042/24287}}

NMR analysis for isomer 3 {{DOI|10042/24288}}

NMR analysis for isomer 4 {{DOI|10042/24289}}

A second NMR analysis was then run this time using a much larger basis set (cc-pVTZ) to investigate if the predicted NMR could be improved, the results have been tabulated below and the files for the calculations can be found here:

Larger basis set NMR analysis for isomer 1 {{DOI|10042/24290}}

Larger basis set NMR analysis for isomer 2 {{DOI|10042/24291}}

Larger basis set NMR analysis for isomer 3 {{DOI|10042/24292}}

Larger basis set NMR analysis for isomer 4 {{DOI|10042/24293}}

For all of the spectra in this table the relavent reference molecule has been used apart from in the case of the F<sup>19</sup> NMR where there was no references in Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V1_F.png]] || [[File:V1_C.png]] || [[File:V1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V2_F.png]] || [[File:V2_C.png]] || [[File:V2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V3_F.png]] || [[File:V3_C.png]] || [[File:V3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:V4_F.png]] || [[File:V4_C.png]] || [[File:V4_H.png]]
|}

The table below contains the same NMR spectra as above but they have been calculated using a higher basis set. The spectra here have been shown to correlate better to the recorded NMR found in literature. To allow analysis of the F<sup>19</sup> NMR a reference molecule was made and the shielding constant (168.5547) was manually entered into Gaussian, the molecule was one of CFCl<sub>3</sub> chosen as it is the same one used in the literature. The output files for the [[Media:CFCL3.LOG|optimization]] and [[Media:CFCL3_NMR.LOG|NMR analysis]] for CFCl<sub>3</sub> can be found at there respective links. The ppm values obtained from Gaussian have been found to be slightly too low, this could be down to the reference calculated or some other area of Gaussian.

{| class="wikitable" border="1"
|+ Table of calculated NMR spectra form the isomers of diflourides calculated using the cc-pVTZ basis set
! JMol of Relevant Molecule !! Flourene NMR Spectra !! Carbon NMR Spectra !! Hydrogen NMR Spectra
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V1_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV1_F.png]] || [[File:2HV1_C.png]] || [[File:2HV1_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V2_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV2_F.png]] || [[File:2HV2_C.png]] || [[File:2HV2_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V3_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV3_F.png]] || [[File:2HV3_C.png]] || [[File:2HV3_H.png]]
|-
| <jmol><jmolApplet><title>Pentahelicene</title><color>white</color>
<size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script>
<uploadedFileContents>V4_OPT_COMP.fchk.cml</uploadedFileContents>
</jmolApplet></jmol> || [[File:2HV4_F.png]] || [[File:2HV4_C.png]] || [[File:2HV4_H.png]]
|}

The NMR data from Liturate has been tabulated below:

{| class="wikitable" border="1"
|+ H<sup>1</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| 2.00-3.30 (m, 2H); || 2.00-2.90 (m, 2H) || 2.35 (tt, 2H) || 2.06 (tdt, 1H)
|-
| 5.22 (ddd, 1H); || 5.68 (ddm, 1H) || 5.78 (ddm, 2H) || 2.40-3.10 (m, 1H)
|-
| 5.6 (ddm, 1H); || 6.00-6.80 (m, 3H) || 5.80-6.40 (m, 2H) || 4.90-5.90 (m, 2H)
|-
| 5.85 (dm, 1H); || || 2.35 (tt, 2H) || 6.18-6.40 (m, 2H)
|-
| 6.80 (m, 1H); || || || 2.06 (tdt, 1H)
|-
|}

{| class="wikitable" border="1"
|+ F<sup>19</sup> NMR data form literature
! Isomer 1 (ppm) !! Isomer 2 (ppm) !! Isomer 3 (ppm) !! Isomer 4 (ppm)
|-
| -176 (ddm, 1F); || -159 (m, 1F) || -171 (m) || -161 (m)
|-
| -187 (m, 1F); || -167 (m, 1F) || ||
|-
|}

=== J coupling ===

To look at the spin coupling for each molecule the following data was extracted from the log files of each of the diflorinated molecules, the origial log files for each can be found above. The data below shows the couplings between each atm, the lableing system relates the the molecule above the data, the light blue atoms are fluorine atoms, the white hydrogen and the grey carbon.

[[File:V1.jpg|300px]]

Isomer 1

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.342866D+02 0.000000D+00
3 0.895875D+01 0.387721D+02 0.000000D+00
4 0.432962D+01 0.357276D+01 0.814371D+02 0.000000D+00
5 0.286622D+02 0.761418D+01 0.168366D+00 0.277392D+02 0.000000D+00
6 0.620195D+01 0.250870D+01 0.154230D+03 0.241025D+01 0.890794D+01
7 0.641252D+01 0.975844D+01 0.233016D+01 0.151755D+03 0.453581D+01
8 -0.356953D+01 0.490619D+01 0.420895D+01 -0.373378D+01 0.118209D+03
9 -0.562801D+01 -0.180511D+01 0.340892D+01 -0.614534D+01 0.112126D+03
10 0.131662D+03 -0.504874D+01 -0.296543D+00 0.105109D+01 -0.136180D+01
11 -0.228247D+03 0.199291D+02 0.648570D+01 0.435993D+01 0.161753D+02
12 0.158580D+02 -0.221931D+03 0.181425D+02 0.275804D+01 0.247006D+01
13 -0.387550D+01 0.133542D+03 -0.281012D+01 0.386991D+01 -0.136352D+01
6 7 8 9 10
6 0.000000D+00
7 0.570798D+01 0.000000D+00
8 -0.239625D+01 0.333843D+01 0.000000D+00
9 -0.377890D+01 0.273722D+01 -0.164174D+02 0.000000D+00
10 0.152419D+00 -0.118905D+00 0.752471D+01 0.513857D+01 0.000000D+00
11 0.114526D+01 0.180493D+01 0.496252D+00 0.209070D+02 0.485841D+02
12 0.243819D+01 -0.284005D+01 0.609967D+00 0.104561D+02 0.227008D+02
13 0.225434D+01 -0.251199D+01 0.230756D+01 0.300313D+01 0.361997D+01
11 12 13
11 0.000000D+00
12 -0.656033D+01 0.000000D+00
13 0.173949D+02 0.493934D+02 0.000000D+00

From this data the most significant couplings have been tabulated below:

{| class="wikitable" border="1"
|+ J coupling summery table
! Coupling atoms !! Coupling (Hz)
|-
| F-F coupling || 0.227008D+02
|-
| cell || cell
|}

The same file for isomer 2 is below:

[[File:V2.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.298057D+02 0.000000D+00
3 0.360005D+01 0.383120D+02 0.000000D+00
4 0.140841D+01 0.568185D+01 0.847547D+02 0.000000D+00
5 0.272228D+02 0.661319D+01 0.146319D+01 0.276719D+02 0.000000D+00
6 0.531289D+01 0.294077D+01 0.154554D+03 0.326074D+01 0.956471D+01
7 0.552333D+01 0.112712D+02 0.331786D+01 0.151972D+03 0.495994D+01
8 -0.540504D+01 0.397276D+01 0.386070D+01 -0.396731D+01 0.116736D+03
9 0.381514D+01 -0.113783D+01 0.287703D+01 -0.488835D+01 0.111760D+03
10 0.884900D+01 -0.227663D+03 0.174540D+02 0.474589D+01 -0.173807D+01
11 0.548960D+01 0.132178D+03 -0.215125D+01 0.257544D+01 -0.786536D+00
12 -0.224697D+03 0.112122D+02 -0.314235D+00 -0.149288D+01 0.150435D+02
13 0.145676D+03 0.312450D+00 0.540799D+01 0.585986D+01 0.177718D+01
6 7 8 9 10
6 0.000000D+00
7 0.541089D+01 0.000000D+00
8 -0.230815D+01 0.333160D+01 0.000000D+00
9 -0.411266D+01 0.255795D+01 -0.176851D+02 0.000000D+00
10 0.241296D+01 -0.149280D+01 0.181811D+00 0.359811D+01 0.000000D+00
11 0.215383D+01 -0.323173D+01 0.133489D+01 0.274682D+01 0.442501D+02
12 -0.119884D-01 -0.683563D-02 0.213811D+02 0.256981D+02 -0.570540D+01
13 0.288938D+00 0.320102D+00 0.497912D-01 0.396887D+01 -0.132042D+01
11 12 13
11 0.000000D+00
12 0.122457D+02 0.000000D+00
13 0.410809D+01 0.492388D+02 0.000000D+00

For isomer 3:

[[File:V31.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.273345D+02 0.000000D+00
3 0.351869D+01 0.357805D+02 0.000000D+00
4 0.351678D+01 0.356759D+01 0.851369D+02 0.000000D+00
5 0.273508D+02 0.784544D+01 0.356356D+01 0.357942D+02 0.000000D+00
6 0.415912D+01 0.232123D+01 0.153275D+03 0.317256D+01 0.115299D+02
7 0.415929D+01 0.115328D+02 0.317046D+01 0.153272D+03 0.232109D+01
8 0.126697D+01 0.766162D+00 0.282143D+01 -0.214675D+01 0.135968D+03
9 0.110154D+02 -0.221170D+03 0.175499D+02 0.268770D+01 -0.224820D+01
10 0.126219D+01 0.135964D+03 -0.214746D+01 0.281796D+01 0.765104D+00
11 0.120768D+03 -0.126794D+01 0.546578D+01 0.546538D+01 -0.126249D+01
12 0.108735D+03 -0.707120D+01 -0.156287D+00 -0.156513D+00 -0.707035D+01
13 0.110113D+02 -0.226057D+01 0.268852D+01 0.175542D+02 -0.221062D+03
6 7 8 9 10
6 0.000000D+00
7 0.509273D+01 0.000000D+00
8 -0.209240D+01 0.221891D+01 0.000000D+00
9 0.250491D+01 -0.292515D+01 0.110507D+02 0.000000D+00
10 0.221853D+01 -0.209470D+01 0.188537D+01 0.483661D+02 0.000000D+00
11 -0.246804D+00 -0.246888D+00 0.628814D+01 0.404899D+00 0.628769D+01
12 -0.122410D+00 -0.120443D+00 0.486518D+01 0.246650D+02 0.486525D+01
13 -0.293299D+01 0.250911D+01 0.483593D+02 0.121202D+02 0.110678D+02
11 12 13
11 0.000000D+00
12 -0.122699D+02 0.000000D+00
13 0.410527D+00 0.246816D+02 0.000000D+00

Isomer 4:

[[File:V4.jpg|300px]]

Total nuclear spin-spin coupling J (Hz):
1 2 3 4 5
1 0.000000D+00
2 0.291101D+02 0.000000D+00
3 0.376865D+01 0.360903D+02 0.000000D+00
4 0.327801D+01 0.501414D+01 0.846316D+02 0.000000D+00
5 0.293380D+02 0.528212D+01 0.261876D+01 0.337271D+02 0.000000D+00
6 0.452981D+01 0.290011D+01 0.152690D+03 0.334557D+01 0.114129D+02
7 0.428822D+01 0.108793D+02 0.372204D+01 0.153433D+03 0.387792D+01
8 0.126708D+02 -0.215381D+03 0.149397D+02 0.209481D+01 0.934862D+01
9 -0.600859D-01 0.134584D+03 -0.146461D+01 0.311426D+01 -0.920073D+00
10 0.117780D+03 -0.161334D+01 0.628257D+01 0.319068D+01 -0.485410D+01
11 0.109076D+03 -0.669288D+01 -0.176798D+00 0.856155D+00 -0.822490D+00
12 0.180918D+02 -0.366872D+01 0.296262D+01 0.774594D+01 -0.211300D+03
13 -0.195171D+00 0.546568D+01 0.457133D+01 -0.927065D+00 0.141349D+03
6 7 8 9 10
6 0.000000D+00
7 0.515899D+01 0.000000D+00
8 0.306287D+01 -0.256222D+01 0.000000D+00
9 0.222974D+01 -0.258174D+01 0.477343D+02 0.000000D+00
10 -0.172590D+00 0.135473D+00 0.311884D+00 0.566856D+01 0.000000D+00
11 -0.605838D+00 -0.518467D+00 0.236849D+02 0.415039D+01 -0.140235D+02
12 -0.434430D+01 0.255227D+01 0.190874D+02 0.799236D+01 0.176430D+02
13 -0.876659D+00 0.260831D+01 0.140782D+00 0.175197D+01 0.551757D-01
11 12 13
11 0.000000D+00
12 0.246213D+02 0.000000D+00
13 0.565082D+01 0.497731D+02 0.000000D+00

=== Vibrational Analysis ===

The optimized molecules for above where then run through vibrational analysis to produce IR spectra, the literature did not run IR spectra which these can be compared to, but it is a helpful technique to check that the compound is has been optimized and to compare any differences that arise (the IR spectra should be the same).

=== References ===
http://ac.els-cdn.com/002211399403190B/1-s2.0-002211399403190B-main.pdf?_tid=930742b8-8a51-11e2-a537-00000aacb362&acdnat=1363009553_0579d0d0ad7eb0ece5d46549b57556e0
http://www.sciencedirect.com/science/article/pii/002211399403190B#