ChemWiki - User contributions [en]

Talk:Mod:Laura91

2013-03-18T13:08:37Z

Pd05: Created page with "Cpd dimers: Excellent, if slightly lengthy, answer. Taxol: The ring junction for your structure 9 is incorrect, it should be cis, so your energy for this structure is incorrec..."

Cpd dimers: Excellent, if slightly lengthy, answer.

Taxol: The ring junction for your structure 9 is incorrect, it should be cis, so your energy for this structure is incorrect! However, your analysis is very.

Carbene: Not sure why you have a screen dump here, it doesn’t seem to show much, especially as you have a jmol of the overlay. Otherwise excellent.

Glycosidation: Burger-Dunitz? Were you thinking of your dinner when you were writing this? Good answer although you could take your analysis further.

Taxol Take 2: Good.

Mini-project: A very enthusiastic attempt. Not sure why you calculated the MOs, especially as you yourself note that this won’t help in the assignment. Overall, a lot of work. Well done.

Overall: An excellent project. However, try to be a little more concise in your writing. It is possible to say more by writing less. But don’t let this comment detract from the fact you did some very good work.

Talk:Mod:AHall Computational Lab Module 1

2013-03-18T13:08:20Z

Pd05: Created page with "Cpd dimers: Good. Taxol: Excellent. Carbene: Again, excellent. Glycosidation: Very close, you could go further in your analyses. This is more than just charge donation an..."

Cpd dimers: Good.

Taxol: Excellent.

Carbene: Again, excellent.

Glycosidation: Very close, you could go further in your analyses. This is more than just charge donation and you need to think more about the differences between the MM2 and MOPAC methods. Also, the angle is very important; can you remember Burgi-Dunitz? Vry good answer though.

Taxol Take 2: Good.

Mini-project: Perhaps a few too many decimal points in use here. Two projects? What’s going on? I’m not sure why you chose two molecules, but well done for the extra work.

Overall: An excellent project.

Talk:Mod:AlexanderGray

2013-03-18T13:07:51Z

Pd05: Created page with "Cpd dimers: Your energies are good. Your explanation and analysis could use a little work though. You put in quite a large table of the breakdown of the MM2 energies but you d..."

Cpd dimers: Your energies are good. Your explanation and analysis could use a little work though. You put in quite a large table of the breakdown of the MM2 energies but you did not use it in your analysis. Before adding large amounts of data to your write up, ask yourself if it is necessary. You could save yourself a lot of time.

Taxol: Good. Any thoughts on hyperstable alkenes?

Carbene: When analysing a structure, try to use technical terms such as ‘exo’ or ‘endo’ to a particular functional group rather than saying ‘left’ or ‘right’. Good to know you’re taking on board the differences between MOPAC and MM2. So what information do the HOMO and LUMO give us about this molecule? And what does the electrostatic potential and vibrational analysis of the molecule tell us? It’s not enough that you simply do the calculations, you need to analyse the results as well.

Glycosidation: Good to see that you realised MOPAC can form new bonds but why is it the case that MOPAC can and MM2 can’t? Good attempt at the energies as well.

Taxol Take 2: Nicely done.

Mini-project: You’ve done a lot of detailed work and this looks good, but the way you’ve presented your result makes it very difficult for me to compare and contrast them with those of the literature. Again, you need to use more technical language, ‘upfield’ and ‘downfield’ are more appropriate descriptors in NMR rather than ‘higher’ and ‘less negative’. Some interesting computational NMR here th[ough.

Overall: Calculations, structures and energies are all good but you were occasionally lacking in analysis. Really to focus on what the question is asking for and ask yourself why you are doing something rather than simply following instructions. Overall, however, this was a good project.

Talk:Mod:ERMGERD

2013-03-18T13:07:33Z

Pd05: Created page with "Cpd dimers: Your energies are good. Your analysis could have been a little clearer. Taxol: Your structures are incorrect! It is also very difficult to tell what’s going o..."

Cpd dimers: Your energies are good. Your analysis could have been a little clearer.

Taxol: Your structures are incorrect! It is also very difficult to tell what’s going on with your 2D chemdraw structures. Where’s the analysis?

Carbene:

Glycosidation:

Taxol Take 2:

Mini-project:

Overall: What happened?

Mod:timetable

2013-02-18T11:07:21Z

Pd05: /* 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 2012-2013 list of groups are available {{pdf|Lab allocations 2013.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 four weeks, during which time you have to attempt '''TWO''' modules and submit '''TWO''' Wiki reports of your experiments. The first of these is due on the Friday at 17.00 at the end of the first two weeks, and the second on the Friday at 17.00 at the end of four weeks.

Dr Hunt, Dr Bearpark and Professor Rzepa will be available for personal discussion as follows and at other times by email or by arrangement with them. However, it is best if you direct your questions to a demonstrator first, as they are on hand and can solve most problems straight away.
*Module 1 [mailto:rzepa@imperial.ac.uk Henry Rzepa (169)] Monday afternoons, Weeks 1-4 of the course, and Friday afternoons, weeks 2 and 4. Paul Dingwall will be available as a demonstrator 1-3 Tuesdays.
*Module 2 [mailto:p.hunt@imperial.ac.uk Patricia Hunt (167)] or [mailto:richard.matthews@imperial.ac.uk Richard Matthews] Tuesday afternoons 2-3, Weeks 1-4 of the course, and Friday 12-1, weeks 2 and 4. Bryan Ward will be available as a demonstrator 12-1 and 3-4 on Thursdays
*Module 3 [mailto:m.bearpark@imperial.ac.uk Michael Bearpark (160a)]. Thursday afternoons, Weeks 1-4 of the course, and as needed throughout the course. Lee Thompson will be available as a demonstrator 12-1 and 3-4 on Mondays.

== Specific times ==

*Week 1 (Monday): Laptop sign-out (12.00-12.30) from Room 237A.
*Day 1 (Monday): Check-up (have you got started) in level 2 computer room, Henry Rzepa.
*Laptop return is four weeks later (Monday) Briscoe lab, 11-12 during the study week following the course.

Although the schedule 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 8 working lab-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 a skill that has to be cultivated, and you will get a chance to do so with this course! 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 at all unsure.

== Report submission ==

Submit the URL for your Wiki report from [https://vle.imperial.ac.uk/webct/logon/5047144695021 this address] by the appropriate deadline. These deadlines are on the Friday of the end of the second week of the course for the first module you attempt, and again on the Friday of the 4th week of the course, at 17.00 for the second module you attempt. You can do the modules in any order you wish provided you hand two reports in over the four week period at the times indicated.

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 attempt to 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 a grade on blackboard within 10 working days. If you have heard nothing and have not received a grade in blackboard, please contact the relevant member of staff for each module (Henry Rzepa for mod 1), Tricia Hunt (Mod 2) or Mike Bearpark (module 3).

'''The coursework hand-in times are fixed, there will be a penalty applied 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]]

Talk:Mod:Skilganon2

2013-02-12T17:02:35Z

Pd05: /* Comments */

Taxol: Your alkene geometries are incorrect and neither structure is truly minimised. Are there any, perhaps six-membered, components of the structure that you think could be in a lower energy conformation?

Carbene: Your overlaid structures link is broken. Just because an IR frequency is intense does not mean it’s interesting, relevant or useful to the analysis you should be conducting. I don’t think a particular IR frequency can cause a reaction to take place. Very little appropriate analysis here.

Glycosidation: Why and how do the MM2 and MOPAC calculations differ? What is the fundamental difference between these methods?

Taxol Take 2: What a lot of decimal points. Poor analysis.

Mini-project: That is not a very good choice of molecule, it has far too much freedom of movement, it will be very difficult to find the lowest energy conformation. Look at all those decimal points, mostly zeroes. I don’t understand what you mean by ‘anomaly’. Do you really think that the addition of contaminants to the literature compound will cause there to be fewer NMR peaks?

Overall: Poorly conducted analyses and a lack of apparent effort really let you down.

Talk:Mod:blackmesa

2013-02-12T17:02:06Z

Pd05: Created page with "Cpd dimers: Good to see you relating energetic terms to structural differences. Not the best explanation of kinetic Vs. thermo control, and you open with an unfinished sentenc..."

Cpd dimers: Good to see you relating energetic terms to structural differences. Not the best explanation of kinetic Vs. thermo control, and you open with an unfinished sentence. Jmols?

Taxol: The geometry of you alkene is wrong so you energy is way out for 9. There is no jmol for 10 so I can’t suggest why the energy is off. Where is the ‘full energy contribution breakdown’?

Carbene: You have a massive table with one whole column empty. I’d like to see the overlay. You’ve written descriptions of each IR motion, why? Does this help complete the objectives you were given?

Glycosidation: Jmols? Okay, so you’ve attempted to analyse the various components of the MM2 output, but does this complete the objective you were given?

Taxol Take 2: You alkene geometry is still incorrect. You’ve attempted a discussion, which is good, and noticed some problems but you haven’t quite grasped the issues.

Mini-project: Not quite, you were asked to find a reaction producing a pair (or more) of isomers so that you could attempt to differentiate between them computationally. And despite the bicyclic component of your molecule, there is still a lot of room for conformational flexibility of the side chain. That said, you have some pretty accurate NMR data. It’s a pity you didn’t find an appropriate example, this is the best part of your project by far.

Overall: Needed a lot more time and thought put into both doing and checking this. In the future, really try to focus your answers on the objectives that you are asked for in the script.

Talk:JadeDamon2

2013-02-12T17:01:53Z

Pd05: Created page with "Cpd dimers: Excellent. Quite an essay though, a couple of paragraphs would have been enough. Taxol: Your link to jmol structure 4 is broken. However, the energy looks fine s..."

Cpd dimers: Excellent. Quite an essay though, a couple of paragraphs would have been enough.

Taxol: Your link to jmol structure 4 is broken. However, the energy looks fine so I’ll assume the structure is correct. Good to see you thinking about the relative energies of each conformation of the six-membered ring, but could you not have calculated and then plotted them for a quantitative analysis?

Carbene: I suspect that, had you chosen slightly different parameters in your overlay, you wouldn’t have seen such a mismatch between the two structures. Excellent discussion, however.

Glycosidation: Good discussion, also good to see you investigating the angle of attack.

Taxol Take 2: Excellent.

Mini-project: Nice visual analysis using bar charts. One point though, try to make the scales on each the same, this emphasises that you have a much better agreement on one isomer than the other. And you don’t have to start the label of a barchart with the word ‘barchart’. Very good project though,

Overall: An excellent project. But for future reference, you don’t get more points the more words you write; try being a little more concise.

Talk:Mod:7521

2013-02-12T17:01:36Z

Pd05: Created page with "Cpd dimers: Excellent. Taxol: Those jmol structures are bizarre, what happened? Your energies are all over the place. Nice discussion on hyper-stable alkenes though. Carben..."

Cpd dimers: Excellent.

Taxol: Those jmol structures are bizarre, what happened? Your energies are all over the place. Nice discussion on hyper-stable alkenes though.

Carbene: Excellent.

Glycosidation: Nice discussion of MM2 vs. MOPAC. You’ve noted the difference in length of C=O bond and a reason why this is, is there anything other potential bonding distance you could measure here?

Taxol Take 2: Nicely done.

Mini-project: Nice choice of molecule and a good discussion of the work. A ‘handwavy argumnet’? Maybe, yes, but is this correct language for a deliverable report? I suspect that in real life, comparison of J values would be the simplest technique to identify between the two. Nice little discussion with the MOs.

Overall: A well written report, shame about the taxol debacle!

Talk:Mod:ilikecake

2013-02-12T17:01:15Z

Pd05: Created page with "Cpd dimers: Excellent. Good to see you relating energetic terms to structural components. Taxol: The geometry of your alkene is incorrect and your structures are definitely n..."

Cpd dimers: Excellent. Good to see you relating energetic terms to structural components.

Taxol: The geometry of your alkene is incorrect and your structures are definitely not minimised. Are there any, perhaps six-membered, components of the structure that you think could be in a lower energy conformation?

Carbene: Well done.

Glycosidation: Good that you’ve noted the difference between MOPAC and MM2, but why is this the case? Interesting use of overlays but we’re really only interested in a small section of the molecule in relation to the question. Where are your MOPAC energies?

Taxol Take 2: Not a huge amount of discussion. Although your calculations look okay.

Mini-project: Maybe not the best choice of molecule, it will be very difficult to minimise properly given the degrees of freedom in its conformation. Not much of a discussion here either.

Overall: A very good start brought up abruptly by what looks like a lack of time. I can’t give you marks for a discussion that isn’t there, but you do have it in you to write well judging by the beginning of the project.

Talk:Mod:ac4610b

2013-02-12T17:00:59Z

Pd05: Created page with "Cpd dimers: Your energies are good but your explanation of thermo vs. kinetic control, while correct, could be a little clearer. Good to see you relating energetic terms to str..."

Cpd dimers: Your energies are good but your explanation of thermo vs. kinetic control, while correct, could be a little clearer. Good to see you relating energetic terms to structural differences.

Taxol: The geometry of your alkene is incorrect! However, it is good to see that you were investigating the geometry of the six membered ring. Looks like you’re missing an energy diagram. Good to see you’re also investigating MMFF94.

Carbene: Nicely done.

Glycosidation: Although it’s nice to see curly arrow diagrams be very careful! You are missing arrows for the electrons pushing into the oxenium! Good attempt at these energies. I like the distance analysis you’ve performed, another aspect to consider is the direction of approach; can you remember Burgi-Dunitz angles? Good to see that you’re considering differences between MM2 and MOPAC.

Taxol Take 2: You’ve got the correct alkene geometry now. Nice analysis.1

Mini-project: Nice choice of molecule. Also, a very thorough and well-presented analysis. Without a diagram, I don’t know which atoms C4 and 7 are. Nice to see you thinking experimentally as well as considering the use of higher basis sets. I imagine, in real life, you would do some 2D NMR to distinguish between these, have you heard of an NOE or NOESY experiment?

Overall: It’s very good to see you introducing each section and trying to make everything relevant. Overall, a lot of work has gone into what is an excellent project, well done.

Talk:Mod:fyl10m1ha

2012-12-14T09:28:15Z

Pd05: Created page with "Cpd dimers: Excellent. Taxol: Your structre for 9 is slightly out, take a look at the bridge hydrogens, resulting in slightly higher energies. Good answer nonetheless. Carb..."

Cpd dimers: Excellent.

Taxol: Your structre for 9 is slightly out, take a look at the bridge hydrogens, resulting in slightly higher energies. Good answer nonetheless.

Carbene: A good answer.

Glycosidation: Very good energies, etc. Those tables of bond lengths are horrible to look at though, maybe just show the really relevant information in the future? What we were really looking for here was an exploration of the differences between MM2 and MOPAC. What are the fundamental differences between the two? On a related note, do you notice any similarities in energies between structures A and B? Excellent answer though.

Taxol NMR: Excellent, good to see you’re specifically highlighting the difference between your results and the literature data. A visually appealing way to display these data would have been in a bar chart.

Mini-project: Yes, I imagine getting just the right conformation may have been a little tricky. Very good discussion. I like that you were also thinking beyond the computations.

Overall: An excellent report, well done.

Talk:Mod:LIUXYLANA1

2012-12-14T09:27:48Z

Pd05: Created page with "Cpd dimers: Excellent. Taxol: It is not good enough to simply state that the alkene is hyperstable, where is your evidence? Good to see you investigating different conformati..."

Cpd dimers: Excellent.

Taxol: It is not good enough to simply state that the alkene is hyperstable, where is your evidence? Good to see you investigating different conformations of the six membered ring, however.

Carbene: You’ve done the calculations, but where is the analysis? Okay, you’ve identified which of the two alkenes are more electron rich, but why has this happened?

Glycosidation: Good energies, but where is the analysis? Your jmol links are broken.

Taxol NMR: Where is the comparison to the literature values?

Mini-project: Some jmols of your structures would have been nice. What ring current? There is no aromatic ring. A better comparison here is needed between your results and the literature. Comparing your results in a table, or better yet a bar chart, would have been good. What’s the conclusion? Was modelling the NMR data useful? Could we use it to tell the isomers apart?

Overall: Your report started off so well, what happened?

Talk:Mod:lyjxiong

2012-12-14T09:26:10Z

Pd05: Created page with "Cpd dimers: It would have been nice to see some jmols of your structures. Good to see you relating energies to structural features of the molecule. Taxol: Good to see you inve..."

Cpd dimers: It would have been nice to see some jmols of your structures. Good to see you relating energies to structural features of the molecule.

Taxol: Good to see you investigating different conformations regarding the six membered ring. However, have you thought that there may actually be further chair conformations? Your explanation of hyperstable alkenes could have been better.

Carbene: Good to see you outlining the weaknesses of MM. Good answer.

Glycosidation: Your explanation of glycosidation is not the full picture, is just SN2 involved here? Think further than ‘electron interactions’, MOPAC can form new bonds whereas MM2 can’t. Can you notice any similarities between energies of A and B?

Taxol NMR: Your analysis could have been a little better. For instance, the comparison of two lots of numbers in a table is not a particularly reader friendly method to show the similarity of your results. A bar chart, in this case, would have been much more useful.

Mini-project: Maybe not the best choice of molecule, there is obviously a lot of conformational freedom in this structure. But good to see you’re trying to investigate a number of different conformations. Again, a clearer analysis of your results would have been beneficial. As a summary, could we actually us the predicted 13C NMR to differentiate between the isomers?

Overall: Your English could use a little work, although it did improve as the report went on. A good effort

Talk:Mod:js71ckl10

2012-12-14T09:25:31Z

Pd05: Created page with "Cpd dimers: Well written and nice discussion. Taxol: Unfortunately, the geometry of your alkene for 9 is incorrect, leading to an incorrect structure and incorrect energies! ..."

Cpd dimers: Well written and nice discussion.

Taxol: Unfortunately, the geometry of your alkene for 9 is incorrect, leading to an incorrect structure and incorrect energies! However, 10 is correct. Nice to see you realising the importance of the 6-membered ring and investigating different conformers. What aromatic ring though?

Carbene: You’re almost there, can you maybe think why one alkene is more electron rich than the other and what the differences between MM2 and MOPAC are that are causing the difference in results?

Glycosidation: So, why do MM2 and MOPAC differ here? What, in terms of boundaries, can molecules do under MOPAC that they cannot do under mechanics? Well done modelling all these compounds though.

Taxol Take 2: A more in-depth analysis would have been welcome.

Mini-project: It would have been good if you could have given a brief introduction to the paper you had found these molecules in. Nice to see you investigating additional conformers. I wouldn’t say all the calculated values agree well, some of them are way off (86.6 to 105.4, is that a good agreement?). Good to see you investigating IR, CD, 1H NMR etc. You have a nice breadth in your results but are a little lacking in analysis. So, as a summary, can we tell the difference between the isomers and what technique would be the best?

Overall: Well written with clearly presented data. Some more in-depth analysis would have been good in some places, however. Overall, a good attempt.

Mod:scan

2012-11-13T14:37:28Z

Pd05: /* Archiving the output into a digital repository */

See also: [[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]],[[Mod:writeup|Writing up]]
===Submitting calculations to the Departmental SCAN Cluster ===

[[Image:export.jpg|thumb|right|Export from Ghemical]]The Chemistry department runs a SCAN (Supercomputer at Night) system, whereby the teaching desktop computers which would otherwise only idle in the middle of the night, can be used to run more time consuming calculations than is possible ''interactively'' on a single computer whilst sitting in front of it.

One far more reliable and quantitative way of modelling a molecule is to subject it to quantum mechanical modelling using '''Density Functional''' theory. In practice, this is implemented here using a program called Gaussian 09. The procedure to submit such a job is as follows:
====Creating an Input file ====

*After you have optimised your sketched molecule using ChemBio3D or Gaussview, as described previously, you will have a Gaussian input file saved in your '''H:''' drive by default.
*[[Image:pentahelicene.jpg|thumb|right|Typical Gaussian input]] The file will have to be edited before it can be submitted. You can do this either with '''Gaussview''' as the program, but a much simpler method is to open the file (''pentahelicene.gjf'' in this example) using eg the Windows Wordpad editor. This is invoked simply by double clicking on the file. Remove any existing lines starting with % or # and replace them with one of the following single lines (the second example also results in the vibrational frequences and from these the entropy being computed, and hence the zero-point and free-energy corrected value, ΔG). This latter option will take significantly longer however. 
<tt># B3LYP/6-31G(d) opt</tt> 
or 
<tt># B3LYP/6-31G(d) opt freq</tt> 
to produce a file that looks like the one shown on the right.
*For a molecule the size of e.g. pentahelicene, the calculation will take about 4-5 hours overnight. If for some reason, your molecule is taking longer, you can always reduce the size of the [[basis set]] to e.g. ''B3LYP/3-21G*'', or submit the job on a Friday, when it will have the entire weekend available to it. If you want greater accuracy (but for longer computing time), try e.g. <tt># B3LYP/cc-pVTZ opt freq</tt>.
====Submitting the Input file ====
*[[Image:scan1.jpg|thumb|right|Create a new job]][https://scanweb.cc.imperial.ac.uk/uportal2/index.php You will have to login as yourself]. You can submit as many jobs as you wish through this mechanism, but you must prepare an input file for each first (.gjf if you want to run Gaussian).
*[[Image:scan2.jpg|thumb|left|Create a project]][[Image:scan3.jpg|thumb|left|Select a pool]]After you are logged in you should organise your jobs by '''project'''. Create a suitable new project, then select '''New job'''. 
*#'''Compchem Lab 1''' runs continuously during the day and night, has a concurrency of 8 and a time limit of 48 hours.

*Next, select an Application. One of one type of Gaussian can be selected: '''Gaussian'''
*Next select the Project you have just created, and press '''Continue'''.
*[[Image:scan5.jpg|thumb|left|Upload your input file]]You now have to find the Gaussian input file, as prepared above. You should '''Browse''' to drive H: to find this file. Add a description which will help you identify the job.
*[[Image:scan6.jpg|thumb|right|The Chemistry Condor Pool]]The job will be added to your list of jobs, and you can view its status, which is either '''running''' if there is a vacant slot in the queue you submitted to, or '''pending''' if there is not (or the queue only runs after 23.00). Unfortunately, you cannot find out how many jobs are in front of yours for a pending job. If a module deadline is approaching, everyone will be submitting jobs, so it is very much in your interest to submit jobs early rather than at the last possible moment! Be aware that the time taken to run a Gaussian job depends critically on the size of the molecule, it scaling at around N4, where N is the number of (non-hydrogen) atoms. Typically, a molecule with around 12 (non-H) atoms will take around 30 minutes, but one with 24 would take around eight hours (or more depending on how ''floppy'' it is, and what kind of basis set you have requested). Calculations of optical rotations also take a long time.
*[[Image:scan8.jpg|thumb|right|Viewing the outputs]]When the job has completed, click on the '''Job List''' link. This will show all available outputs. Download the program Log file (this will help you chart whether the calculation was successfull) or the Gaussian Formatted Checkpoint file onto the desktop of the computer you are using, and the file should open up '''Gaussview''', where the molecule can be viewed and checked. You can use the latter file to e.g. plot molecular orbitals for the molecule, view vibrational modes, etc. Full details of these procedures are described in the [http://www.gaussian.com/g_tech/gv5ref/gv5ref_toc.htm Gaussview] and [http://www.gaussian.com/g_tech/g_ur/g09help.htm Gaussian] manuals.
*It is possible also to preview any output prior to downloading it. This will open up a Jmol Window (FireFox only) showing a 3D model of the molecule in question.

====Archiving the output into a digital repository ====

[[Image:Dspace-mod.jpg|thumb|right|Depositing an entry in DSpace]]A very recent innovation is the '''Institutional digital repository''', a resource for permanently archiving calculations, spectra and crystal structures. You can get a flavour of this by archiving your own calculation in the '''SPECTRa''' digital repository. To the right of the Portal display is a link termed '''Publish'''. If you click on this, and the calculation is actually in a state to be published (it may for example have failed for some reason) then appropriate ''metadata'' for the calculation is collected, and the collection deposited into the repository. From here, it can be retrieved in future, and it can also be cited in the manner of a DOI, i.e. '''http://dx.doi.org/10042/to-ABCD''' where ABCD are the four integers representing your deposition ID. In a Wiki, cite this in the form of {{DOI|10042/to-2253}}

====A Note on Publishing to D-Space ====

In order to publish to an archive, you must first select the archive you want to publish to:

1. Log in to the HPC

2. Click on "Profile" in the bottom left

3. Tick the "Publish to DSpace" box

4. Click "Update"

When you click "Publish" in your job list, your files will now publish to the archive you have chosen.

=== Retaining the Calculations ===

Do not delete any completed jobs from the submission pages until your report has been graded. You may be asked to show individual jobs (via the input, or outputs) if for example the calculation has not succeeded in the manner you expected and you would like feed back on this or any other errors.

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

Mod:phys3

2012-11-13T13:57:55Z

Pd05: /* Optimizing the "Chair" and "Boat" Transition Structures */

See also:[[Mod:timetable|Timetable]], [[Mod:lectures|Intro lecture]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:phys3|Module 3]], [http://www.gaussian.com/g_tech/gv5ref/gv5ref_toc.htm Gaussian Online User Manual] | [http://faculty.ycp.edu/~jforesma/educ/visual/index.html Visualization Tutorials]
= Module 3 =

In this set of computational experiments, you will characterise transition structures on potential energy surfaces for the Cope rearrangement and Diels Alder cycloaddition reactions.

There are two parts:
a) tutorial material: how to use the programs and methods,
b) more challenging examples, with guidelines but fewer explicit instructions.



In the second year physical chemistry laboratory, you may have carried out dynamics calculations using model potential energy surfaces to explore transition states. In that computational experiment, the total energy could quickly be calculated for different geometries of a triatomic system using an analytical function of the atomic coordinates (for more information, see for example [http://books.google.com/books?id=T8IZ1aa_FRkC&pg=RA1-PA36&lpg=RA1-PA36&dq=%22lake+eyring%22&source=web&ots=OXY00lSZ7D&sig=Ld_MTNwNjUDNGzB_5w1IxaMBMPU&hl=en&sa=X&oi=book_result&resnum=7&ct=result here] and [http://www.rsc.org/ejarchive/DC/1979/DC9796700007.pdf here]).

In this experiment, you will be studying transition structures in larger molecules. There are no longer fitted formulae for the energy, and the molecular mechanics / force field methods that work well for structure determination cannot be used (in general) as they do not describe bonds being made and broken, and changes in bonding type / electron distribution. (This is the main difference from Module 1). Instead, we use molecular orbital-based methods, numerically solving the Schrodinger equation, and locating transition structures based on the local shape of a potential energy surface. As well as showing what transition structures look like, reaction paths and barrier heights can also be calculated.

==The Cope Rearrangement Tutorial==



''This part of the module is described as a 'tutorial' because it's an introduction to various computational techniques for locating transition structures on potential energy surfaces. It's different to the GaussView tutorial you may have worked through earlier: it's an exercise where you're given specific instructions, see if you can follow them, and also whether there are problems or better ways of carrying the exercise out. Please include this part in your write-up. Marks will be given for correct answers, the documentation showing how you got these, discussion, and how you went about solving any problems you encountered.''

In this tutorial we will use the Cope rearrangement of 1,5-hexadiene as an example of how to study a chemical reactivity problem.

Your objectives are to locate the low-energy minima and transition structures on the C6H10 potential energy surface, to determine the preferred reaction mechanism.

[[Image:pic1.jpg|right|thumb|Cope rearrangement]]

This [3,3]-sigmatropic shift rearrangement has been the subject of numerous experimental and computational studies (e.g. Houk et al. {{DOI|10.1021/ja00101a078}}), and for a long time its mechanism (concerted, stepwise or dissociative) was the subject of some controversy. Nowadays it is generally accepted that the reaction occurs in a concerted fashion via either a "chair" or a "boat" transition structure, with the "boat" transition structure lying several kcal/mol higher in energy. The B3LYP/6-31G* level of theory has been shown to give activation energies and enthalpies in remarkably good agreement with experiment. In this tutorial we will show how these can be calculated using Gaussian.

 

{| align="center"
|- align="center"
|
[[Image:pic2a.jpg]]
|
[[Image:pic2b.jpg]]
|- align="center"
| align="center" | ''Chair Transition State''
| align="center" | ''Boat Transition State''
|}

 

===Optimizing the Reactants and Products===

'' In this section you will learn how to optimize a structure, symmetrize it to find its point group, calculate and visualize vibrational frequencies and correct potential energies in order to compare them with experimental values. It is assumed that you are already familiar with using the builder in GaussView. ''

 

(a) Using GaussView, draw a molecule of 1,5-hexadiene with an "anti" linkage (aproximately a.p.p conformation) for the central four C atoms . Clean the structure using the '''Clean''' function under the '''Edit''' menu.

Now we will optimize the structure at the '''HF/3-21G''' level of theory. Select '''Gaussian''' under the '''Calculate''' menu, click on the '''Job Type''' tab and choose '''Optimization'''. The default method should already be Hartree Fock and the default basis set is 3-21G, so there should be no need to change these. You can check this by clicking on the '''Method''' tab. Change the %mem under the '''Link 0''' tab to 250 MB (though this could be increased to 500 MB). Submit the job by clicking on the '''Submit''' button at the bottom of the window and give the job a meaningful name (e.g. react_anti).

When the job has finished, you will be asked if you want to open a file. Select '''Yes''' and choose the checkpoint (chk) file with the name of the job you have just run (e.g. react_anti.chk). This checkpoint file is a binary file that stores data calculated by Gaussian. The name of the chk file should have been assigned by default, but by default, this file will be created in the C:\Windows\G03\Scratch folder. Once the file has been opened, click on the '''Summary''' button under the '''Results''' menu and make a note of the energy.


Does your final structure have symmetry? Select '''Symmetrize''' under the '''Edit''' menu (note that sometimes it is necessary to relax the search criteria under the '''Point Group''' menu). Make a note of the point group.

 

(b) Now draw another molecule of 1,5-hexadiene with a "gauche" linkage for the central four C atoms. Would you expect this structure to have a lower or a higher energy than the anti structure you have just optimized? Optimize the structure at the '''HF/3-21G''' level of theory and compare your final energy with that obtained in (a). Again, check if the molecule has symmetry and make a note of the point group.

 

(c) Normally, calculated activation energies and enthalpies use the lowest energy conformation of a reactant molecule as a reference. Based on your results from above, try to predict what the lowest energy conformation of 1,5-hexadiene might be. Test out your hypothesis by drawing the structure and optimizing it.

 

(d) A table containing the low energy conformers of 1,5-hexadiene and their point groups is shown in [[Mod:phys3#Appendix 1|Appendix 1]]. Compare the structures that you have optimized with those in the table and see if you can identify your structure.

 

(e) Draw the Ci ''anti2'' conformation of 1,5-hexadiene (unless you have already located it). Optimize it at the '''HF/3-21G''' level of theory and make sure it has Ci symmetry. Compare your final energy to the one given in the table.


 

(f) When you are happy that your structure is the same as the one in the table, reoptimize it at the '''B3LYP/6-31G*''' level (6-31G* is equivalent to 6-31G(d) by selecting '''DFT''' under the '''Method''' menu and '''B3LYP''' from the box with the functionals on the right-hand side. Now select '''Link 0''' and change the name of the chk file to the name of the DFT optimization that you are about to run. Note that it is always advisable to do this when re-using or modifying existing structures to ensure that the original chk file is not overwritten. Run the job and make a note of the energy. Now compare the final structures from the '''HF/3-21G''' calculation with that at the higher level of theory. How much does the overall geometry change?

 

(g) The final energies given in the output file represent the energy of the molecule on the bare potential energy surface. To be able to compare these energies with experimentally measured quantities, they need to include some additional terms, which requires a frequency calculation to be carried out. The frequency calculation can also be used to characterize the critical point, i.e. to confirm that it is a minimum in this case: that all vibrational frequencies are real and positive.

Starting from your optimized B3LYP/6-31G* structure, run a frequency calculation at the same level of theory. You can do this by selecting '''Frequency''' under the '''Job Type''' tab. Ensure that the method is still correctly specified under the '''Method''' tab (''caution: on Windows, sometimes 'scrf=(solvent=water,check)' is incorrectly added!'') and then change the name of the chk file under the '''Link 0''' tab to the name of the frequency job that you are about to run. Run the job. Once the job has finished, open the log file this time. Select '''Vibrations''' under the '''Results''' menu. A list of all the vibrational frequencies modes should appear. Check that there are no imaginary frequencies, only real ones. You can visualize some of these vibrations under this menu and simulate the infrared spectrum.


Now, select '''View File''' under the '''Results''' menu and open the output file in the visualizer. Scroll down to the section beginning '''Thermochemistry'''. Under the vibrational temperatures a list of energies should be printed. Make a note of (i) the sum of electronic and zero-point energies, (ii) the sum of electronic and thermal energies, (iii) the sum of electronic and thermal enthalpies, and (iv) the sum of electronic and thermal free energies. The first of these is the potential energy at 0 K including the zero-point vibrational energy (E = Eelec + ZPE), the second is the energy at 298.15 K and 1 atm of pressure which includes contributions from the translational, rotational, and vibrational energy modes at this temperature (E = E + Evib + Erot + Etrans), the third contains an additional correction for RT (H = E + RT) which is particularly important when looking at dissociation reactions, and the last includes the entropic contribution to the free energy (G = H - TS). It is important to make sure that you select the correct energy/enthalpy term to compare to your experimental values. Note that these corrections can also be calculated at other temperatures using the '''Temperature''' option in Gaussian, If you have time, try re-calculate these quantities at 0 K as shown in the [[mod:gv_advanced | Advanced GaussView Tutorial]].

 

===Optimizing the "Chair" and "Boat" Transition Structures ===

'' In this section you will learn how to set up a transition structure optimization (i) by computing the force constants at the beginning of the calculation, (ii) using the redundant coordinate editor, and (iii) using QST2. You will also visualize the reaction coordinate and run the IRC (Intrinisic Reaction Coordinate) and calculate the activation energies for the Cope rearrangement via the "chair" and "boat" transition structures. ''

 

The "chair" and "boat" transition structures for the Cope rearrangement are shown in [[Mod:phys3#Appendix 2|Appendix 2]]. Both consist of two C3H5 allyl fragments positioned approximately 2.2 Å apart, one with C2h symmetry and the other with C2v symmetry.

 

(a) Draw an allyl fragment (CH2CHCH2) and optimize it using the '''HF/3-21G''' level of theory. Your structure should look like one half of the transition structures shown below.

Now open a new GaussView window by going to the '''File''' menu and selecting '''New''' and then '''Create MolGroup'''. Copy the optimized allyl structure from the first calculation by selecting '''Copy''' under the '''Edit''' menu, and then paste it twice into the new window by selecting '''Paste''' and then '''Append Molecule'''. Now orient the two fragments so that they look roughly like the chair transition state below by using the '''Shift Alt keys + Left Mouse button''' to translate one fragment with respect to the other and the '''Alt key + Left Mouse button''' to rotate it. The distance between the terminal ends of the allyl fragments should be approximately 2.2 Å apart. Save this structure to a Gaussian input file with a meaningful name (e.g. chair_ts_guess).

We are now going to optimize this transition state manually in two different ways. Transition state optimizations are more difficult than minimizations because the calculation needs to know where the negative direction of curvature (i.e. the reaction coordinate) is. If you have a reasonable guess for your transition structure geometry, then normally the easiest way to produce this information is to compute the force constant matrix (also known as the Hessian) in the first step of the optimization which will then be updated as the optimization proceeds. This is what we will try to do in the next section. However, if the guess structure for the transition structure is far from the exact structure, then this approach may not work as the curvature of the surface may be significantly different at points far removed from the transition structure. In some cases, a better transition structure can be generated by freezing the reaction coordinate (using '''Opt=ModRedundant''' and minimizing the rest of the molecule. Once the molecule is fully relaxed, the reaction coordinate can then be unfrozen and the transition state optimization is started again. One advantage of doing this, is that it may not be necessary to compute the whole Hessian once this has been done, and just differentiating along the reaction coordinate might give a good enough guess for the initial force constant matrix. This can save a considerable amount of time in cases where the force constant calculation is expensive.

 

(b) Use Hartree Fock and the default basis set 3-21G for parts (b) to (f).

Create a new MolGroup ('''File → New → Create MolGroup''') and copy and paste your guess structure into the window. Now set up a Gaussian optimization for a transition state. Go to the '''Gaussian''' menu under '''Calculate''' and click on the '''Job Type''' tab. Select '''Opt+Freq''' and then change '''Optimization to a Minimum''' to '''Optimization to a TS (Berny)'''. Choose to calculate the force constants '''Once''' and in the Additional keyword box at the bottom, type '''Opt=NoEigen'''. The latter stops the calculation crashing if more than one imaginary frequency is detected during the optimization which can often happen if the guess transition structure is not good enough. Submit the job. If the job completes successfully, you should have optimized to the structure shown in [[Mod:phys3#Appendix 2|Appendix 2]] and the frequency calculation should give an imaginary frequency of magnitude 818 cm-1. Animate the vibration and ensure that it is the one corresponding to the Cope rearrangement.

 

(c) Now we will try optimizing the transition structure again using the frozen coordinate method. Create a new MolGroup ('''File → New → Create MolGroup''') and copy and paste your guess structure into the window again. Now select '''Redundant Coord Editor''' from the '''Edit''' menu. Click on the highlighted file icon at the top left-hand corner (Create a New Coordinate) and a line should appear below saying '''Add Unidentified (?, ?, ?, ?)'''. Now go back to the GaussView window and select two of the terminal carbons from the allyl fragments which form/break a bond during the rearrangement. Return to the coordinate editor and select '''Bond''' instead of '''Unidentified''' and select '''Freeze Coordinate''' instead of '''Add'''. Now click on the icon again to generate another coordinate. This time select the opposite two terminal atoms and again select '''Bond''' and '''Freeze Coordinate'''. Click OK. Now set up the optimization as if it were a minimum and you should see the option '''Opt=ModRedundant''' already included in the input line. Submit the job.

'''Note:''' GaussView allows you to produce an input file with the frozen coordinate specified as e.g. <tt>B 5 1 2.200000 F</tt>. Unfortunately, a recent update to the Gaussian program means it does not recognise this syntax, and just ignores this line. This means that the coordinate ends up being optimised rather than frozen. Therefore do not use this method, but ensure the guess structure has suitable guess transition bond distances(~2.2 Å) using the ''Modify Bond'' tool in GaussView --[[User:Rzepa|Rzepa]] 14:39, 29 October 2012 (UTC)

 

(d) When the job has finished, open the chk file. You should find that the optimized structure looks a lot like the transition you optimized in section (b), except the bond forming/breaking distances are fixed to 2.2 Å. Now we are going to optimize them too. Open the '''Redundant Coord Editor''' from the '''Edit''' menu again and create a new coordinate as before by clicking on the icon, Select one of the bonds that was previously frozen and this time choose '''Bond''' instead of '''Unidentified''' and '''Derivative''' instead of '''Add'''. Repeat the procedure for the other bond. This time you need to set up a transition state optimization but we are not going to calculate the force constants as we did in section (b) (so we leave this option as '''Never'''), instead we will use a normal guess Hessian modified to include the information about the two coordinates we are differentiating along. Change the name of the chk file in '''Link 0''' if you do not want to write over the previous calculation and submit the job. When the calculation has finished, open the chk file, check the bond forming/bond breaking bond lengths and compare the structure to the one you optimized in section (b).

 

(e) Now we will optimize the boat transition structure. We will do this using the '''QST2''' method. In this method, you can specify the reactants and products for a reaction and the calculation will interpolate between the two structures to try to find the transition state between them. You must make sure that your reactants and products are numbered in the same way. Therefore, although our reactants and products are both 1,5-hexadiene, we will need to manually change the numbering for the product molecule so that it corresponds to the numbering obtained if our reactant had rearranged.

e.g.

<center>[[Image:pic3.jpg|200px]]</center>

Open the chk file corresponding to the optimized Ci reactant molecule (''anti2'' in [[Mod:phys3#Appendix 1|Appendix 1]]). Now open a second window and create a new MolGroup. Copy the optimized reactant molecule into the new window. In the same window, now select '''File → New → Add to MolGroup'''. The original molecule should disappear and a green circle should appear at the top left-hand corner with a '''2''' next to it. Clicking on the down arrow by the '''2''' will take you back to the original window and you will see your molecule again. This is how we read multiple geometries into GaussView. Go back to window '''2''', and copy and paste the reactant molecule a second time. This is going to be the product molecule and will be the molecule on which we need to change the numbering. If you now click on the icon showing two molecules side by side, then you can view both molecules simultaneously.

Now go to the '''View''' menu and select '''Labels''' so that you can see the numbering on both structures. Orient the two structures separately so they look something like the following:

{| align="center"
|- align="center"
|
[[Image:pic4a.jpg|200px]]
|
[[Image:pic4b.jpg|200px]]
|- align="center"
| align="center" | ''Reactant''
| align="center" | ''Product''
|}

 

Now click on the product structure. Go to the '''Edit''' menu and select '''Atom List'''. Starting from Atom 1 on the reactant, go through and renumber all the atoms on the Product so that they match the reactant molecule, e.g. for the numbering above you would start by changing atom '''6''' on the product molecule to atom '''3'''. The other atom numbers will update as you do this so make sure you do it in the correct order. At the end, the numbering on your two molecules should correspond to each other in the following way:

 

{| align="center"
|- align="center"
|
[[Image:pic5a.jpg|200px]]
|
[[Image:pic5b.jpg|200px]]
|- align="center"
| align="center" | ''Reactant''
| align="center" | ''Product''
|}

 

Now we will set up the first '''QST2''' calculation. Go to the '''Gaussian''' menu and select '''Job Type''' as '''Opt+Freq''', and optimize to a transition state. This time you will have two options - '''TS (Berny)''' which we used in the previous calculations and '''TS (QST2)'''. Select '''TS (QST2)'''. Submit the job.

You will find that the job fails. To see why, open the chk file you created and view the structure. You will see that it looks a bit like the chair transition structure but more dissociated. In fact when the calculation linearly interpolated between the two structures, it simply translated the top '''allyl''' fragment and did not even consider the possibility of a rotation around the central bonds. It is clear that the QST2 method is never going to locate the boat transition structure if we start from these reactant and product structures.

Now go back to the original input file where you set up your QST2 calculation. We will now modify the reactant and product geometries so that they are closer to the boat transition structure. Click on the reactant molecule first and select the central '''C-C-C-C''' dihedral angle (i.e. '''C2-C3-C4-C5''' for the molecule above) and change the angle to 0o. Then select the inside '''C-C-C''' (i.e. '''C2-C3-C4''' and '''C3-C4-C5''' for the molecule above) and reduce them to 100o. Do the same for the product molecule. Your reactant and product molecules should now look like the following:

 

{| align="center"
|- align="center"
|
[[Image:pic6a.jpg|200px]]
|
[[Image:pic6b.jpg|200px]]
|- align="center"
| align="center" | ''Reactant''
| align="center" | ''Product''
|}

 

Set up the QST2 calculation again, renaming both the chk file under '''Link 0''' and the input file. Run the job again. This time it should converge to the boat transition structure. Check that there is only one imaginary frequency and visualize its motion.

The object of this exercise is to illustrate that although the QST2 method is has some advantages because it is fully automated, it can often fail if your reactants and products are not close to the transition structure. There is another method, the '''QST3''' method, that allows you to input the geometry of a guess transition structure also and this can often be more reliable. If you have time, you can try generating a guess boat transition structure and see if you can get the calculation to converge using the original reactant and product molecules. Remember to check the atom numbers in the transition structure are in the right order.

 

(f) Take a look at your optimized chair and boat transition structures. Which conformers of 1,5-hexadiene do you think they connect? You will find that it is almost impossible to predict which conformer the reaction paths from the transitions structures will lead to. However, there is a method implemented in Gaussian which allows you to follow the minimum energy path from a transition structure down to its local minimum on a potential energy surface. This is called the '''Intrinsic Reaction Coordinate''' or '''IRC''' method. This creates a series of points by taking small geometry steps in the direction where the gradient or slope of the energy surface is steepest.

Open the chk file for one of your optimized chair transition structures. Under the '''Gaussian''' menu, select '''IRC''' under the '''Job Type''' tab. You will be presented with a number of options. The first is to decide whether to compute the reaction coordinate in one or both directions. As our reaction coordinate is symmetrical, we will only choose to compute it in the forward direction. Normally you would do both forward and reverse, either in one job or in two separate jobs. You are also given the option to calculate the force constants once, at every step along the IRC or to read them from the chk file. You would use the latter option if you have previously run a frequency calculation. In this case, to avoid confusion with chk files, we will just recompute them at the beginning of the calculation. (The '''IRCMax''' option can also be specified here. This takes a transition structure as its input, and finds the maximum energy along a specified reaction path, taking into account zero-point energy etc., and produces all the quantities needed for a variational transition state theory calculation. We will leave this unchecked for the purposes of this exercise.) The final option to consider is the number of points along the IRC. The default is '''6''' but this is normally never enough. Let's change this to 50 and see how the calculation progresses. Change the name of the chk file under '''Link 0''' and submit the job. The job will take a while so now is a good time to take a coffee break...

When the IRC calculation has finished, open the chk file with all the intermediate geometries and see how the calculation has progressed. You will find that it hasn't reached a minimum geometry yet. This leaves you three options: (i) you can take the last point on the IRC and run a normal minimization; (ii) you can restart the IRC and specify a larger number of points until it reaches a minimum; (iii) you can redo the IRC specifying that you want to compute the force constants at every step. There are advantages and disadvantages to each of these approaches. Approach (i) is the fastest, but if you are not close enough to a local minimum, you may end up in the wrong minimum. Approach (ii) is more reliable but if too many points are needed, then you can also veer off in the wrong direction after a while and end up at the wrong structure. Approach (iii) is the most reliable but also the most expensive and is not always feasible for large systems. You can try any or all of these approaches and see which conformation you end up in.

 

(g) Finally we need to calculate the activation energies for our reaction via both transition structures. To do this we will need to reoptimize the chair and boat transition structures using the '''B3LYP/6-31G*''' level of theory and to carry out frequency calculations. You can start from the HF/3-21G optimized structures. Once the calculations have converged, compare both the geometries and the difference in energies between the reactants and transition states at the two levels of theory. What you should find is that the geometries are reasonably similar, but the energy differences are markedly different.

As a consequence of this, it is often more computational efficient to map the potential energy surface using the low level of theory first and then to reoptimize at the higher level as we have done in this exercise.

The experimental activation energies are 33.5 ± 0.5 kcal/mol via the chair transition structure and 44.7 ± 2.0 kcal/mol via the boat transition structure at 0 K. If you take the values computed at 0 K, how close are they to the experimental values? You can also find the energies with thermal correction at 298.15 K under the Thermochemistry data in the output file. If you have time, you can recompute them at higher temperature. Alternatively, you can use the utility program '''FreqChk''' to obtain energies at a different temperature. This only requires the chk file from a frequency calculation and allows you to retrieve frequency and thermochemistry data as well as calculating them with an alternate temperature, pressure, scale factor, and/or isotope substitutions. The '''FreqChk''' utility program can be accessed from '''Gaussian03W'''. Launch '''Gaussian03W'''. Select '''utilities''' from the menu and click on '''FreqChk''' to launch the utility program. You will be prompted for a chk file. Select your chk file from the C:\G03W\Scratch directory and follow the instructions from this [http://www.gaussian.com/g_tech/g_ur/u_freqchk.htm web link] to proceed.

 

=== Appendix 1 ===

 

{| border="1" cellpadding="5"
|- align="center"
| width="150" | '''Conformer'''
| width="150" | '''Structure'''
| width="100" | '''Point Group'''
| width="200" | '''Energy/Hartrees HF/3-21G'''
| width="200" | '''Relative Energy/kcal/mol'''
|- align="center"
| ''gauche1''
|
[[Image:gauche1.jpg|150px]]
| C2
| -231.68772
| 3.10
|- align="center"
| ''gauche2''
|
[[Image:gauche2.jpg|150px]]
| C2
| -231.69167
| 0.62
|- align="center"
| ''gauche3''
|
[[Image:gauche3.jpg|150px]]
| C1
| -231.69266
| 0.00
|- align="center"
| ''gauche4''
|
[[Image:gauche4.jpg|150px]]
| C2
| -231.69153
| 0.71
|- align="center"
| ''gauche5''
|
[[Image:gauche5.jpg|150px]]
| C1
| -231.68962
| 1.91
|- align="center"
| ''gauche6''
|
[[Image:gauche6.jpg|150px]]
| C1
| -231.68916
| 2.20
|- align="center"
| ''anti1''
|
[[Image:anti1.jpg|150px]]
| C2
| -231.69260
| 0.04
|- align="center"
| ''anti2''
|
[[Image:anti2.jpg|150px]]
| Ci
| -231.69254
| 0.08
|- align="center"
| ''anti3''
|
[[Image:anti3.jpg|150px]]
| C2h
| -231.68907
| 2.25
|- align="center"
| ''anti4''
|
[[Image:anti4.jpg|150px]]
| C1
| -231.69097
| 1.06
|}

 

=== Appendix 2 ===

{| cellpadding="5"
|- align="center"
|
[[Image:appendix2a.jpg|300px]]
|- align="center"
| ''C2h Chair Transition State''
|- align="center"
|- align="center"
|- align="center"
|
[[Image:appendix2b.jpg|300px]]
|- align="center"
| ''C2v Boat Transition State''
|}

 

=== Results Table ===

 

''' Summary of energies (in hartree) '''

{| border="1" cellspacing="1" cellpadding="10"
|-
| ''' '''
!colspan="3"|'''HF/3-21G'''
!colspan="3"|'''B3LYP/6-31G*'''
|-
| ''' '''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
| width="125" align="center" | '''Electronic energy'''
| width="125" align="center" | '''Sum of electronic and zero-point energies'''
| width="125" align="center" | '''Sum of electronic and thermal energies'''
|-
| ''' '''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| ''' '''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
|-
| '''Chair TS'''
| align="center" | -231.619322
| align="center" | -231.466705
| align="center" | -231.461346
| align="center" | -234.556983
| align="center" | -234.414919
| align="center" | -234.408998
|-
| '''Boat TS'''
| align="center" | -231.602802
| align="center" | -231.450929
| align="center" | -231.445300
| align="center" | -234.543093
| align="center" | -234.402340
| align="center" | -234.396006
|-
| '''Reactant (''anti2'')'''
| align="center" | -231.692535
| align="center" | -231.539539
| align="center" | -231.532566
| align="center" | -234.611710
| align="center" | -234.469203
| align="center" | -234.461856
|}

 *1 hartree = 627.509 kcal/mol 

''' Summary of activation energies (in kcal/mol) '''

{| border="1" cellspacing="1" cellpadding="10"
|-
| ''' '''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''HF/3-21G'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''B3LYP/6-31G*'''
| width="125" align="center" | '''Expt.'''
|-
| ''' '''
| width="125" align="center" | '''at 0 K '''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
| width="125" align="center" | '''at 298.15 K'''
| width="125" align="center" | '''at 0 K'''
|-
| '''ΔE (Chair)'''
| align="center" | 45.70
| align="center" | 44.69
| align="center" | 34.06
| align="center" | 33.17
| align="center" | 33.5 ± 0.5
|-
| '''ΔE (Boat)'''
| align="center" | 55.60
| align="center" | 54.76
| align="center" | 41.96
| align="center" | 41.32
| align="center" | 44.7 ± 2.0
|}

 

==The Diels Alder Cycloaddition==

In this exercise, you will characterise transition structures using any of the methods described above in the tutorial: the choice is up to you. In addition, you will look at the shape of some of the molecular orbitals. To help you structure your report, there is a data/discussion sheet at the end of this section.

[[Image:mb_da1.jpg |right|thumb|Diels Alder cycloaddition]]
The Diels Alder reaction belongs to a class of reactions known as pericyclic reactions. The π orbitals of the dieneophile are used to form new σ bonds with the π orbitals of the diene. Whether or not the reactions occur in a concerted stereospecific fashion ('''allowed''') or not ('''forbidden''') depends on the number of π electrons involved. In general the HOMO/LUMO of one fragment interacts with the HOMO/LUMO of the other reactant to form two new bonding and anti-bonding MOs. The nodal properties allow one to make predictions according to the following rule:

''If the HOMO of one reactant can interact with the LUMO of the other reactant then the reaction is '''allowed'''.''

''The HOMO-LUMO can only interact when there is a significant overlap density. If the orbitals have different symmetry properties then no overlap density is possible and the reaction is '''forbidden'''.''

If the dieneophile is substituted, with substituents that have π orbitals that can interact with the new double bond that is being formed in the product, then this interaction can stabilise the regiochemistry (i.e. head to tail versus tail to head) of the reaction. In this exercise you will study the nature of the transition structure for the Diels Alder reaction, both for the prototypical reaction and for the case where both diene and dieneophile carry substituents, and where secondary orbital effects are possible. Clearly, the factors that control the nature of the transition state are quantum mechanical in origin and thus we shall use methods based upon quantum chemistry.

 

Shown on the right is a diagram of the transition state for the Diels-Alder reaction between ethylene and butadiene. The ethylene approaches the cis form of butadiene from above.
[[Image:mb_da2.jpg |right|thumb|Ethylene+Butadiene cycloaddition]]

Before beginning our quantitative study, it is helpful to discuss the interaction of the π orbitals in a simple qualitative way.

''You will confirm some of these considerations in your computations.''

The principal orbital interactions involve the π/ π* orbitals of ethylene and the HOMO/LUMO of butadiene. It is referred to as [4s + 2s] since one has 4 π orbitals in the π system of butadiene. The orbitals of ethylene and butadiene and ethylene can be classified as symmetric '''s''' or anti-symmetric '''a''' with respect to the plane of symmetry shown.

The HOMO of ethylene and the LUMO of butadiene are both '''s''' (symmetric with respect to the reflection plane) and the LUMO of ethylene and the HOMO of butadiene are both '''a'''. Thus it is the HOMO-LUMO pairs of orbital that interact, and energetically, the HOMO of the resulting adduct with two new σ bonds is '''a'''.

 

=== Exercise ===

Use the the AM1 semi-empirical molecular orbital method for these calculations (to start with).

i) Use GaussView to build cis butadiene, and optimize the geometry using Gaussian. Plot the HOMO and LUMO of cis butadiene and determine its symmetry (symmetric or anti-symmetric) with respect to plane.

''There are two ways to do this in GaussView. One is: Select '''Edit→MOs'''. Select the HOMO and the LUMO from the MO list (highlights it yellow). Click the button '''Visualise''' (not Calculation), then '''Update'''. Alternately, having calculated the surface for this orbital, you can display it in the main GaussView window for the molecule, from the '''Results→Surfaces''' menu. Select '''Surface Actions→Show Surface'''. Having displayed the surface this way, you can also select '''View→Display Format→Surface''', and change '''Solid''' to '''Mesh'''.''

 

ii) Computation of the Transition State geometry for the prototype reaction and an examination of the nature of the reaction path.

[[Image:mb_da3.jpg |right|thumb|]]

The transition structure has an envelope type structure, which maximizes the overlap between the ethylene π orbitals and the π system of butadiene. One way to obtain the starting geometry is to build the bicyclo system (b) and then remove the -CH2-CH2- fragment. One must then guess the interfragment distance (dashed lines) and optimize the structure, but use any method you wish, based on the tutorial above, to characterise the transition structure. Confirm you have obtained a transition structure for the Diels Alder reaction!

[[Image:mb_da4.jpg |right|thumb|guessing the transition structure]]

Once you have obtained the correct structure, plot the HOMO as in (i). Rotate the molecule so that the symmetry and nodal properties of the system can be interpreted, and save a copy of the image.

 

(iii) To Study the regioselectivity of the Diels Alder Reaction

Cyclohexa-1,3-diene '''1''' undergoes facile reaction with maleic anhydride '''2''' to give primarily the endo adduct. The reaction is supposed to be kinetically controlled so that the exo transition state should be higher in energy.

[[Image:Bearpark_pic_edit_by_jm906.JPG |right|thumb|regioslectivity]]

Locate the transition structures for both 3 and 4. Compare the energies of the endo and exo forms.

Measure the bond lengths of the partly formed σ C-C bonds and the other C-C distances. Make a sketch with the important bond lengths. Measure the orientation, (C-C through space distances between the -(C=O)-O-(C=O)- fragment of the maleic anhydride and the C atoms of the “opposite” -CH2-CH2- for the exo and the “opposite” -CH=CH- for the endo). The structure must be a compromise between steric repulsions of the -CH2-CH2- fragment and the maleic anhydride for the exo versus secondary orbital interactions between the π systems of -CH=CH- and -(C=O)-O-(C=O)- fragment for the endo.

Plot the HOMO as in the previous exercise. Examine carefully the nodal properties of the HOMO between the -(C=O)-O-(C=O)- fragment and the remainder of the system. What can you conclude about the so called “secondary orbital overlap effect”?

=== Suggested Discussion ===

Use this template as a guide. Screen images can be saved from the GaussView '''File''' menu.

''For cis butadiene'': 
Plot the HOMO and LUMO and determine the symmetry (symmetric or anti-symmetric) with respect to the plane.

''For the ethylene+cis butadiene transition structure'': 
Sketch HOMO and LUMO, labeling each as symmetric or anti symmetric.

Show the geometry of the transition structure, including the bond-lengths of the partly formed σ C-C bonds.

What are typical sp3 and sp2 C-C bondlengths? What is the van der Waals radius of the C atom? What can you conclude about the C-C bondlength of the partly formed σ C-C bonds in the TS.

Illustrate the vibration that corresponds to the reaction path at the transition state.
Is the formation of the two bonds synchronous or asynchronous?
How does this compare with the lowest positive frequency?

Is the HOMO at the transition structure '''s''' or '''a'''?

Which MOs of butadiene and ethylene have been used to form this MO?
Explain why the reaction is allowed.

''For the cyclohexa-1,3-diene reaction with maleic anhydride'': 
Give the relative energies of the exo and endo transition structures.
Comment on the structural difference between the endo and exo form. Why do you think that the exo form could be more strained?
Examine carefully the nodal properties of the HOMO between the -(C=O)-O-(C=O)- fragment and the remainder of the system. What can you conclude about the so called “secondary orbital overlap effect”?
(There is some discussion of this in Ian Fleming's book 'Frontier Orbitals and Organic Chemical Reactions').

''Further discussion'': 
What effects have been neglected in these calculations of Diels Alder transition states?

Look at published examples and investigate further if you have time.
(e.g. {{DOI|10.1021/jo0348827}})

----
See also: [[Mod:timetable|Timetable]],[[Mod:lectures|Intro lecture]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:phys3|Module 3]]

© 2008-2011, Imperial College London

Talk:Mod:pdg08mod1

2012-03-05T10:39:25Z

Pd05: Created page with " Cpd dimers: Energies are correct. Good answer. Taxol: Good to see you thinking through and analysing the most obvious conformers. Carbene: Analysis? Glycosidat..."

Cpd dimers: Energies are correct. Good answer.

Taxol: Good to see you thinking through and analysing the most obvious conformers.

Carbene: Analysis?

Glycosidation: ?

Mini-project: ?

Overall: What happened? Where’s the rest of your project?

Talk:Mod:rjg286

2012-03-05T10:39:17Z

Pd05: Created page with " Cpd dimers: Your calculations are correct but you’ve got the isomers mixed up! A discussion of thermo/kinetic control would have been nice to show you really understand the..."

Cpd dimers: Your calculations are correct but you’ve got the isomers mixed up! A discussion of thermo/kinetic control would have been nice to show you really understand the concepts involved. This logic isn’t entirely sound, it’s possible for the kinetic and thermodynamic product of a reaction to be the same thing.

Taxol: Your energies are way off, and your jmol of 10 is definitely not in a chair as you state.

Carbene: Try getting used to using nomenclature like ‘syn’ and ;anti’ rather than ‘closer’ or ‘further away’. Did you notice any issues with symmetry when calculating the MOs?

Glycosidation: ?

Mini-project: ?

Overall: What happened to the rest of your project? It started off so well.

Talk:Mod:kandyrocks1

2012-03-05T10:39:06Z

Pd05: Created page with " Cpd dimers: Good discussion and excellent answer. Taxol: Good to see you analysing the three most obvious conformers of the molecule. Another very good discussion and an..."

Cpd dimers: Good discussion and excellent answer.

Taxol: Good to see you analysing the three most obvious conformers of the molecule. Another very good discussion and answer.

Carbene: Great answer.

Glycosidation: The excellence continues . . .

Mini-project: Glad to see you’ve chosen your own project. Excellent presentation of your NMR results. Hmmm, ‘blah blah blah stretches’? Those sound interesting, would you care to elaborate? I’m also interested in the presence of blah and blah, I’ve never heard of these functional groups before. Careless!

Overall: Excellent introductions throughout. A great piece of coursework significantly let down by your mini project! Did you run out of time? Proof your work properly in the future.

Talk:Mod:mod1 aal109

2012-03-05T10:38:39Z

Pd05: Created page with " Cpd dimers: Excellent answer. Taxol: Nice to see the reaction mechanism. Good to see you producing such a thorough analysis. However, do I really need to see the bond an..."

Cpd dimers: Excellent answer.

Taxol: Nice to see the reaction mechanism. Good to see you producing such a thorough analysis. However, do I really need to see the bond angle for the entire molecule? Think about an organic paper, all the vital information is in the paper itself whereas extraneous, although potentially important, information is in the SI. Highlighting just the important and necessary information will also allow you to convey your results to a reader with more impact. Still, excellent answer.

Carbene: Excellent.

Glycosidation: Excellent discussion on MM2/MOPAC. Did you notice any similarities between structures/energies of 9/11?

Mini-project: Possibly the best mini-project I’ve ever had the pleasure to mark. An interesting problem and very well analysed. It’s a difficult problem, I wonder what Venkateswarlu have actually made?

Overall: Very well done.

Talk:Mod:RM13Q4

2012-03-05T10:38:18Z

Pd05: Created page with " Cpd dimers: “Observed experimentally” is a preferable phrase to “been seen”. Jmols? It would have been nice to have an in depth explanation of thermo/kinetic control ..."

Cpd dimers: “Observed experimentally” is a preferable phrase to “been seen”. Jmols? It would have been nice to have an in depth explanation of thermo/kinetic control but it reads as if you understand the concepts involved. A very in depth analysis here.

Taxol: I do like mechanisms to be incorporated. The structures of you higher energy conformer is incorrect (look at the bicyclic rings). Still, you have a thorough and detailed discussion. Good work.

Carbene: Nice to see you caught the lack of orbital symmetry. This is actually caused by a bug in the implementation of PM6 is ChemBio. Can you think of a reason why there is such a pronounced difference between the two alkenes? The reason for the change in IR spectra is a lot simpler that you think. Remember, you were asked to model the orbitals of the molecule. Is there any sort of interaction or donation that could explain all the observations?

Glycosidation: If you plan to have so many figures, it might be an idea to label them in the future. A nice, slightly off tangent, MO investigation but a good way to highlight the differences between MM2 and MOPAC methods. However, you could have explored this a little further. Do you notice any similarities between A and C, say, when using MOPAC? Perhaps you should think of the system in terms of nucleophilic attacks. Still, this is a good, and quite enthusiastic, exploration of computational chemistry.

Mini-project: A shame you didn’t choose your own project. Good to see a graphical presentation of the differences involved. I wouldn’t worry too much about the OR, the calculations are never that accurate. Good to see you thinking of the selectivity involved in the reaction to make cubebol.

Overall: Excellent introduction and quite thorough referencing. It’s a personal (and journal specific if you look in the literature) preference but I prefer all the references to be collected at the end; still, this is entirely up to you. A very enthusiastic project, I liked you further explorations, although it seems they sometimes took preference over a more detailed exploration of the given problem.

Talk:COOKIESANDCREAM

2012-03-05T10:37:33Z

Pd05: Created page with " Cpd dimers: Good outline of the differences between dimer energies. Hmmm, missing a reference here are we? Good discussion of thermo/kinetic control. Taxol: Twist coat?..."

Cpd dimers: Good outline of the differences between dimer energies. Hmmm, missing a reference here are we? Good discussion of thermo/kinetic control.

Taxol: Twist coat? Is this a new type of conformer I’ve never heard of? Why just chair and twist boat? Where’s the boat conformation? “Stabler:” is not a word, “more stable” is the phrase you were looking for. Not a bad answer though.

Carbene: Good to see you caught the PM6 symmetry bug. Where’s the analysis though?

Glycosidation: Your energies look okay but again, where’s the discussion or analysis?

Mini-project: This is not a finished piece of work. You essentially state this at the end. Poor effort.

Overall: Nice name, however, it doesn’t quite make up for the lack of an introduction. Could have been proofed a little better as well (Hint: I find that initially labelling references, figure or table numbers as XX and then searching the document for XX before you submit is an easy way to be sure you’ve correctly inserted everything). It feels like you really ran out of time after taxol. If you don’t offer any discussion or analysis I can’t give you marks.

Talk:Mod1GL1990

2012-03-05T10:37:02Z

Pd05: Created page with " Cpd dimers: Could be written a little more concisely, but very good answers nonetheless. Taxol: Your 9 chair jmol is definitely not a chair. Why analyse just the chair and..."

Cpd dimers: Could be written a little more concisely, but very good answers nonetheless.

Taxol: Your 9 chair jmol is definitely not a chair. Why analyse just the chair and twist boat, what happened to the boat? Reduces what strain exactly?

Carbene: Good to see you noticed the issue of PM6 and orbital symmetry. I like your moving jmols.

Glycosidation: Okay, MM2 and MOPAC take into account different factors, but why do they do this? What is the basic, fundamental difference between the two methods? Do you notice any similarities between the energies of the different isomers when using the different methods? How will the difference in the methods affect the calculated energies? Not a bad attempt though. As an aside, “produce products” is a terrible phrase to use.

Mini-project: A shame you didn’t choose your own project. Nice introduction though. Good to see you highlighting the difference in NMR shifts. A good way to visually highlight data like this to a reader is through the use of a graph; say a bar chart. A little brief, but a good attempt all the same.

Overall: A pretty good attempt. It feels like you slightly ran out of time for the glycosidation and mini-project, the analysis there was a little brief but still, well done.

Talk:Mod:lg1109mod1

2012-03-05T10:36:24Z

Pd05: Created page with " Cpd dimers: Instead of ‘according to the table’, say something like ‘according to our calculations’, the table is not the source of the answers, your calculations are...."

Cpd dimers: Instead of ‘according to the table’, say something like ‘according to our calculations’, the table is not the source of the answers, your calculations are. Good to see you clearly outlining the differences in your table and that you’re relating energies to structural features. You could have done with a better description of kinetic/thermodynamic control.

Taxol: Where are the jmols? I’d have liked to examine your structures. It is better to show that one conformation is lower in energy than another with the results of calculations, rather than breezing over the fact in your text. No mention of hyperstable alkenes?

Carbene: “Will give lots of information” is not the most scientific of language. You state that the molecule has Cs symmetry. Is this observed in your calculated orbitals?

Glycosidation: Good to see you’ve included jmols and that you’ve minimised the structures, but where’s the analysis?

Mini-project: Five tables and three sentences do not a mini-project make.

Overall: Disappointing. If you don’t engage with the problem and offer some sort of analysis or evaluation of the problem then I can’t give you any marks

Talk:Mod:Sabrina

2012-03-05T10:34:34Z

Pd05: Created page with " Cpd dimers: Good to see you analysing the energies in terms of structural effects, but do you really think this is the origin of the kinetic control observed? Taxol: Will ..."

Cpd dimers: Good to see you analysing the energies in terms of structural effects, but do you really think this is the origin of the kinetic control observed?

Taxol: Will the relative energies of the structures give you insight into which product is formed faster? Maybe just poor wording but this does not demonstrate a strong understanding of kinetic/thermodynamic control. Why assume that the twist-boat does not exist? Try to model it, see if it does. And what happened to the boat conformation? The thermodynamic product of a reaction can also be the kinetic product! Read up on this! Good to see you investigating the differences between MM2 and MMFF94. Very good discussion of hyperstable alkenes.

Carbene: You shouldn’t have to explain the meaning of syn, knowledge of its meaning should be assumed. You also don’t really need to explain the processes you went through to run a file on SCAN (think of this as an organic paper, this info would be kept to the experimental or SI unless it was vital to the understanding of the discussion). Very good discussion otherwise.

Glycosidation: Very good discussion on choice of protecting group and the differences between MM2 and MOPAC. Very good discussions all round in fact, taking into account the differences mentioned above and the burgi-dunitz angle.

Mini-project: I’m glad you chose your own project. A discussion (and arrows) of the reaction mechanism would have been nice. Excellent observation of the differences in planarity at the nitrogen. An excellent, well presented (and reader friendly) analysis of your NMR results. But shy didn’t you simply renumber the atoms yourself so they made more sense? Eugh, Hartrees? Why suddenly use them when you’ve been on kcal mol-1 for the rest of your document? You generally use IR to identify particular functional groups, therefore I imagine it would actually be quite useful in real life to determine between the two isomers.

Overall: The whole thing got better the more I read. One of the better mini-projects I’ve read in a while, it read like you actually engaged with and thought about what you were doing, and an excellent attempt overall. Although it’s a pity about the first couple of sections, you certainly have it in you to have done a better job on them. Make sure to read up on kinetic/thermodynamic control!

Talk:Mod:jgh001

2012-03-05T10:34:21Z

Pd05: Created page with " Cpd dimers: Well written. Very good discussion. However, it would have been nice to view some jmols of your structures. Taxol: Good to see you’re thinking in terms of..."

Cpd dimers: Well written. Very good discussion. However, it would have been nice to view some jmols of your structures.

Taxol: Good to see you’re thinking in terms of obvious structural rearrangements rather than randomly moving atoms around. It would have been good to include both the breakdown of energies, rather than just showing the totals, and jmol structures of the other taxol configurations. Out of interest, could you find any further conformations of the 6-membered ring? What were the energies of those?

Carbene: Excellent discussion.

Glycosidation: Good answer but just missing the full picture. Why, perhaps in terms of a nucleophilic attack, would A be lower in energy than A’? What, in terms of boundaries, can molecules do under MOPAC that they cannot do under mechanics? Good effort though.

Mini-project: A shame you didn’t chose your own project. Another good introduction though. When presenting comparisons of data like this, you have to think of the best way to present it, rather than plonking it in a table. What we’re interested in here is the accuracy of your results, meaning the difference between yours and those in the literature. A further exploration of this would have been beneficial. Good to see you examining the H spectra.

Overall: Well written introductions and discussions. Overall, a very good effort.

Talk:Mod:GD409 module1

2012-02-06T12:51:37Z

Pd05: Created page with " Cpd dimers: Your explanation of endo selectivity is a little meandering. Try to be more concise. Good to see you relating energies to structural features. And that you are a..."

Cpd dimers: Your explanation of endo selectivity is a little meandering. Try to be more concise. Good to see you relating energies to structural features. And that you are aware of the limitations of MM2.

Taxol: The rotation is not around the carbonyl bond! Again, your answer is a little meandering.

Carbene: Well answered. However, look at your MOs. With a plane of symmetry in your molecule, would you not expect the MOs to be symmetrical as well?

Glycosidation: Is that the real reason you didn’t choose H? If you mention something earlier in your work you should say where. Good that you noticed similarities in MOPAC energies. Your discussion could have expanded on this a little. Particularly on why this is not true for MM2 (you mention only that the two methods use different parameters; what are these parameters and why should they give different answers?).

Mini-project: A shame you didn’t choose your own project. The sum of the differences between your calculated and the literature values will NOT tell you anything relevant about the accuracy of your calculations and will NOT tell you which isomer is preferred! This is a major flaw in your analysis! Very accurate optical rotation calculation; I’d say they are amazingly, rather than reasonably, close.

Overall: You seem to understand the questions, your answers are largely correct, but your English is letting you down. Really try to phrase things properly and concisely; shorten your sentences and try not to needlessly repeat yourself.

Talk:Mod:chilong module1

2012-02-06T12:50:50Z

Pd05: Created page with " Cp dimers: Your explanation could be a little more concise. Nice to see you realise the limitations of an MM approach. Try to use either numbers or letters to label your str..."

Cp dimers: Your explanation could be a little more concise. Nice to see you realise the limitations of an MM approach. Try to use either numbers or letters to label your structures, not both.

Taxol: Good to see you exploring different conformations of the molecule and comparing the differences.

Carbene: Good that you’ve noticed a bug in the programme. Nice discussion.

Glycosidation: I wouldn’t say ‘not as good’, its just a different approach. Good to see that you’ve noticed A and C are equivalent for MOPAC but a more in depth discussion on the differences of MOPAC and MM2 would have been nice. You’ve discussed angle of attack but you’ve not mentioned what this is usually called! Drew is the past form of draw and is incorrectly used here, you should be using drawn, the past participle. You draw a bond or you drew a bond, however, a bond is drawn.

Mini-project: Good to see you’ve chosen your own project, quite a nice one as well. Very good graphical representation of the difference between the literature and your calculated NMR spectra. If you calculated the H spectra, why didn’t you put them in? Nice to see you’re not taking what’s in the literature as gospel. A very good project.

Overall: Your English could use a little bit of work and your explanations could be a little more concise (although they got better towards the end). However, your answers and analyses were generally pretty good. Well done.

Talk:La409Mod1

2012-02-06T12:50:02Z

Pd05:

Cp dimers: Good to see you relating energies to structural features of the molecule.

Taxol: Good discussion.

Carbene: Good that you’ve noticed the lack of symmetry in the PM6 results. Good discussion.

Glycosidation: ‘More negative’ isn’t the best English. Your discussion on the differences between MM2 and MOPAC, a t a fundamental level, could have been a little more in depth. Still, you stated the results of the difference. Can you think of a better name for the stabilising interaction you’ve mentioned? Good work.

Mini-project: Glad to see you’ve chosen your own molecule. A more reader-friendly approach to analysing differences between a long list f numbers would be by way of a graph. Nice discussion and inclusion of CD.

Overall: Some good discussions and excellent work. Well done.

Talk:La409Mod1

2012-02-06T12:49:25Z

Pd05: Created page with " Cp dimers: Good to see you relating energies to structural features of the molecule. Taxol: Good discussion. Carbene: Good that you’ve noticed the lack of symmetry i..."

Talk:Mod:elablablagdb

2012-02-06T12:48:55Z

Pd05: Created page with " 1.2.1 Cp dimers: Excellent. Taxol: Another excellent discussion. Carbene: A Baeyer-villager reaction as well? Seems like you almost had too much time on your hands. ..."

1.2.1 Cp dimers: Excellent.

Taxol: Another excellent discussion.

Carbene: A Baeyer-villager reaction as well? Seems like you almost had too much time on your hands. Excellent work.

Glycosidation: Another very thorough well discussed answer.

Mini-project: Mmmm, adamantane. This is an interesting problem you’ve chosen, well worth the extra bit of time it took to find.

Overall: What can I say? You make this marking malarkey easy. Very well done.

Talk:Mod:Ab mod1

2012-02-06T12:48:35Z

Pd05: Created page with " Cp dimers: The endo rule is an empirical observation, not scientific fact. FO are the real reason this is observed, keep this in mind! Would have been nice to see an analysi..."

Cp dimers: The endo rule is an empirical observation, not scientific fact. FO are the real reason this is observed, keep this in mind! Would have been nice to see an analysis based on the breakdown of energies related to structural features of the molecule.

Taxol: Saying something “thus may be” isn’t the greatest English. Out of interest, how would you be able to tell which isomer is the kinetic product? Nice discussion.

Carbene: Read that first sentence again! Glad you noticed the lack of symmetry delivered by PM6.

Glycosidation: You’ve stated that MOPAC and MM2 consider different aspects of the molecule in their calculations. Take this forward another step. How does this to into account, say, bond formation for the two methods? Does this have any implications for the calculation? Good effort though.

Mini-project: Glad to see you choosing your own molecule. Excellent attempt.

Overall: Good discussions, although a little bit skimpy at times. A good piece of work.

Talk:Module 1 - ceg09

2012-02-06T12:48:04Z

Pd05: Created page with " Cpd dimers: Excellent discussion. Good use of jmols. Taxol: Another excellent discussion. Carbene: Glad you noticed the PM6 bug. Good work. Glycosidation: Good t..."

Cpd dimers: Excellent discussion. Good use of jmols.

Taxol: Another excellent discussion.

Carbene: Glad you noticed the PM6 bug. Good work.

Glycosidation: Good to see you discussing the implications of mechanics versus QM.

Mini-project: A bit of a shame you didn’t choose your own molecule for the project. Still, a good piece of work. Nice to see you analysing the difference in NMRs, graphically, although you don’t really have to state that a graph displays data graphically. A thorough analysis.

Overall: An excellent project, and very well written too.

Talk:Mod:clc09

2012-02-06T12:47:41Z

Pd05: Created page with " Cpd dimers: Although your answers are correct, your discussion could use a little more work. It’s a tad brief, try to flesh your answers out, even use more diagrams or jmol..."

Cpd dimers: Although your answers are correct, your discussion could use a little more work. It’s a tad brief, try to flesh your answers out, even use more diagrams or jmols to describe what you mean.

Taxol: All in all, you have the right ideas but it’s a little sketchy. Are there any other conformations the cyclohexane ring can take? How does this affect the energy of the molecule? What does the breakdown of energies of both isomers tell you about each conformation? Although it’s good to keep things concise try expanding on your answers with a fuller and more thorough analysis.

Carbene: Nice use of jmols. Again, though, your answer is lacking analysis. It’s not enough to simply state what is going on. Why is one alkene more electron rich than the other?

Glycosidation: Calculations but no analysis. If you don’t analyse your results then you’re missing out on a whole bucket full of (pretty easy) marks.

Mini-project: A pity you didn’t chose your own project. Nice to see you trying N and H NMR. Good use of jmols for the IR section. You state that NMR spectra are enough to differentiate between the molecules, if you make a statement like this you really need to back it up with evidence. It is not enough to simply paste spectra and tables, you must guide the reader through your analysis and thought process. For instance, compare the differences between your calculated spectra and that of the literature. Where are the differences? Why are there differences? Is the calculation accurate enough? Think of the best way to display this data to the reader (hint: graphs are useful, endless tables of numbers are mind-numbing)

Overall: Your answers were correct overall but largely lacking in analysis. Would also have been nice to see some introductions. Has the feeling of being slightly rushed.

Talk:Mod:ja2209module1

2012-02-06T12:46:51Z

Pd05: Created page with " Cpd dimers: I like your detailed jmols. Taxol: It’s not entirely relevant to compare the hydrogenated product to the alkene, as they are not isomers, but good to see you..."

Cpd dimers: I like your detailed jmols.

Taxol: It’s not entirely relevant to compare the hydrogenated product to the alkene, as they are not isomers, but good to see you trying.

Carbene: I like your solution to the PM6 bug. Good discussion.

Glycosidation: Good to see you’ve noticed that A and C and also B and D are identical for PM6. Also good to see you’re reasoning through reasons for this and why this is not true for MM2. Good discussion.

Mini-project: A shame you didn’t choose your own project, especially given that you had the time to do so. Still, you’ve done a good job. Nice to see an attempt at a more user friendly, visual analysis of the difference in NMRs.

Overall: Could have been proofed a little better. Excellent, if slightly overenthusiastic, referencing. Good introductions all round. Excellent project.

Talk:Sunkiss pl1208 01

2011-03-11T11:30:25Z

Pd05: New page: 1.2.1 Cp dimers: That’s quite a lengthy answer, it’s a good one though. 1.2.2 NAD: Good to see you presenting your minimisation graphically. Excellent analysis. 1.2.3 Taxol: A ver...

1.2.1 Cp dimers: That’s quite a lengthy answer, it’s a good one though.

1.2.2 NAD: Good to see you presenting your minimisation graphically. Excellent analysis.

1.2.3 Taxol: A very good analysis. However, your structure for A is not fully optimised (the energy should be around 48 kcal mol-1).

1.3.1 Carbene: Good to see you’ve picked up on the bug in PM6 and that you are contrasting and comparing the results of more than one method. Another lengthy but thorough analysis.

Mini-project: Good introduction and exploration of the mechanism. A good presentation of your results as well. Some fantastically accurate calculations here. Some well presented conclusions too. An excellent project.

Overall: : We’re not looking for essays, your answers really were FAR too long and I found them rather difficult to wade through after a while; I’m sure you could have summarised the salient points into something less half the length. Although it’s a matter of personal taste, I find rotating Jmols incredibly irritating. Despite the over-enthusiastic length, a very good piece of work.

Talk:Mod:FolarinDuduyemi

2011-03-11T11:30:02Z

Pd05: New page: 1.2.1 Cp dimers: Jmols? Is this supposed hindrance the sole reason behind the kinetic/thermo selectivity? What are the structural features relating to the energy differences between 3/4?...

1.2.1 Cp dimers: Jmols? Is this supposed hindrance the sole reason behind the kinetic/thermo selectivity? What are the structural features relating to the energy differences between 3/4?

1.2.2 NAD: Your MM2 energy looks okay but your structure is incorrect, the carbonyl should be pointing ‘up’. If you had included a jmol I may have been able to find out what was going on.

1.2.3 Taxol: Good energies and structures. Note that it is not valid to compare the alkene/alkane of 9 as they are not isomers.

1.3.1 Carbene: Your molecule has a plane of symmetry yet your orbitals are not symmetrical. This is something I would have expected you to pick up on. The problem is caused by a bug in MOPAC PM6. Moral of the story: question the results the computer gives you, learn to identify these errors and how cope with them. Your IR results are not well presented, your analysis is fine though.

Mini-project: It’s a real pity you couldn’t pick your own project. I don’t really need to see the spectra, the values alone would suffice. It would be much better to have presented the differences between your calculated and the experimental NMR values in a graph in order to discuss the accuracy of your calculations.

Overall: Where were the jmols? It would also have been much better for you to choose your own mini-project from the literature. The presentation of your results could use some work, I found it very difficult to contrast and compare your data, especially as you were leaving almost all of this work up to me.

Talk:Mod 1: CouchMA

2011-03-11T11:29:34Z

Pd05: New page: 1.2.1 Cp dimers: Energies and structures are fine. Could you give a more quantitative answer for 3/4 hydrog? Note that it is not valid to compare 1/2 or 3/4 or5 as they are not isomers....

1.2.1 Cp dimers: Energies and structures are fine. Could you give a more quantitative answer for 3/4 hydrog? Note that it is not valid to compare 1/2 or 3/4 or5 as they are not isomers.

1.2.2 NAD: Good.

1.2.3 Taxol: Energies and structures are fine.

1.3.1 Carbene: Good to see you’ve picked up on the lack of symmetry in the PM6 orbitals. Can you think of why this happened? Good discussion.

Mini-project: That’s quite a flexible molecule and perhaps not the best choice if no 13C data was available. Good to see you’ve tried to predict the 1H spectra.

Overall: Perhaps not the best choice in molecule for your mini-project but a decent attempt nonetheless. Overall, a good piece of work.

Talk:Mod1:jc808

2011-03-11T11:29:18Z

Pd05: New page: 1.2.1 Cp dimers: Energies and structures are fine. What is the basis of the endo rule? It is not valid to compare 5 to 4/3 because they are not isomers. 1.2.2 NAD: Good to see you’re...

1.2.1 Cp dimers: Energies and structures are fine. What is the basis of the endo rule? It is not valid to compare 5 to 4/3 because they are not isomers.

1.2.2 NAD: Good to see you’re presenting your minimisation as a graph. Good discussion.

1.2.3 Taxol: Excellent energies and structures.

1.3.1 Carbene: Your molecule has a plane of symmetry yet your orbitals are not symmetrical. This is something I would have expected you to pick up on. The problem is caused by a bug in MOPAC PM6. Moral of the story: question the results the computer gives you, learn to identify these errors and how cope with them.

Mini-project: Cinchona, not cinchoma. That’s a rather flexible molecule. Jmols? Actually, it’s fair to expect errors of 5-6 ppm in these calculations, so your values are not that bad at all. Good to see you attempting to find a reasoning behind these differences though. A better way to present your data would have been to plot a graph of the differences between your calculated and the experimental NMR data. Are there any other techniques that could determine between the enantiomers? Good project.

Overall: A very good piece of work.

Talk:Hoss.Module1

2011-03-11T11:29:02Z

Pd05: New page: 1.2.1 Cp dimers: The reason lay, not lied. Good discussion but a little meandering, could have been structured better. 1.2.2 NAD: You’re missing a Jmol for 5. A better way to pres...

1.2.1 Cp dimers: The reason lay, not lied. Good discussion but a little meandering, could have been structured better.

1.2.2 NAD: You’re missing a Jmol for 5. A better way to present your minimisation would be by using a graph, ie energy vs. dihedral angle. This would also allow you to highlight the energy minima, as opposed to simply quoting a number. Although it can adopt many conformations, there IS a single, global minima for 7.

1.2.3 Taxol: It would be much nicer to have jmols of all your conformations. Excellent energies and good discussion. What structural features cause a higher strain in the parent alkane?

1.3.1 Carbene: Your molecule has a plane of symmetry yet your orbitals are not symmetrical. This is something I would have expected you to pick up on. The problem is caused by a bug in MOPAC PM6. Moral of the story: question the results the computer gives you, learn to identify these errors and how cope with them.I don’t really need to see the IR spectra. Good discussion.

Mini-project: Personal taste, but I’m not sure how interesting the mechanism of the Diels-Alder reaction is . . . Excellent analysis. However, it’s not conformational rigidity that imbues chemical equivalence but symmetry. Good to see you’re thinking about other techniques (having worked with similar bicyclic compounds, I can tell you that the endo/exo isomers are very easy to distinguish by 1H NMR, once you’ve assigned which is which using a technique like NOESY). A very good project.

Overall: It really is a much better idea to include your jmols as popup windows, especially if your marker is using a tired out old college machine to view your wiki (don’t worry, you didn’t lose any marks due to the departments tight purse strings). This was a very good project.

Talk:Mod 1: Tom Campling

2011-03-11T11:28:45Z

Pd05: New page: 1.2.1 Cp dimers: Energies and structures are fine. What is the basis of the endo rule? What are the structural features causing the difference in bending strain between 3 and 4? 1.2.2 ...

1.2.1 Cp dimers: Energies and structures are fine. What is the basis of the endo rule? What are the structural features causing the difference in bending strain between 3 and 4?

1.2.2 NAD: It’s not quite that MM2 can’t recognise just metals. A better way to display your minimisation would be in a graph of total energy vs dihedral angle. Your answers are correct but a little brief.

1.2.3 Taxol: Your energies are correct but where is your analysis? You need to take me through the work you’ve been doing, show your working.

1.3.1 Carbene: Good to see you’ve picked up on the bug in PM6 and found a way around it. Much better analysis here.

Mini-project: What reaction made these isomers? NMR spectra, not readings. If you’re going to number the atoms in a table, I’m going to have to know which ones are which on the molecule. Nice to see you’re graphically comparing your calculated and experimental shifts but a better property to compare would be the difference alone (say, in a bar chart). So can 13C NMR be applied to distinguish between these isomers? What about any other analytical thechniques?

Overall: Your answers were rather brief and, at times, didn’t really explore the problems at hand. But your structures and energies were all spot on so you obviously understood what you were doing. A strong piece of work.

Talk:Mod:com7

2011-03-11T11:28:32Z

Pd05: New page: 1.2.1 Cp dimers: Jmols? Good energies. Exactly what structural features cause the differences in energies? Where did hydroboration come from? 1.2.2 NAD: Looks good. 1.2.3 Taxol:...

1.2.1 Cp dimers: Jmols? Good energies. Exactly what structural features cause the differences in energies? Where did hydroboration come from?

1.2.2 NAD: Looks good.

1.2.3 Taxol: Excellent energies. Nice to see you examining both MM2 and MMF94.

1.3.1 Carbene: Excellent, you are aware of the bug in MOPAC and you’ve found a way around it. Another very good discussion. But how does the C-Cl bond affect the IR spectra?

Mini-project: Presenting the differences in calculated and experimental NMR data in a table would have been a better way to display the accuracy of your calculations. Have you not assigned the carbons? A mixture of isomers in an NMR would produce two different peaks, not an averaging of one signal. So if 13C and IR are not very good, what will be?

Overall: Your analyses were sometimes a little convoluted and long-winded, the layout of your writing was also sometimes a little hard to follow. Otherwise, some very good work.

Talk:Mod:eb108m1

2011-03-11T11:28:20Z

Pd05: New page: 1.2.1 Cp dimers: Your energies look good, your discussion is also good. 1.2.2 NAD: A better way to present your minimisation to a reader would have been graphically (ie, energy vs. di...

1.2.1 Cp dimers: Your energies look good, your discussion is also good.

1.2.2 NAD: A better way to present your minimisation to a reader would have been graphically (ie, energy vs. dihedral angle). Still, your discussions are good.

1.2.3 Taxol: Excellent energies and discussion.

1.3.1 Carbene: Your molecule has a plane of symmetry yet your orbitals are not symmetrical. This is something I would have expected you to pick up on. The problem is caused by a bug in MOPAC PM6. Moral of the story: question the results the computer gives you, learn to identify these errors and how cope with them.. Excellent discussion otherwise.

Mini-project: That’s not the most conformationally constrained of molecules. Very detailed mechanistic discussion. Good to see you displaying your results graphically, although a bar chart of the differences would have had more impact in commenting on the accuracy of your calculations. Are there any other analytical techniques which would have been of use to you? I imagine simple 1H NMR would be much better than IR or 13C NMR to distinguish between these molecules.

Overall: A very good piece of work.

Talk:Mod:Sc2108 Module 1

2011-03-11T11:28:09Z

Pd05: New page: 1.2.1 Cp dimers: Your jmols for molecules 1 and 2 are the same. Some discussion about kinetic/thermodynamic control would have been nice. 1.2.2 NAD: You don’t really need to highlight...

1.2.1 Cp dimers: Your jmols for molecules 1 and 2 are the same. Some discussion about kinetic/thermodynamic control would have been nice.

1.2.2 NAD: You don’t really need to highlight atoms like this, it should be obvious to your audience from the mechanism alone what is happening. Nice to see a graphical presentation of your minimisation. The graph would also have done alone, there is little need for the table. How come your dihedral angle minimisation is so less detailed for 7? Your jmol for 7 is broken. Good discussion though.

1.2.3 Taxol: These are twist boats, not boats! Good energies though. It is not valid to directly compare the energies of the Taxol intermediates as alkenes and alkanes as they are not isomers.

1.3.1 Carbene: Why do you think PM6 returned incorrect results? Good to see you’re not blindly accepting the results the computer throws at you. Your orbital overlap explanation is a little convoluted. I don’t really need to see the spectra, a table of pertinent peaks would be fine

Mini-project: It’s a real pity you haven’t chosen your own project. It’s good to see you attempted to model the 1H spectra. However, there is absolutely no analysis of the data here or any sort of conclusion.

Overall: A little more proof reading would have been nice. I’m not sure I understand when you say you tried three reactions and they didn’t work, it would still have been good to see what you were attempting, especially if you did spend a lot of time on them. Mini[project aside, a very good piece of work.

Talk:Mod:wyc08

2011-03-11T11:27:35Z

Pd05: New page: 1.2.1 Cp dimers: You don’t really need to give energies in two units, kcal mol-1 is the standard and would do alone. The endo rule does is not always followed! Good to see you relatin...

1.2.1 Cp dimers: You don’t really need to give energies in two units, kcal mol-1 is the standard and would do alone. The endo rule does is not always followed! Good to see you relating energies to structural components. Excellent discussion.

1.2.2 NAD: ‘Methyl ligand’ is not entirely the correct terminology. How did you come by Conformer 2 and 3? How does your analysis prove conformer 1 is of the lowest energy (with respect to dihedral angle)?

1.2.3 Taxol: Excellent energies and good discussion.

1.3.1 Carbene: Great to know you spotted the lack of symmetry in the PM6 computed orbitals. Can you think of a reason for this? The syn bond has a higher electron density so will be stronger than the anti C=C and will also be attacked preferentially by an electrophile. Some good work.

Mini-project: I like your graphical analysis, although you forgot to label which carbon atom corresponds to which bar. It’s not really necessary to show me the calculated spectra, your table is enough. Your analysis here is a little brief. Are there any other analytical techniques which could have been (experimentally) performed? It’s a pity you didn’t have enough time to run any further calculations.

Overall: A good piece of work. It’s a pity you didn’t investigate your project any further.

Talk:Mod1:ch1508

2011-03-11T11:27:19Z

Pd05: New page: 1.2.1 Cp dimers: You really think the endo conformation is that strange? Would have been nice to have a little more about kinetic/thermo control. Excellent discussion and nice to see a ...

1.2.1 Cp dimers: You really think the endo conformation is that strange? Would have been nice to have a little more about kinetic/thermo control. Excellent discussion and nice to see a quantitative analysis of strain.

1.2.2 NAD: A better way to comment on your minimisation (and to show off how much work you did) would be to plot a graph of energy vs. dihedral angle. Sterics and electronic repulsion are not the same thing.

1.2.3 Taxol: Your discussion is good but a little on the short side. Energy for B is correct but A is slightly out as your structure is incorrect (look at the hydrogens on the cyclohexane). Are there any particular interactions which would cause higher strain after hydrogenation of the alkene?

1.3.1 Carbene: Your molecule has a plane of symmetry yet your orbitals are not symmetrical. This is something I would have expected you to pick up on. The problem is caused by a bug in MOPAC PM6. Moral of the story: question the results the computer gives you, learn to identify these errors and how cope with them. A deeper analysis of the interactions between the MOs would have been nice.

Mini-project: They could have used DEPT to assign the carbons, NOE will be the best way. Good to see you graphically analysing the differences in calculated and experimental NMR. That’s a lovely bit of Paint work you’ve done there. Good to see you’re thinking practically about other analytical techniques. Having worked with very similar molecules, I can tell you that the best NOE interactions to observe are between the methylene group and the protons you’ve labelled C or D (if you want to differentiate between endo/exo isomers at least).

Overall: Discussions earlier in your report are perhaps a little low level (you should assume by now your audience does know something about chemistry), this doesn’t detract from the fact that they are good discussion though. It is also good practice to number your compounds sequentially throughout rather than naming them (‘proline derivative’, ‘starting material’ etc). A good report.

Talk:Mod:cb208

2011-03-11T11:27:06Z

Pd05: New page: 1.2.1 Cp dimers: Jmols? Not the clearest explanation of kinetic vs thermodynamic control, or the endo rule. Your energies are good. 1.2.2 NAD: Nice minimisation. Your answers are goo...

1.2.1 Cp dimers: Jmols? Not the clearest explanation of kinetic vs thermodynamic control, or the endo rule. Your energies are good.

1.2.2 NAD: Nice minimisation. Your answers are good, if a little brief.

1.2.3 Taxol: Your cyclohexane in 9 is not in a twist-boat, it’s a chair! Your energies are spot on.

1.3.1 Carbene: Jmols? Your molecule has a plane of symmetry yet your orbitals are not symmetrical. This is something I would have expected you to pick up on. The problem is caused by a bug in MOPAC PM6. Moral of the story: question the results the computer gives you, learn to identify these errors and how cope with them.

Mini-project: An actual mechanism in the ‘Reaction Mechanism’ section would have been nice. It’s a very lucky man who finds any assignments for 13C in the literature. Nice to see you presenting the differences in a graph, pity it’s between the experimental NMRs and not between your predictions and the experimental values. Do you really think C16 will resonate at 218ppm? The molecule would not change its structure!

Overall: Your explanations were a tad shaky in places, you need to be more thorough in your writing to demonstrate a deeper understanding (do not confuse this with adding waffle for the sake of it!). Some good work here though.

Talk:00554846 Org1

2011-03-11T11:26:47Z

Pd05: New page: 1.2.1 Cp dimers: You’ve got your answer the wrong way around! Nice to see a quantitative analysis of the relative alkene strains. 1.2.2 NAD: The information in tables 3 and could have...

1.2.1 Cp dimers: You’ve got your answer the wrong way around! Nice to see a quantitative analysis of the relative alkene strains.

1.2.2 NAD: The information in tables 3 and could have been better presented graphically. Good discussion however.

1.2.3 Taxol: Your energies seem good.

1.3.1 Carbene: Although the molecule has a plane of symmetry, your orbitals are not symmetrical. This is caused by a bug in the MOPAC program. You did notice that something was wrong when comparing your results to the literature, you just got the reason wrong. Programs do have bugs and you need to learn to identify and cope with them. I don’t really need to see the whole IR spectra, your table is fine alone. Your analysis of the IR is a tad confusing. Orbital mixing is not the correct terminology!

Mini-project: A good choice of molecule. Good to see you’re highlighting and presenting the differences between your results and the experimental results. However, this could have been presented much better graphically (ie a bar chart). Would m.p. analysis really be a good way of identifying between the isomers? While x-ray crystallography would allow you to differentiate, the technique comes with a wide range of caveats. 1H NMR would almost certainly be the best method. While there are large inaccuracies involved with predicting these spectra your molecule is very constrained and might not be as bad as you think. This was a good attempt, well done.

Overall: It’s a matter of personal taste but I find rotating Jmols incredibly irritating. Typically, answers should be quoted to 2 d.p. only.

Talk:Mod:md308

2011-03-11T11:26:23Z

Pd05: New page: 1.2.1 Cp dimers: Good results and discussion. 1.2.2 NAD: Nice to see you’re thinking of ways around the lack of support for Mg in MM2. Did you optimise the geometry in terms of the d...

1.2.1 Cp dimers: Good results and discussion.

1.2.2 NAD: Nice to see you’re thinking of ways around the lack of support for Mg in MM2. Did you optimise the geometry in terms of the dihedral angle for 8 as well? Where is the graph? A good, if somewhat brief, discussion.

1.2.3 Taxol: Again, a brief but good answer,

1.3.1 Carbene: Excellent that you noticed the lack of symmetry in the orbitals and attempted to find a way around the bug in MOPAC, even if it appears to be a compromise. I don’t really need to see the IR spectra, your table would be enough. Excellent discussion.

Mini-project: Personally, working with organocatalysts, I’d say a 10 mol% loading isn’t all that bad for a catalyst. Although this is subjective. Good to see you’re questioning the assignment in the literature. It would have been nice to see a more in depth analysis of the deviations between your calculated results and the literature results. This data could easily have been presented graphically. Are there any other analytical methods you can think of that would allow differentiation between the isomers?

Overall: It’s a matter of personal taste but I find rotating Jmols incredibly irritating. Good to see references to appropriate literature throughout. Why the sudden change in writing style (‘I will . . .’)? Your answers were good but slightly thin on the ground in places. Still, a very good report.