ChemWiki - User contributions [en]

Talk:Mod:MRTSFN89 phys

2011-11-28T10:59:35Z

Ajthom: Created page with "Cope Rearrangement Presentation: Data clearly tabulated. Good use of images/diagrams. Use of Jmol where appropriate. Animations to show vibrational frequencies. Use of file sha..."

Cope Rearrangement

Presentation:

Data clearly tabulated. Good use of images/diagrams. Use of Jmol where appropriate. Animations to show vibrational frequencies. Use of file sharing?

Results:

Investigated almost all of the anti and gauche conformers – v.good. Student has correctly noted gauche 3 as the lowest energy isomer. Would you expect this? An explanation considering vdW interactions, MOs etc would assist the report. Anti conformer was reoptimised and thermochemical data is provided for 298K and 0K – good. IR spectrum?

Chair/boat TS: Results generally v.good. Transition states found and IRC calculations carried out for both using a number of different methods. Activation energies calculated for chair and boat using both levels of theory. The table is a little confusing as the titles within the table don’t apply to the values inside it. Were activation energies calculated at 0K? Converting these values to kcal/mol would have perhaps made it easier to visualise.

Understanding:

Very thorough introduction with good use of primary literature. The student has a good understanding of the levels of theory used and why they have been applied in this study. The student also has a good grasp on the use of keywords and what they instruct the calculation to do. The student has gone beyond what was asked and investigated a potential stepwise reaction.

Diels Alder

Presentation:

As above. Data sometimes not tabulated but hidden in script, making it harder to read.

Results:

MOs of reactants good, correct symmetries noted, and thorough explanation of HOMO/LUMO interactions. TS MOs good – student has given additional thought to the HOMO TS. Correctly noted that the TS shows a bond is partially formed as the C-C distance is < 2 x vdW radius of C.

Endo/exo: Results generally good. Correctly noted endo is lower in energy and explained by considering steric reasoning and the secondary orbital overlap effect. This effect could be explained further, although good use of a diagram has been made. Apply this effect to your results? Is this effect really apparent in your results for the endo? Additional work carrying out the IRC calculations adds individual thought to this report.

Understanding:

Again, a v.thorough introduction explaining what will be covered in this section. The results have been analysed well: The student has a good understanding of HOMO/LUMO interactions and allowed/forbidden reactions and this is explained well with use of diagrams. Also steric interactions for the endo/exo states have been well considered. As mentioned above – student could expand on the secondary orbital overlap effect. Perhaps a little rushed towards the end without a conclusion, but in general this report was very good and extremely thorough.

Talk:Mod:ht309mod3

2011-11-28T10:58:37Z

Ajthom: Created page with " Cope Rearrangement Presentation: Data generally tabulated (but TS section have to look through document to find important values). Good use of images/Jmol. Animations for i..."

Cope Rearrangement

Presentation:

Data generally tabulated (but TS section have to look through document to find important values). Good use of images/Jmol. Animations for imaginary frequencies good. Files shared where appropriate.

Results:

All anti and gauche conformers investigated – v.thorough. Correctly noted gauche 3 as lowest energy conformer at this level of theory – what reasoning for this could there be? Could consider MOs, vdW interactions etc. All isomers then reoptimised at higher level of theory at noted gauche 3 not lowest energy conformer at higher level of theory – v.good. Frequency analysis for anti 2 does not appear to have been put in.

Chair/boat TS: Results generally good. TSs found. IRC calculations carried out for chair and boat using a number of different methods. Activation energies calculated for chair and boat for both levels of theory at 0K and 298K – v.good.

Understanding:

Good introduction. Steps taken very clear – could explain further why these steps/methods/keywords were used. Good conclusion, showing some individual thought in the calculations.

Diels Alder

Presentation:

Slightly muddled ordering, but otherwise v.good. Data tabulated. Good use of images/Jmol. Animations for imaginary frequencies good. Files shared where appropriate.

Results

MOs of reactants good, correct symmetries assigned and diagrams of orbitals v.useful. MOs of TS good- HOMO/LUMO interactions clearly understood. Also included IRC calculations as additional work .

Endo/exo: Results generally good. TS found and MOs correct. Correctly noted endo lower in energy. Carried our additional work with IRC calculations – good. Discussed secondary orbital overlap – and applied this to results – v.good! Why do you think this effect is apparent in the LUMO+2?

Understanding

Concise introduction, but no conclusion. Steps taken clear – again explanation as to why these steps were taken would be beneficial. Good analysis of results: HOMO/LUMO interactions considered – could also mention allowed/forbidden reactions. Student also mentions thermodynamic and kinetic control – good. You could compare what your results tell you to what is experimentally known. Good understanding of secondary orbital overlap – and have considered this when looking at your results – v.good. Could also consider steric effects for the endo/exo.

Talk:Mod:jlm2014

2011-11-28T10:56:28Z

Ajthom: Created page with "Cope Rearrangement Presentation: Data generally tabulated – good! Limited use of images. No use of Jmol or animations. Tables and figures not given legends. Links to files? ..."

Cope Rearrangement

Presentation:

Data generally tabulated – good! Limited use of images. No use of Jmol or animations. Tables and figures not given legends. Links to files?

Results:

A number of anti and gauche conformers investigated, including gauche 3 which is correctly noted as the lowest energy isomer at this level of theory. Explanation as to why this might be? Anti 2 reoptimised. Difference in geometry noted. Frequency analysis carried out – IR spectrum? Thermochemical data provided for 298K, results for 0K?

Boat/chair TS: Chair TS optimised. Steps taken very vague with ‘1st method’ and ‘2nd method’ - explain what these methods are and how they differ! Results for boat TS? IRC calculations? Activation energies calculated for both levels of theory at 298K and 0K – very good.

Understanding:

No introduction to topic. Steps taken are not stated or explained. Results that are provided are generally good – but what do these tell us? Although it is correct to predict the chair TS, this is not because it is closer to its experimental value, it is due to the lower activation energy for the chair TS!

Diels Alder:

Presentation:

Data tabulated – good. MO images good. Again no use of Jmol. Animation of vibrational frequency good. Files where calculations failed would be useful so I can see what went wrong.

Results:

MOs for reactants good and correct symmetries assigned. Haven’t actually labelled what these are MOs of. MOs of TS good and HOMO/LUMO interactions explained. Activation energy calculated – good.

Results for the regioselectivity of the Diels Alder reaction?

Understanding:

No introduction or conclusion. Steps taken provided. Would be good to include why these steps/methods/levels of theory/keywords were used.

Talk:Mod:3rdyearchemist

2011-11-28T10:54:58Z

Ajthom: Created page with "Cope Rearrangement Presentation: Report is very clearly laid out. Data all tabulated. Good use of Jmol/images. Animations for vibrational frequencies? Links to dspace? Resu..."

Cope Rearrangement

Presentation:

Report is very clearly laid out. Data all tabulated. Good use of Jmol/images. Animations for vibrational frequencies? Links to dspace?

Results:

A number of anti and Normal 0 false false false MicrosoftInternetExplorer4

Cope Rearrangement

Presentation:

Report is very clearly laid out. Data all tabulated. Good use of Jmol/images. Animations for vibrational frequencies? Links to dspace?

Results:

A number of anti and gauche conformers studied – v.good. Correctly noted gauche 3 is lowest energy conformer – why? Anti 2 isomer reoptimised as well as a number of the other low energy conformers – v.good. Noted at a higher level of theory gauche 3 is no longer the lowest energy conformer. This is explained well using hyperconjugation and MOs. Vibrational analysis was also carried out for these isomers and thermochemical data provided for both levels of theory – excellent.

Chair/boat TS: Results good. TSs found. IRC calculations carried out using a number of different methods for chair. Same for boat? Activation energy calculated for chair and boat for DFT level of theory. Results for HF? At 0K?

Understanding:

Good introduction. Steps taken clear – could expand on reasons why these steps were taken/levels of theory used/keywords etc. Generally good analysis of the results obtained. Would benefit from a concluding paragraph summarising findings.

Diels Alder

Presentation:

As above.

Results:

MOs of reactants good and correct symmetries assigned. Obtained transition states – MOs good and assigned correct symmetries. Diagrams very good at explaining LCAO theory – but a written explanation would help.

Endo/exo: MOs for reactants good – a shame ran out of time for TSs. Understood balance of steric hindrance and secondary orbital overlap, but couldn’t apply to your results as calculations weren’t run.

Understanding:

Good introduction. Steps taken are not mentioned. Results are good, but there is no written explanation for these. What do the results tell you? Report feels rushed towards the end, as the first section was very thorough.

gauche conformers studied – v.good. Correctly noted gauche 3 is lowest energy conformer – why? Anti 2 isomer reoptimised as well as a number of the other low energy conformers – v.good. Noted at a higher level of theory gauche 3 is no longer the lowest energy conformer. This is explained well using hyperconjugation and MOs. Vibrational analysis was also carried out for these isomers and thermochemical data provided for both levels of theory – excellent.

Chair/boat TS: Results good. TSs found. IRC calculations carried out using a number of different methods for chair. Same for boat? Activation energy calculated for chair and boat for DFT level of theory. Results for HF? At 0K?

Understanding:

Good introduction. Steps taken clear – could expand on reasons why these steps were taken/levels of theory used/keywords etc. Generally good analysis of the results obtained. Would benefit from a concluding paragraph summarising findings.

Diels Alder

Presentation:

As above.

Results:

MOs of reactants good and correct symmetries assigned. Obtained transition states – MOs good and assigned correct symmetries. Diagrams very good at explaining LCAO theory – but a written explanation would help.

Endo/exo: MOs for reactants good – a shame ran out of time for TSs. Understood balance of steric hindrance and secondary orbital overlap, but couldn’t apply to your results as calculations weren’t run.

Understanding:

Good introduction. Steps taken are not mentioned. Results are good, but there is no written explanation for these. What do the results tell you? Report feels rushed towards the end, as the first section was very thorough.

User talk:Ds2909mod3

2011-11-28T10:54:03Z

Ajthom: Created page with "Cope Rearrangement Presentation: Very clearly laid out. Data tabulated. Good use of Jmol and animations for imaginary vibrations. File sharing? Results: Investigated anti a..."

Cope Rearrangement

Presentation:

Very clearly laid out. Data tabulated. Good use of Jmol and animations for imaginary vibrations. File sharing?

Results:

Investigated anti and gauche conformers. Correctly noted gauche 3 is lowest energy conformer and explained well with the use of MOs. Also explained the relative energies of the other conformers using hyperconjugation and orbital interactions – v.good. Anti 2 conformer reoptimised and frequency analysis carried out – IR spectrum and thermochemical data provided. Thermochemical data at 0K?

Boat/chair TS: Results v. good. IRC calculations carried out for both chair and boat – v.good. Activation energies calculated for chair and boat at both levels of theory. Results for 0K and 298K?

Understanding:

Good introduction to topic. Steps taken in investigation clear. Good understanding of levels of theory. Results analysed well – explaining what your results tell you. A summarising paragraph at the end about what was found out in this study would have enhanced report.

Diels Alder:

Presentation:

As above

Results:

MOs of butadiene good. MOs of ethylene images not given, but correct symmetries assigned – ran out of time? TS MOs good. Correct symmetries assigned and HOMO/LUMO interactions explained well. Analysis of geometry of TS good, and noted C-C bond forming distance is less than 2 x the vdW radius of C, showing shared electron density.

Endo/exo: Results good. Correctly noted endo lower in energy. Good explanation considering steric reasoning and secondary orbital overlap – these are applied to YOUR results – v.good!

Understanding:

Good introduction – little gaps in sentences which I presume you meant to fill in. Steps taken clear and understood - could expand reasoning why these methods/levels of theory/keywords were used. Analysis of results very thorough – good explanation of HOMO/LUMO interactions and allowed/forbidden reactions. Good consideration of steric repulsion and secondary orbital overlap for endo/exo structures.

Talk:Mod:CSWmodule3

2011-11-28T10:46:31Z

Ajthom: Created page with " Cope Rearrangement Presentation: Data generally tabulated – would be useful to put vibrational frequencies/energies into tables also (where found in text) for ease of readi..."

Cope Rearrangement

Presentation:

Data generally tabulated – would be useful to put vibrational frequencies/energies into tables also (where found in text) for ease of reading. Good use of Jmol. Animations provided for boat TS, same for chair? Files shared where appropriate.

Results:

A number of anti and gauche conformer considered. Correctly noted gauche 3 conformer is lowest energy at the HF level of theory – try to explain this? Reoptimised anti 2 isomer as well as gauche 3 – good. Noted the difference in energetic ordering at higher level of theory – v.good. Frequency analysis for anti 2 v.good – included IR spectra and thermochemical data at 0K and 298K.

Chair/boat TS: Results generally good – TSs found. IRC calculations carried out for chair and boat. Mis-labelling of IRC graphs? Activation energies calculated for chair and boat at both levels of theory at 0K and 298K – v.good.

Understanding:

Good introduction to overall report and cope rearrangement section. A summarising paragraph as to what was found out in this investigation and the path the reaction takes would be useful. Steps taken clear – could expand on reasoning why certain methods/keywords etc. were used. Good understanding of using higher levels of theory and the computational expense associated with these. Results commented on appropriately.

Diels Alder

Presentation:

Generally as above. Data and symmetries all tabulated. A little strange ordering in the exo/endo section, with energies only provided in the conclusion.

Results:

MOs of reactants good and correct symmetries noted. MOs of TS also good and HOMO/LUMO interactions of reactants explained.

Endo/exo: Results generally good. Correctly noted endo is lower in energy than exo. Student has done extra work, by carrying out IRC calculations – good. What do these calculations tell us?

Understanding:

Good introduction to topic. Steps taken explained, but again could further comment on why. HOMO/LUMO interactions explained well. Considered kinetic and thermodynamic control of reaction. For exo/endo student understands the balance of steric repulsion vs. the secondary orbital overlap effect – apply these to your results – are these apparent?

Talk:Mod3:MJW11

2011-11-28T10:44:03Z

Ajthom: Created page with " Cope Rearrangement Presentation: Data generally tabulated. Good use of Jmol and animations. Would have been nice to include these directly inserted into the report and not as..."

Cope Rearrangement

Presentation:

Data generally tabulated. Good use of Jmol and animations. Would have been nice to include these directly inserted into the report and not as tabs for ease of reading. File sharing?

Results:

Investigated anti and gauche conformers – including gauche 3 which was correctly noted as the lowest energy conformer at this level of theory. Student should consider why this could be by considering vdW interactions, MOs etc.

Anti 2 conformer reoptimised . Note, you cannot compare energies between different methods (HF and DFT), they’re calculated on different energy scales. Frequency analysis good, inc. IR spectra and thermochemical data at 298K and 0K – v.good.

Chair/boat TS: Results good. TS states obtained for both. Images for optimized chair TS? And associated energies for optimized chair/boat TS? IRC calculations carried out for both chair and boat using a number of methods – v.good. Activation energies were calculated for chair and boat and 0K and 298K and compared to experiment. Results for HF level of theory?

Understanding:

Good introduction. Conclusion goes into further detail about the TS the reaction goes through. Useful diagrams and reference to primary literature. Steps taken clear – could expand on reasoning why certain methods/level of theory/keywords etc. were used.

Diels Alder

Presentation

As above.

Results

MOs of reactants good – correct symmetry assigned. HOMO/LUMO interactions explained. TS MOs good. Analysis of geometry of TS good. Could have noted the C-C distance of bind forming is < 2 x vdW radius of C, thus suggesting bond forming.

Endo/exo: Results good. Correctly noted endo is lower in energy. Considered steric interactions vs. secondary orbital overlap to explain this. Carried out further work by doing IRC calculations for endo and exo – v.good!

Understanding

Good introduction. Could expand on explaining the steps that were taken and WHY. Results generally explained well: HOMO/LUMO interactions explained, could expand this onto allowed/forbidden reactions. Good explanation ofsteric interactions and secondary orbital overlap for endo/exo. Apply this secondary orbital overlap effect to your results – is it apparent? Good consideration of thermodynamic/kinetic control. And student has seen limitations, and suggested higher level of theory to improve the study – v.good.

Talk:Mod:BYL109 module 3

2011-11-28T10:42:53Z

Ajthom: Created page with " Cope Rearrangement Presentation: Data all clearly tabulated. Good use of diagrams. Jmol used appropriately. Slightly funny order with IRC calculations after activation ene..."

Cope Rearrangement

Presentation:

Data all clearly tabulated. Good use of diagrams. Jmol used appropriately. Slightly funny order with IRC calculations after activation energies. Appropriate links to files.

Results:

Investigated anti and gauche conformers including gauche 3 – correctly noting it as the lowest energy conformer at this level of theory. Rationalised this well with use of hyperconjugation and MOs. Reoptimised anti 2 isomer – note: you cannot compare energies between different methods (HF and DFT), they’re calculated on different energy scales. Frequency analysis included: IR spectra? Thermochemical data at 0K?

TS: Results generally good. IRC carried out for both chair and boat TS – v.good. Activation energies calculated for chair and boat for both levels of theory at 0K and 298K.

Understanding:

Good introduction. The steps taken are clear – could expand on why certain methods/levels of theory/keywords etc. Conclusion for this section given at very end of report – generally good, but seems to be a little muddled e.g. the comment ‘The Cope Rearrangement occurs via either a chair or boat transition state, the mechanism of which is not defined’ – but you CAN comment on this, as you have actually investigated it in this work!

Diels Alder

Presentation:

As above

Results:

MOs of reactants good with correct symmetries noted. TS MOs also good – with a good explanation of HOMO/LUMO interactions. Noted the C-C bond forming distance is < 2 x radius of C, suggesting this bond is forming.

Endo/exo: TS MOs good. Correctly note endo is lower in energy. Have considered steric effects and secondary orbital overlap. Apply the secondary orbital overlap effect to your results…is it apparent?

Understanding:

Good introduction to the section. Steps taken clear, again could expand on reasoning why. HOMO/LUMO interactions and allowed/forbidden reactions considered well. For endo and exo have considered secondary orbital overlap – but is this effect apparent in your results?

Talk:Mod:ms mod3

2011-11-28T10:41:30Z

Ajthom: Created page with "Cope Rearrangement: Presentation: Data clearly tabulated. Good use of Jmol. Animations used to show imaginary frequencies – v.good. All images and tables given appropriat..."

Cope Rearrangement:

Presentation:

Data clearly tabulated. Good use of Jmol. Animations used to show imaginary frequencies – v.good. All images and tables given appropriate legends. Links to files where appropriate.

Results:

Anti and gauche conformers both investigated including gauche 3 which is correctly noted as the lowest energy conformer at this level of theory. This is explained well with the use of MOs. Anti 2 is reoptimised and frequency analysis carried out. IR spectra? Thermochemical data provided for 298K – good. Results for 0K?

Chair/boat TS – results good. Found transition states and shown imaginary frequencies. Carried out IRC calculations for both chair and boat – very thorough. Activation energies calculated for chair and boat, for both levels of theory at 0K and 298K – excellent. Good comparison to literature values.

Understanding:

Good introduction. Steps taken clear and the levels of theory/keywords etc. used are understood. Generally good analysis of results obtained. A paragraph summarising the reaction pathway would assist report.

Diels Alder:

Presentation:

As above

Results:

MOs of reactants good, and correct symmetry noted. HOMO/LUMO interactions well explained and TS MOs good. Correctly noted C-C bond forming distance is < 2 x vdW radius, suggesting this bond is forming in the TS.

Exo/endo: MOs for endo/exo states good. Correctly show endo is lower in energy from your calculations but no comment on this. Looked for secondary orbital overlap, but noticed not apparent in the results – v.good. Could have considered the exo/endo state by discussing the balance between steric effects and secondary orbital overlap.

Understanding:

V.good introduction to this section. Steps taken clear again – could expand on why certain methods/levels of theory etc. were chosen. HOMO/LUMO interactions explained well, could discuss allowed/forbidden reactions here. Endo/exo results very good, but lacking discussion as to whether the endo/exo state is favoured and why this might be? Overall the report is very good, but perhaps a little rushed towards the end.

Talk:Mod:LS1109crashbangwallopwhatavideo

2011-11-28T10:40:01Z

Ajthom: Created page with " Cope Rearrangement Presentation: Data all clearly tabulated. Excellent use of images and diagrams. Jmol used throughout. Appropriate use of file sharing. Animations assist ..."

Cope Rearrangement

Presentation:

Data all clearly tabulated. Excellent use of images and diagrams. Jmol used throughout. Appropriate use of file sharing. Animations assist report very well. All tables and images given appropriate legends.

Results:

Investigated a number of anti and gauche conformers - Gauche 3 correctly noted as lowest energy conformer according to the HF method. Frequency analysis carried out for anti 2 isomer- included IR spectra and thermochemical data. Thermochemical data also provided for a number of the lowest energy conformers at 0K – fantastic extra work. Also investigated how the thermochemical data varies with temperature – excellent!

Chair/boat TS – results good. IRC calculations carried out for both chair and boat using a number of methods. Activation energies calculated for both boat and chair at both levels of theory, at 0K and 298K – v.good. These results are then compared to the literature values.

Understanding:

Excellent introduction to report. Nice use of conclusion, and mini-conclusions in between. Steps taken very clear, as are the reasonings why. Good analysis of the results obtained. Rationalises lowest energy conformers well using vdW interactions, MOs, hyperconjugation – excellent! And good comparison to literature. Good understanding of the thermochemical data and what it represents. Student goes beyond what is asked of them and carries out some extremely interesting extra work. Mention in mini conclusion ‘AM1 level of theory’ – however I believe this is just a slip up as earlier you mention you use HF.

Diels Alder:

Presentation:

As above.

Results:

MOs for reactants good and correct symmetries noted. Optimised the TS state using 2 different levels of theory. Correctly noted C-C bond forming distance is < 2 x vdW radius of C suggesting bond forming. HOMO/LUMO interactions explained well. For TS HOMO from 6-31g* study, you’ve noted as antisymmetric, but this isn’t what the image shows – accidentally put in wrong image?

Endo/exo: MOs for reactants and TS good – correct symmetry assigned. Correctly noted endo is lower in energy. Analysis of secondary orbital overlap very good – applied to results. Student has also carried out additional work doing IRC calculations

Understanding:

V. good introduction and conclusion again. Appropriate references to primary literature. Steps taken clear and again well explained. Results analysed well : Good explanation of HOMO/LUMO interactions, could expand a bit on allowed/forbidden reactions. Good explanation of secondary orbital overlap vs. steric effects. Kinetic and thermodynamics control considered. Student also suggests improvements for this study, by using a higher level of theory ( and correctly noting the computational expense associated with this).

Overall this report was excellent. The results were analysed very well and the use of additional work has really enhanced this report.

Talk:Mod3:YJY1234

2011-11-28T10:38:07Z

Ajthom: Created page with "Cope Rearrangement: Presentation: Data generally tabulated. Images provided - would have been easier to assign images to the different conformers at the beginning rather than..."

Cope Rearrangement:

Presentation:

Data generally tabulated. Images provided - would have been easier to assign images to the different conformers at the beginning rather than having to scroll back. Good use of animations for vibrational frequencies. Use of Jmol would be useful in places to visualise molecules from different angles. Use of file sharing?

Results:

Optimized gauche and anti structures and correctly noted gauche 3 is lowest energy conformer at this level of theory. Reasoning why? Could consider vdW interactions, MOs, etc. Anti 2 reoptimised and frequency analysis carried out. IR spectra – good, and thermochemical data provided. Same for 0K?

Chair/boat TS : Results ok. Energies for the boat and chair TSs? IRC carried out – would be good to include the graphs for these, to see if have reached a minimum. Same for boat? Activation energies calculated for both levels of theory for chair and boat. Activation energies at 0K? Note, you cannot compare energies between different methods (HF and DFT), they’re calculated on different energy scales.

Understanding:

No introduction or conclusion. Steps taken clear. Could expand on reasoning for methods/levels of theory/use of keywords etc. Perhaps a little confused here ‘The first method is to use Hartree Fock and the default basis set 3-21G . The second method is the frozen coordinate method.’ The HF/3-21g is the level of theory. The frozen co-ordinate method is a method of optimisation – they are not mutually exclusive.

Diels Alder:

Presentation:

As above. Have included some file sharing in this section. Use of animations for vibrational frequencies?

Results:

HOMO/LUMO of cis-butadiene good and correct symmetries assigned. Same for ethylene? Included MOs of TS. Would you expect the HOMO TS to be symmetric? Good explanation of HOMO/LUMO interactions.

Endo/exo: Reactants and TS MOs provided. Assigned HOMO of exo as symmetric, are you sure? Correctly noted endo as lower in energy. Have rationalised this using steric reasoning as well as secondary orbital overlap. This is explained very well with the use of diagrams. Have considered kinetic and thermodynamic control – good. When analysing C-C distances could have noticed C-C bond forming distance is <2 x vdW radius of C, suggesting a bond is forming.

Understanding:

No introduction. Steps taken provided, again explanation as to why certain methods/levels of theory etc. were used could be expanded on. HOMO/LUMO interactions for TS well understood – could expand onto allowed/forbidden reactions. Good explanation of results from endo/exo – and nice conclusion to this section.

Talk:Mod:gjsmodule3 jackanackanory

2011-11-28T10:37:03Z

Ajthom: Created page with "Cope Rearrangement: Presentation: Data clearly tabulated. Good use of images and Jmol. Animations of imaginary frequencies v. good. Results: Considered all anti and gauche..."

Cope Rearrangement:

Presentation:

Data clearly tabulated. Good use of images and Jmol. Animations of imaginary frequencies v. good.

Results:

Considered all anti and gauche conformers– v. thorough. Correctly noted gauche 3 is lowest energy isomer for HF optimisation. Reoptimised a number of the lowest energy isomers, showing at a higher level of theory gauche 3 is no longer the lowest energy isomer – v.good. Very thorough investigation for the reasoning behind the energetic ordering including considering MOs and vdW interactions – excellent! Frequency analysis carried out for multiple isomers at 298K and 0K.

Chair/boat TS – Results v.good. TSs found. IRC carried out for both and minimums found. Activation energies calculated for both levels of theory for chair and boat TS. Results for both 0K and 298K?

Understanding:

Good concise introduction. Conclusion? Steps taken clear and well understood. Why certain steps were taken, levels of theory/keywords used etc. are explained well.

Diels Alder:

Presentation:

As above

Results:

MOs of reactants good- correct symmetries noted, and 2 different levels of theory investigated – v.good! MOs of TS good and HOMO/LUMO interactions well understood. For TS correctly noted C-C bond forming distance is < 2 x vdW radius of C, suggesting bond forming.

Endo/exo: Correctly noted endo lower in energy. Considered steric reasoning as well as secondary orbital overlap to understand their relative energies. Applied these reasonings to results obtained, looking at a number of the MOs - excellent.

Understanding:

Good concise introduction. Steps taken clear. Good analysis of results: HOMO/LUMO interactions and allowed/forbidden reactions well understood. Good suggestion of improving the study by using a higher level of theory.

Talk:Mod3:BMWWiki

2011-11-28T10:36:08Z

Ajthom: Created page with " Cope Rearrangement: Presentation: Data generally tabulated (TS state section could be made clearer). Good use of Jmol. Animations of negative vibrations v.good. Appropriate..."

Cope Rearrangement:

Presentation:

Data generally tabulated (TS state section could be made clearer). Good use of Jmol. Animations of negative vibrations v.good. Appropriate use of file-sharing.

Results:

Optimised both anti and gauche conformers, correctly noted gauche 3 as lowest energy isomer. Reoptimised a number of isomers using B3LYP to show gauche 3 is not the lowest energy isomer at a higher level of theory – v.good. More reasoning for why certain conformers may be lower in energy e.g. using vdW interactions, MOs etc. to explain would enhance report. Frequency analysis for anti 2 v. good – included IR spectra and thermochemical data for 298K and 0K.

Chair/Boat TS: Results generally good and TSs found. Investigated using the QST3 method as additional work – v.good. IRC calculatations carried out for chair AND boat! Activation energy table a little confusing, but calculated for both chair and boat TSs using both levels of theory at 0K and 298K, using both anti 1 and anti 2 as reactant – v.thorough. Is the activation energy for the boat TS at 0K missing?

Understanding:

Good concise introduction and conclusion. Steps taken clear and well understood. Good understanding of the levels of theory/methods used and why. A lot of individual thought has been put into this work – well done.

Diels Alder:

Presentation:

As above.

Results:

MOs of reactants and TS good and correct symmetry noted. Good explanation of HOMO/LUMO interactions. Good analysis of C-C bond distances. Could have noted C-C bond forming distance is < 2 x vdW radius suggesting a bond is forming/showing shared electron density.

Endo/exo: Thorough investigation of TSs. Correctly noted endo lower in energy. Good analysis of the MOs. As additional work has carried out IRC calculations and calculated activation energies! Has also taken into consideration kinetic and thermodynamic control of the reaction – excellent! Good consideration of secondary orbital overlap (why do you think this is apparent in LUMO+1? Unsure what is meant by ‘IRC also shows endo to be the most thermodynamically stable product, when exo should be’

Understanding:

Could do with a brief introduction, but very good conclusion. Good analysis of results. Clear explanation of HOMO/LUMO interactions and allowed/forbidden reactions. As well as making improvements to the script, student has also suggested further improvements including using higher levels of theory.

Student has clearly carried out lots of extra work significantly improving the investigation – Well done!

Talk:Mod:pikachu

2011-11-28T10:35:03Z

Ajthom: Created page with " Cope Rearrangement Presentation: Data clearly tabulated. Jmol used appropriately. Animations of vibrational frequencies for TS would assist report. Good use of file-sharing. ..."

Cope Rearrangement

Presentation:

Data clearly tabulated. Jmol used appropriately. Animations of vibrational frequencies for TS would assist report. Good use of file-sharing.

Results:

A number of anti and gauche conformers considered. Noted gauche 1 as the lowest energy conformer; however visualisation and comparison of its energy with the appendix suggests it is in fact gauche 3. However the fact it is lowest in energy is explained very well with use of vdW interactions, MOs (diagrams v.useful) and hyperconjugation.

Reoptimised a number of isomers using B3LYP. This included reoptimising anti2 (as asked in the script), however you’ve named it anti 3! Note, you cannot compare energies between different methods (HF and DFT) - they’re calculated on different energy scales! Differences in geometry well considered. Frequency analysis for anti 3 (actually anti 2) carried out, inc. IR spectra and thermochemical data for 0K and 298K – v. good!

Chair/Boat: Results v. good. Have additionally investigated optimising the boat TS using QST3 – great! IRC carried out for chair and boat. Activation energies calculated for chair and boat for both levels of theory. Results at 298K?

Understanding:

Very good introduction and conclusion (particularly justifying why the chair TS is lower in energy). Steps taken clearly stated, and reasons why explained. Good understanding of levels of theory, methods, keywords etc. Only slight confusion is the difference of naming in the report to the appendix.

Diels Alder

Presentation:

Same as above.

Results:

MOs of reactants good, and correct symmetries assigned. Good understanding of HOMO/LUMO interactions in TS. Are images muddled for the TS? As the assigned symmetry for the HOMO is symmetric, but the assigned diagram for this is anti-symmetric . Correctly noted C-C bond forming distance is < 2 x vdW radius of C, therefore implying the bond is forming.

Endo/exo: Correctly noted endo is lower in energy. Considered why this is so using steric reasoning and the secondary orbital overlap effect . Has looked to see if this effect is apparent in their results – v.thorough. Additionally have carried out IRC calculations as further work.

Understanding:

Very good introduction and conclusion. Excellent explanation of HOMO/LUMO interactions and allowed/forbidden reactions. Good use of (and comparison to) primary literature throughout. Suggested improvements to the study, such as using a higher level of theory, are provided.

User talk:Xx108(module 3)

2011-11-28T10:34:10Z

Ajthom: Created page with " Cope Rearrangement Presentation: Data clearly tabulated. Good use of images and Jmol. Could do with animations to show imaginary vibrations. Links to some of the original f..."

Cope Rearrangement

Presentation:

Data clearly tabulated. Good use of images and Jmol. Could do with animations to show imaginary vibrations. Links to some of the original files provided.

Results:

Many anti and gauche conformers considered. Correctly noted gauche 3 is lowest in energy and rationalised using MOs – good.

Anti 2 – Reoptimised. Note, you cannot compare energies between different methods (HF and DFT) - they’re calculated on different energy scales. Good comparison of geometries for both. Thermochemical data provided. Thermochemical energies (e.g. sum of electronic and thermal energies, sum of electronic and thermal enthalpies) at 0K should all be the same as thermal energies should all be 0. The link to the 0K calculation does not appear to be the right one, as there is no frequency analysis, or setting the temperature in this file.

Boat/Chair TS: Results good. IRC calculations for chair – have attempted a number of methods. Boat? Activation energies calculated for chair and boat at both levels of theory at 0K and 298K – v. good.

Understanding:

Good concise intro and conclusion. Steps taken very clear, and have rationalised these steps and the advantages/disadvantages of different approaches – good. Also good explanation of results obtained. Appropriate references made to primary literature.

Diels Alder

Presentation:

Same as above

Results:

MOs of reactants good with correct symmetry assigned. Interactions of these MOs and allowed reactions mentioned. MOs of TS – good with correct symmetry. Correctly noted the C-C bond bonding distance is < 2 x vdW radius of C, suggesting bond forming. Calculated activation energy using 2 different levels of theory as extra work and compared to literature value – excellent!

Endo/exo – results v. good. Investigated 2 different levels of theory for TS optimisation. Correctly noted endo is lower in energy. Good consideration of steric reasoning vs. secondary orbital overlap effect.

Understanding:

Nice introduction. Good understanding of the work being done and limitations of the calculations carried out. The method of TS optimisation has been carefully considered looking at the advantages/disadvantages of each. Suggestions for possible further work also mentioned . Results well analysed including considering HOMO/LUMO interactions and allowed/forbidden reactions. Also provided a very good explanation of secondary orbital overlap with use of diagrams – but are these apparent in your MOs?

Talk:Mod:HAS1503

2011-11-28T10:28:27Z

Ajthom: Created page with "Cope Rearrangement Presentation: Data tabulated. Images generally good. Have numbered images and tables, and given them appropriate legends. However, could have shown animatio..."

Cope Rearrangement

Presentation:

Data tabulated. Images generally good. Have numbered images and tables, and given them appropriate legends. However, could have shown animations – particularly for illustrating the imaginary frequencies for TS. File sharing would be useful, particular where things didn’t work as expected.

Results:

Anti and gauche conformations considered. Thorough thought to the contributing stabilising factors such as vdW interactions, MO orbitals etc. – v.good. It’s difficult to see why your results don’t correlate with those in the appendix without submission of files.

Anti 2 conformer – Note, you cannot compare energies between different methods (HF and DFT); they’re calculated on different energy scales. Differences in geometry well considered. Frequency analysis – good. Included IR spectra and thermochemical data. Calculations at 0K?

Chair/boat TS- Results for chair good. Would’ve been useful to include files for boat optimization so could see what was going wrong. Were you optimizing to a minimum not TS? IRC calculations for chair good, considered different approaches. Could have calculated the activation energy for the chair, even without data for the boat.

Understanding:

Very good introduction to the topic no conclusion though. Steps taken generally clear. It’s a shame you didn’t use file-share, so we could see what went wrong with the calculations.

Diels Alder

Presentation:

Data tabulated. MOs presented well. Again, animations for the vibrational frequencies would be good.

Results:

HOMO and LUMO of cis-butadiene good – correct symmetries assigned. MOs for ethylene? Good explanation of HOMO/LUMO interactions. Would you expect the HOMO TS to be symmetric?

Analysis of C-C distances shows C-C distance of bond forming is less than twice the VdW radius of carbon, therefore suggests bond forming – good!

Limited results for the ‘Regioselectivity of the Diels alder reaction’ section.

Understanding:

Very good introduction again. HOMO/LUMO interactions and allowed/forbidden reactions well-understood. I am guessing you were running out of time towards the end, as it begins to feel rushed and is missing the last section.

Talk:Mod:wearethewalri

2011-11-28T10:00:46Z

Ajthom: Created page with "Cope Rearrangement Presentation: Good use of images. Data tabulated. Captions? Could have made greater use of animations. Some links to original files provided. Results: I..."

Cope Rearrangement

Presentation:

Good use of images. Data tabulated. Captions? Could have made greater use of animations. Some links to original files provided.

Results:

Investigated anti and gauche conformations. Correctly noted gauche 3 as lowest energy isomer and considered vdW interactions and MOs to explain – very good!

Reoptimised anti 2 – Note, you cannot compare energies between different methods (HF and DFT) - they’re calculated on different energy scales. Differences in geometry? Frequency analysis good. IR spectra? Calculations at 0K?

Chair/Boat TS – Results good. IRC calculated for chair using multiple methods – v.good analysis of different methods. Boat?

Activation energies calculated for both levels of theory at 0K and 298K – v.good. Compared to experimental data.

Understanding:

Very good introduction. Could do with conclusion. Steps taken very clear and generally understood. Could do with further reasoning at points as to why certain methods/keywords etc. were used. Very good analysis of results obtained – explaining and rationalising what is seen.

Diels Alder

Presentation:

Data tabulated. Images of structures given. Good use of animations. Use of Jmol?

Results:

MOs of cis-butadiene good. However symmetries incorrectly assigned. MOS for ethylene?

TS – MOs good. HOMO/LUMO interactions covered briefly in legends and diagram, but needs more explanation. Correctly notes C-C bond forming distance is < 2 x vdW radius of C, suggesting bond forming.

Endo/exo: Very thorough. Correctly note endo as lower energy conformation. Additional work calculating IRC for both and activation energies – v.good. Good explanation of HOMO/LUMO interactions here. Delves into kinetic and thermodynamic control. Considers steric effects vs. secondary orbital overlap – and applies this to actual results – Excellent.

Understanding:

Could do with an introduction. Steps taken clear. Further reasoning for these steps/levels of theory/keywords etc. would be useful. Lots of additional work has been carried out to help understand the reaction. Good consideration of endo vs. exo – including discussion of steric reasoning and secondary orbital overlap. These considerations were then applied to the results obtained – v.good. In the conclusion have considered alternative approaches included using solvent in calculations and higher levels of theory.

Talk:Mod:YYTmod3

2011-11-28T09:58:54Z

Ajthom: Created page with "Cope Rearrangement Presentation: Data clearly tabulated. Figures and Tables given appropriate legends. Animations would be useful at times (e.g. to illustrate imaginary freque..."

Cope Rearrangement

Presentation:

Data clearly tabulated. Figures and Tables given appropriate legends. Animations would be useful at times (e.g. to illustrate imaginary frequencies). Appropriate links to files given. Note you have misquoted 3-21g as 3-21 a number of times in the script.

Results:

Optimized anti and gauche conformers inc. gauche 3 - good. This is the lowest energy isomer according to these calculations, would you expect this? For the HF and B3LYP optimised anti-2 conformer you cannot compare energies between different methods (HF and DFT) - they’re calculated on different energy scales! Further comment on their geometries? Included IR spectra and thermochemical data – good. Calculations at 0K?

Chair/Boat TS: Results generally good. Images of optimised structures would be useful. Also please note the frozen co-ordinate method is a 2 step approach – the reason the structure/energy from the ’2nd’ optimization is different to the ‘1st’ and ‘3rd’ is because bond lengths are constrained in this stage. Once the whole molecule is optimised free of constraints (in the 3rd optimisation) the chair TS has a similar energy and structure to that from the TS Berny method. IRC calculations carried out for the chair structure using a range of methods – good. Could do the same for the boat structure.

Activation energies calculated for both levels of theory at 0K and 298K – very good. Good comparison to experimental data.

Understanding:

Good concise introduction and have summarised findings well at end. Steps taken clear. Could comment more on why these steps were taken, why a certain level of theory was used, use of keywords etc. Good explanation of the IRC method.

Diels Alder

Presentation:

Data clearly tabulated. Good use of images and Jmol. Animation of TSs would be useful. Appropriate links to original files provided.

Results:

MOs of butadiene good – correct symmetry noted. MOs for ethylene?

TS – Results generally good. See above for comments on frozen co-ordinate method. Correctly noted the C-C bond forming distance is < 2 x vdW radius of C, thereby showing shared electron density. Good explanation of the interaction of the reactants – diagrams assist explanation well.

Exo/endo: Results generally good. Correctly noted endo lower in energy. Could comment on the symmetry of the TSs and comment on the interaction of the MOs of the reactants as in the previous section. Have reasoned endo is lower energy due to secondary orbital overlap effect – good. Can you see this effect in the MO diagrams?

Understanding:

Could do with more than a line for the introduction/conclusion. Steps taken generally clear. Could add reasoning as to why these steps were taken, e.g. why use of opt=noeigen in TS optimisation? Interactions between MOs of reactants and allowed/forbidden reactions good. As mentioned above, secondary orbital overlap effect is discussed – would be good to apply to your results.

Talk:Mod:fs1309module 3

2011-11-28T09:57:52Z

Ajthom: Created page with "Cope Rearrangement Presentation: Data clearly tabulated. Good use of animations to show imaginary frequency for chair. Use of Jmol would have allowed visualisation of structur..."

Cope Rearrangement

Presentation:

Data clearly tabulated. Good use of animations to show imaginary frequency for chair. Use of Jmol would have allowed visualisation of structures at different angles. Appropriate use of file sharing.

Results:

Investigated many of the anti/gauche conformers inc. gauche 3 – good. Would you expect gauche 3 to be the lowest energy conformer? Some explanation would be useful here. Included detailed analysis of difference in geometry of anti-2 isomer using HF and B3LYP methods. Note, you cannot compare energies between different methods (HF and DFT), they’re calculated on different energy scales. Frequency analysis good, including IR spectra and thermochemical data at 298K – Results for 0K?

Boat/Chair TS: Results good, TSs found. IRC calculated for chair using multiple methods – good! Could also consider boat. Activations energies calculated for both levels of theory at 298K and 0K – v.good. Where is result for B3LYP method at 298K? I think in the table ‘Summary of energies and transition structure obtained from HF/3-21G’, for the column ‘sum of electronic and ZPE’ the title should be ‘sum of electronic and thermal energies’ and for each of the literature values here you have written 234 instead of 231. Maybe this is where some of the confusion came from?

Understanding:

Good overall introduction. A more thorough conclusion would be useful. Sometimes steps taken confusing, and have to refer back to original script with instructions as student has named things ‘method b’ etc. More explanation as to why steps were taken would also help report, e.g. what is the use of IRC?

Diels Alder

Presentation:

Generally OK. Data clearly tabulated. Animations of TS would be good, as sometimes arrows hard to visualise. Again use of Jmol would be useful.

Results:

MOs for butadiene good, correct symmetry noted. MOs for ethylene?

TS – Results good with explanation of HOMO/LUMO interactions - Good use of diagrams here. Correctly noted C-C bond forming distance is < 2 x vdW radius of C, implying bond forming.

Endo/exo: Results generally good. Investigated using 2 levels of theory – good. Endo is lower in energy than exo for BOTH levels of theory according to your results; they do not have ‘opposite results’. Have explained secondary orbital overlap – but is this effect apparent in your results?

Understanding:

An introduction to the topic would be good. Steps taken mentioned, but reasoning behind these steps (e.g. use of keywords, why certain levels of theory were used etc.) was a little lacking. Very good explanation to allowed/forbidden reactions. Secondary orbital overlap explained well, but could’ve been applied to results.

Talk:Mod:mw1409module3

2011-11-28T09:57:02Z

Ajthom:

Cope Rearrangement

Presentation:

Generally good use of images, with appropriate legends. Could have included images of the chair TS. Limited use of Jmol which would be useful at times to view the molecules from different angles. Good use of animations to illustrate IRC, animations for TS? Data not always tabulated, have to look through script to find values. Useful links to files.

Results:

Investigated anti and gauche conformers. Why didn’t you investigate gauche 3, which in Appendix 1 is the lowest energy conformer when optimising using HF/3-21g? Would you expect this to be the lowest energy conformer? You’ve mentioned that the lowest energy conformer would be expected to be anti.

Have re-optimized the anti 2 conformer – quite a large difference between the 2 structures, would you still describe the B3LYP optimised isomer as anti 2? Thermochemical data provided – good. Could have also run these frequency calculations at 0K. IR spectra?

Optimisation of chair/boat TS: Results good, images would be useful here. IRC present for chair and boat – with a number of methods investigated – v. good. Given data required to calculate activation energies. However it is unclear what activation energies were calculated. Value given for the activation energy for the chair TS at 0K using the B3LYP level of theory, and for the boat – is this also at 0K and using B3LYP? Could have calculated activation energies for both levels of theory at both temperatures and compared them to experimental data.

Understanding:

Brief intro given – could have been expanded (the same goes for the conclusion). Has explained why the steps were taken, and has an understanding of the methods used and their limitations.

Diels Alder

Presentation:

Good use of Jmol, and animations for TS. Data clearly tabulated. Useful links to files.

Results:

HOMO and LUMO provided for cis-butadiene, what about ethylene? Correct symmetries noted for cis-butadiene. Interactions between reactants for transition states good – could go into further detail here about allowed/forbidden reactions etc. Correctly noted C-C bond forming distance is <2xC vdW radius apart, therefore suggesting bond forming.

Endo/Exo: Results generally good. Correctly noted endo as lower in energy. Good animation of imaginary frequency and analysis of geometries. HOMO and LUMOs for exo and endo all antisymmetric – good. Interaction of reactants explained well.

Understanding:

Intro and conclusion a little too brief. Steps taken clear – perhaps include more justification for these steps – such as why certain methods chosen. Secondary orbital overlap and steric hindrance considered (could explain this a little further). Looked for secondary orbital overlap effect in results and showed not apparent in them. Very good use of reference to explain endo selectivity!

Talk:Mod:mw1409module3

2011-11-28T09:55:31Z

Ajthom: Created page with " Normal 0 false false false MicrosoftInternetExplorer4 Cope Rearrangement Presentation: Generally good use of images, with appropriate legends..."

Normal 0 false false false MicrosoftInternetExplorer4

Cope Rearrangement

Presentation:

Generally good use of images, with appropriate legends. Could have included images of the chair TS. Limited use of Jmol which would be useful at times to view the molecules from different angles. Good use of animations to illustrate IRC, animations for TS? Data not always tabulated, have to look through script to find values. Useful links to files.

Results:

Investigated anti and gauche conformers. Why didn’t you investigate gauche 3, which in Appendix 1 is the lowest energy conformer when optimising using HF/3-21g? Would you expect this to be the lowest energy conformer? You’ve mentioned that the lowest energy conformer would be expected to be anti.

Have re-optimized the anti 2 conformer – quite a large difference between the 2 structures, would you still describe the B3LYP optimised isomer as anti 2? Thermochemical data provided – good. Could have also run these frequency calculations at 0K. IR spectra?

Optimisation of chair/boat TS: Results good, images would be useful here. IRC present for chair and boat – with a number of methods investigated – v. good. Given data required to calculate activation energies. However it is unclear what activation energies were calculated. Value given for the activation energy for the chair TS at 0K using the B3LYP level of theory, and for the boat – is this also at 0K and using B3LYP? Could have calculated activation energies for both levels of theory at both temperatures and compared them to experimental data.

Understanding:

Brief intro given – could have been expanded (the same goes for the conclusion). Has explained why the steps were taken, and has an understanding of the methods used and their limitations.

Diels Alder

Presentation:

Good use of Jmol, and animations for TS. Data clearly tabulated. Useful links to files.

Results:

HOMO and LUMO provided for cis-butadiene, what about ethylene? Correct symmetries noted for cis-butadiene. Interactions between reactants for transition states good – could go into further detail here about allowed/forbidden reactions etc. Correctly noted C-C bond forming distance is <2xC vdW radius apart, therefore suggesting bond forming.

Endo/Exo: Results generally good. Correctly noted endo as lower in energy. Good animation of imaginary frequency and analysis of geometries. HOMO and LUMOs for exo and endo all antisymmetric – good. Interaction of reactants explained well.

Understanding:

Intro and conclusion a little too brief. Steps taken clear – perhaps include more justification for these steps – such as why certain methods chosen. Secondary orbital overlap and steric hindrance considered (could explain this a little further). Looked for secondary orbital overlap effect in results and showed not apparent in them. Very good use of reference to explain endo selectivity!

Mod:demonstrators

2011-11-10T14:53:25Z

Ajthom: /* Timetable for computational experiments */

== Timetable for computational experiments ==

The course runs for five weeks, with key dates as follows;
Start dates are
*Mon 10 Oct ...(handout 11-12 Tricia/Alex)
*Mon 14 Nov ...(handout 11-12 Tricia/Bao)
*Mon 16 Jan ...(handout 11-12 Mike/Henry)
*Mon 20 Feb ...(handout 11-12 Mike/Henry)

*Term 1: Bao/Tricia/Alex Admin: Tricia
*Term 2: Henry/Richard/Mike Admin: Mike

:PG Demonstrators present 3hrs a day 12-1,2-4 mon,thur, 12-1,2-4 tue,fri
:''2 Staff present for the first monday of each session 11-12 and 2-4'' and then module leader 1hr a day 2-3pm

Timetable
<table border=1 cellpadding=5px>
<tr align=center bgcolor="#99CC99">
<th width=60px>Week</th>
<th width=120px>Mon staff: 2-3 PG demo: 12-1, 2-4 students: 11-5</th>
<th width=120px>Tues staff: 2-3 PG demo: 12-1, 2-4 students: 12-5</th>
<th width=30px bgcolor="#CCCCCC">Wed</th>
<th width=120px>Thurs staff: 2-3 PG demo: 12-1, 2-4 students: 11-5</th>
<th width=120px>Fri sstaff: 2-3 PG demo: 12-1, 2-4 students: 12-5</th>
</tr>
<tr>
<td>Week 1</td>
<td bgcolor="#66CCFF">laptop issue 11-12 introduction 2-4 2 Staff</td>
<td>Module 1: Henry/Bao</td>
<td bgcolor="#CCCCCC"></td>
<td>Module 1: Henry/Bao</td>
<td>Module 1: Henry/Bao</td>
</tr>
<tr>
<td>Week 2</td>
<td>Module 1: Alan/Henry/Bao</td>
<td>Module 1: Alan/Henry/Bao</td>
<td bgcolor="#CCCCCC"></td>
<td>Module 1: Alan/Henry/Bao</td>
<td bgcolor="#FF9999">Module 1 Due 5pm</td>
</tr>
<tr>
<td>Week 3</td>
<td>Module 2: Tricia/Richard </td>
<td>Module 2: Tricia/Richard </td>
<td bgcolor="#CCCCCC"></td>
<td>Module 2: Tricia/Richard </td>
<td>Module 2: Tricia/Richard </td>
</tr>
<tr>
<td>Week 4</td>
<td>Module 2: Tricia/Richard </td>
<td bgcolor="#FF9999">Module 2 Due 5pm</td>
<td bgcolor="#CCCCCC"></td>
<td>Module 3: Mike/Alex </td>
<td>Module 3: Mike/Alex </td>
</tr>
<tr>
<td>Week 5</td>
<td>Module 3: Mike/Alex </td>
<td>Module 3: Mike/Alex </td>
<td bgcolor="#CCCCCC"></td>
<td bgcolor="#66CCFF">Module 3: Mike/Alex laptop hand-in: 3-4 TBD </td>
<td bgcolor="#FF9999">Module 3: Mike/Alex </td>
</tr>
</table>

'''PG Demonstrators'''
<table border=1 cellpadding=5px>
<tr align=center>
<th width=120px>Section</th>
<th width=120px>Organic</th>
<th width=120px>Inorganic</th>
<th width=120px>Physical</th>
</tr>
<tr>
<td>Staff</td>
<td>Henry Rzepa and Alan Armstrong</td>
<td>Patricia Hunt</td>
<td>Mike Bearpark</td>
</tr>
<tr>
<td>PG Demonstrators
 10 Oct
 14 Nov
 16 Jan
 20 Feb
</td>
<td>Allocated sessions
 Matt Hughes
 Matt Hughes
 Paul Dingwall
 Paul Dingwall
</td>
<td>Allocated sessions
 Abdihakim Hassan
 Bryan Ward
 Precious Ugbomah
 TBD
</td>
<td>Allocated sessions
 Sarah Rosen
 William Vigor
 Richard Bradshaw
 Lee Thompson
</td>
</tr>
</table>

'''PG Markers'''
<table border=1 cellpadding=5px>
<tr align=center>
<th width=120px>Section</th>
<th width=120px>Organic</th>
<th width=120px>Inorganic</th>
<th width=120px>Physical</th>
</tr>
<tr>
<td>Marking</td>
<td>Module 1 marking: 1. Matt Hughes 2. Matt Hughes 3. Paul Dingwall 4. Paul Dingwall</td>
<td>Module 2 marking: compulsory section 1. Abdihakim Hassan 2. Abdihakim Hassan 3. Bryan Ward 4. Bryan Ward
 project section: Tricia/Richard</td>
<td>Module 3 marking: 1. Sarah Rosen 2. Richard Bradshaw 3. Sarah Rosen 4. Richard Bradshaw</td>
</tr>
</table>

Rep:Mod:AJWT1

2011-09-28T09:52:56Z

Ajthom:

Module 1
bicyclos:

bicylco 1
Total Energy: 31.8765 kcal/mol

bicyclo 2
Total Energy: 33.9975 kcal/mol

bicyclo 3
Total Energy: 35.9266 kcal/mol
Stretch: 1.2351
Bend: 18.9430
Stretch-Bend: -0.7610
Torsion: 12.1195
Non-1,4 VDW: -1.5003
1,4 VDW: 5.7274
Dipole/Dipole: 0.1631

bicyclo 4
Total Energy: 31.1520 kcal/mol
Stretch: 1.0968
Bend: 14.5245
Stretch-Bend: -0.5493
Torsion: 12.4979
Non-1,4 VDW: -1.0702
1,4 VDW: 4.5117
Dipole/Dipole: 0.1406

pyr5

------------MM2 Minimization------------
Pi System: 6 2 1 3 5 4 12 19
Warning: Some parameters are guessed (Quality = 1).
Iteration 2: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.4901
Bend: 8.3132
Stretch-Bend: 0.1420
Torsion: 14.8202
Non-1,4 VDW: -1.5017
1,4 VDW: 16.6653
Charge/Dipole: 12.5201
Dipole/Dipole: -7.4298
Total Energy: 45.0194 kcal/mol
Calculation completed
------------------------------------

pyr5_2

------------MM2 Minimization------------
Separating coincident atoms: Lp(20)-Lp(22)
Pi System: 6 2 1 3 5 4 12 19
Warning: Some parameters are guessed (Quality = 1).
Iteration 545: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.4890
Bend: 8.3059
Stretch-Bend: 0.1424
Torsion: 14.8198
Non-1,4 VDW: -1.5007
1,4 VDW: 16.6707
Charge/Dipole: 12.5226
Dipole/Dipole: -7.4300
Total Energy: 45.0196 kcal/mol
Calculation completed
------------------------------------

pyr5_3

------------MM2 Minimization------------
Pi System: 6 2 1 3 5 4 12 19
Warning: Some parameters are guessed (Quality = 1).
Iteration 227: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.4871
Bend: 7.2752
Stretch-Bend: 0.1054
Torsion: 15.5569
Non-1,4 VDW: -2.2916
1,4 VDW: 16.7887
Charge/Dipole: 12.8151
Dipole/Dipole: -7.3972
Total Energy: 44.3396 kcal/mol
Calculation completed
------------------------------------

pyr5_4

------------MM2 Minimization------------
Pi System: 6 2 1 3 5 4 12 19
Warning: Some parameters are guessed (Quality = 1).
Iteration 255: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.4887
Bend: 8.3056
Stretch-Bend: 0.1416
Torsion: 14.8266
Non-1,4 VDW: -1.5036
1,4 VDW: 16.6655
Charge/Dipole: 12.5235
Dipole/Dipole: -7.4284
Total Energy: 45.0194 kcal/mol
Calculation completed
------------------------------------

pyr5_5

------------MM2 Minimization------------
Pi System: 6 2 1 3 5 4 12 19
Warning: Some parameters are guessed (Quality = 1).
Iteration 554: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.4895
Bend: 8.3164
Stretch-Bend: 0.1420
Torsion: 14.8116
Non-1,4 VDW: -1.4989
1,4 VDW: 16.6690
Charge/Dipole: 12.5205
Dipole/Dipole: -7.4307
Total Energy: 45.0195 kcal/mol
Calculation completed
------------------------------------

pyr5_6
------------MM2 Minimization------------
Pi System: 6 2 1 3 5 4 12 19
Warning: Some parameters are guessed (Quality = 1).
Iteration 185: Minimization terminated normally because the gradient norm is less than the minimum gradient norm
Stretch: 1.4881
Bend: 7.2771
Stretch-Bend: 0.1052
Torsion: 15.5489
Non-1,4 VDW: -2.2903
1,4 VDW: 16.7926
Charge/Dipole: 12.8162
Dipole/Dipole: -7.3981
Total Energy: 44.3397 kcal/mol
Calculation completed
------------------------------------

pyr5_3 and pyr5_6 are probably stereoisomers.

Model: bicy12

Mopac Job: AUX AM1 CHARGE=0 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.07234 (< 0.10000) Heat of Formation = 32.19982 Kcal/Mol
-----------------------------------------

------------ Mopac Interface ------------
Model: bicy12

Mopac Job: AUX PM6 CHARGE=0 EF GNORM=0.100 SHIFT=80
Finished @ RMS Gradient = 0.08300 (< 0.10000) Heat of Formation = 19.74028 Kcal/Mol
-----------------------------------------
HOMO no component on C=C. Mostly C-Cl pi * looking

Rep:Mod:AJWT1

2011-09-24T11:59:07Z

Ajthom: Created page with " Module 1 bicyclos: bicylco 1 Total Energy: 31.8765 kcal/mol bicyclo 2 Total Energy: 33.9975 kcal/mol bicyclo 3 Total Energy: 35.9266 kcal/mol..."

Mod:timetable

2011-09-24T09:38:40Z

Ajthom: /* Timetable for computational experiments */

See also: [[Mod:timetable|Timetable]],[[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]],[[Mod:writeup|Writing up]]

= Timetable for computational experiments =

The 2011-12 list of groups are available {{pdf|3-2011.pdf|here:}}. If for whatever reason you have swapped a course, please let us know so that we do not allocate zero marks for you. For each group, the course runs for five weeks, with key dates as follows;

[[Mod:Hunt_Research_Group/compchemlab|PG Demonstrators]] present 3hrs a day 12-1, 2-4 Mon, Tue, Thur and Fri in the tutorial room.

Staff will be available for their module 2-3pm, mon, tue, thur and fri

<table border=1 cellpadding=5px>
<tr align=center>
<th width=60px>Week</th>
<th width=120px>Mon 11-5</th>
<th width=120px>Tues 12-5</th>
<th width=30px bgcolor="#CCCCCC">Wed</th>
<th width=120px>Thurs 11-5</th>
<th width=120px>Fri 12-5</th>
</tr>
<tr>
<td>Week 1</td>
<td bgcolor="#66CCFF">11-12 laptop issue 
2-4.30 introduction</td>
<td>Module 1</td>
<td bgcolor="#CCCCCC"></td>
<td>Module 1</td>
<td>Module 1</td>
</tr>
<tr>
<td>Week 2</td>
<td>Module 1</td>
<td>Module 1</td>
<td bgcolor="#CCCCCC"></td>
<td>Module 1</td>
<td bgcolor="#FF9999">Module 1 Due 5pm [http://course_link_placeholder submit Module 1]</td>
</tr>
<tr>
<td>Week 3</td>
<td>Module 2</td>
<td>Module 2</td>
<td bgcolor="#CCCCCC"></td>
<td>Module 2</td>
<td>Module 2</td>
</tr>
<tr>
<td>Week 4</td>
<td>Module 2</td>
<td bgcolor="#FF9999">Module 2 Due 5pm [http://course_link_placeholder submit Module 2]</td>
<td bgcolor="#CCCCCC"></td>
<td>Module 3</td>
<td>Module 3</td>
</tr>
<tr>
<td>Week 5</td>
<td>Module 3</td>
<td>Module 3</td>
<td bgcolor="#CCCCCC"></td>
<td bgcolor="#66CCFF">Module 3 
3-4 laptop hand-in</td>
<td bgcolor="#FF9999">Module 3 Due 5pm [http://course_link_placeholder submit Module 3]</td>
</tr>
</table>
*Day 1 Laptop sign-out and familiarisation (study area, level 2) laptop issue (11-12), laptop set-up (12-2)
*Day 1 "A Rough Guide to Successful Computational Chemistry" (2.00-4.30):
::#Why computational chemistry?
::#Molecular Mechanics
::#Basis sets and Methods
::#Optimisation and Frequency analysis
::#Open for questions
*Module 1: Structural chemistry investigations using Molecular mechanics and semi-empirical MO methods.
*Module 2: Bonding analyses using ''Ab initio'' and Density functional techniques.
*Module 3: Reaction mechanisms and transition states.
*Laptop hand-in day, Rm 167 (C2) between 3-4pm, use the computers in the study area to complete your final report.

Although the schedule above shows activity for only Mon, Tue, Thur and Fri of any week, you are of course free to use your laptop 24/7 and to work at times which best suit you. We strongly recommend you attend the first day's introductory sessions, these will tell set you up for the rest of the lab. The timetable above is a guideline. You should spend approximately 6 working days per module, using your judgement on how you can make most effective use of your time (thus you might decide to interleave two modules concurrently). Previous groups have shown that '''time management''' is an issue. It is up to you to manage your time, not to do too much and not to do too little. Ask a staff member if you are unsure.

Specific staff are available to answer questions (including those e-mailed) 14.00-15.00 during each module, for module 1 [mailto:b.nguyen@imperial.ac.uk Bao Nguyen] or [mailto:a.armstrong@imperial.ac.uk Alan Armstrong], for module 2 [mailto:p.hunt@imperial.ac.uk Tricia Hunt] and for module 3 [mailto:a.thom@imperial.ac.uk Alex Thom]. Student demonstrators are available in the up-stairs computer lab as outlined above. While you can work on the lab when you like, the demonstrators and staff are available at specific times of the day. They may choose to answer e-mails outside of this time.

If we do not receive the URL of your report (submitted via the Blackboard system, and '''NOT''' emailed to the individual members of the course team), we will contact you by email within one working day (Mon-Fri) of the deadline to check it has not gone missing. You should expect to get an email informing you of your grade within 10 working days. If you have heard nothing, please contact the relevant member of staff for each module (Alan Armstrong, Henry Rzepa for mod 1), Tricia Hunt (Mod 2) or Alex Thom (module 3).

'''The coursework hand-in times are fixed, there will be a 15% penalty for every 24hrs after 5pm of the submit date.''' Any sections completed by the hand-in date will be assessed for full marks, additional material added after this will incur a penalty. If you are having problems, are ill or have extenuating circumstances please see [mailto:p.hunt@ic.ac.uk Dr Hunt] as early as possible, extensions may be granted and will be determined on a case-by-case basis.

----
See also: [[Mod:timetable|Timetable]], [[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]], [[Mod:writeup|Writing up]]