ChemWiki - User contributions [en]

Talk:Mod:xxyte35134

2010-11-30T12:47:37Z

Alana:

Another outstanding piece of work! Lots of interesting discussion.

Epoxidation of 3: you've over-complicated this with your orbital analysis...the epoxidation simply goes on the more electron rich alkene (the other one is electron poor because it's conjugated to the ester). Great discussion of the hydrogenation, including the possibility of epimerisation. I expect the "top" face (near the N-bridge) is more accessible than the other (near the 2-carbon bridge).

For your 13C analysis, it would have been good to try to quantify the "fit" with the lit data.

Well done!

Talk:Mod:xxyte35134

2010-11-30T12:41:17Z

Alana: New page: Another outstanding piece of work! Epoxidation of 3: you've over-complicated this with your orbital analysis...the epoxidation simply goes on the more electron rich alkene (the other one i...

Another outstanding piece of work!
Epoxidation of 3: you've over-complicated this with your orbital analysis...the epoxidation simply goes on the more electron rich alkene (the other one is electron poor because it's conjugated to the ester). Great discussion of the hydrogenation, including the possibility of epimerisation. I expect the "top" face (near the N-bridge) is more accessible than the other (near the 2-carbon bridge).

Talk:Mod:xxyte35133

2010-11-30T12:31:34Z

Alana: New page: Wow - amazingly detailed. Well done!

Wow - amazingly detailed. Well done!

Talk:Mod:xxyte35132

2010-11-30T12:14:59Z

Alana: New page: Excellent. Again, would have been good to give the energy value for each isomer, rather than the difference between them, to allow me to check them!

Excellent. Again, would have been good to give the energy value for each isomer, rather than the difference between them, to allow me to check them!

Talk:Mod:xxyte35131

2010-11-30T12:09:48Z

Alana:

Again, great presentation and lots of detail. Note that the reaction is stereoselective, not stereospecific, even if it gives one isomer. Also, attack from both faces would NOT give a racemic product - it would give a mixture of diastereomers (there is one pre-existing stereocentre always "fixed" in the molecule).

Talk:Mod:xxyte35131

2010-11-30T12:07:33Z

Alana: New page: Again, great detail. Note that the reaction is stereoselective, not stereospecific, even if it gives one isomer. Also, attack from both faces would NOT give a racemic product - it would...

Again, great detail. Note that the reaction is stereoselective, not stereospecific, even if it gives one isomer. Also, attack from both faces would NOT give a racemic product - it would give a mixture of diastereomers (there is one pre-existing stereocentre always "fixed" in the molecule).

Talk:Mod:xxyte35130

2010-11-30T12:03:55Z

Alana: New page: Spectacular presentation with a lot of extra information! Would have been good to give the total energy for each structure, to enable comparison, rather than just quoting the difference.

Spectacular presentation with a lot of extra information! Would have been good to give the total energy for each structure, to enable comparison, rather than just quoting the difference.

Talk:Mod:elle0000

2010-11-30T11:52:50Z

Alana:

Cp: Good

NAD: Good

Taxol: Your two structures both have the carbonyl "down", which is why they are so similar in energy!

CCl2: HOMO and LUMO look a little odd. Vibrations OK

Mini-project: Interesting choice! You were brave to tackle 4 isomers (2 would have been enough). Your ChemDraw drawings of the isomers are not very clear, and I don't think they match the JMols. Good to have calculated all the 13C spectra, but it would have been good to try to quantify how well each calculated set matches the experimental. Why is the second C=O for pseudococaine so far off? Could you tell which-is-which with confidence from the 13C? What about other spectroscopic techniques - what would have been useful to distinguish the isomers?

Talk:Mod:elle0000

2010-11-30T11:41:45Z

Alana:

Cp: Good

NAD: Good

Taxol: Your two structures both have the carbonyl "down", which is why they are so similar in energy!

CCl2: HOMO and LUMO look a little odd. Vibrations OK

Mini-project:

Talk:Mod:elle0000

2010-11-30T11:36:22Z

Alana: New page: Cp: Good NAD: Good Taxol: Your two structures both have the carbonyl "down", which is why they are so similar in energy!

Cp: Good
NAD: Good
Taxol: Your two structures both have the carbonyl "down", which is why they are so similar in energy!

Talk:Grt07:breakyourself

2010-11-30T11:14:55Z

Alana:

Cp: Structures and energies good. Why is the endo-isomer kinetically preferred?

NAD: Good

Taxol: Your "up" isomer's energy is too low...hard to tell for sure without a JMol structure, but I think you've accidentally drawn the "trans" ring isomer

CCl2: Orbitals and vibrations good. Discussion of bond stretch vs reactivity a little confused - lower frequency doesn't necessarily mean more reactive - depends on the reaction!

Mini-project: Nice choice. Note that other stereoisomers are possible - you could form the cis-decalins (yours are both trans-decalins). It's odd that the two forcefields predict different relative stabilities for your two isomers - are there any obvious differences in the minimised structures? I have no idea why your 13C values are so far out - a pity! J values would definitely be a good way of telling the isomers apart. Your Table is a bit confusing as I don't know what the numbering system you've used is. It would have been good to expand the J-value analysis a bit more, and include pics to show the values. The IR and rotation would probably not be much use.

Overall good, but shame about the 13C!

Talk:Grt07:breakyourself

2010-11-30T11:08:08Z

Alana:

Talk:Grt07:breakyourself

2010-11-30T11:04:26Z

Alana:

Talk:Grt07:breakyourself

2010-11-30T10:59:05Z

Alana:

Talk:Grt07:breakyourself

2010-11-30T10:54:11Z

Alana: New page: Cp: Structures and energies good. Why is the endo-isomer kinetically preferred? NAD:

Cp: Structures and energies good. Why is the endo-isomer kinetically preferred?

NAD:

Talk:Mod:shaneomar

2010-11-30T10:48:35Z

Alana:

Cp: Energies and structures good. Why is the endo-TS lower in energy?

NAD: Good

Taxol: Energy and structure for "down" isomer are good. For the "up" isomer, the energy is higher than expected, although it does look OK - maybe you have the "wrong" chair conformation of the 6-ring. Discussion good. Apart from angle strain, are there any other undesirable interactions in the hydrogenation products?

CCl2: Orbitals look good. Pity you couldn't get the vibrations...very odd!

Mini-project: Nice choice. Although it's good to see you've tried to compare the experimental and calculated data for each isomer, you should have compared them to each other to see whether the 13C could have been used to tell them apart with confidence! I agree that 1H J values might do the trick, although it would have been good for you to estimate them by modelling and compare to the experimental.

Overall good - shame about the missing vibration data.

Talk:Mod:shaneomar

2010-11-30T10:44:30Z

Alana:

Talk:Mod:shaneomar

2010-11-30T10:41:29Z

Alana:

Talk:Mod:shaneomar

2010-11-30T10:36:55Z

Alana: New page: Cp: Energies and structures good. Why is the endo-TS lower in energy? NAD:

Cp: Energies and structures good. Why is the endo-TS lower in energy?

NAD:

Talk:Mod:tb12

2010-11-30T10:33:41Z

Alana:

Cp: Energies and structures fine. Why is the endo isomer kinetically preferred? Why is 3 strained?

NAD: Good

Taxol: Structure 10 OK, but your 9 has a trans-ring junction (rather than cis) and a boat conf. for the 6 ring. What structural features make the alkene "hyperstable"?

CCl2: Good

Mini-project: Interesting structures, and a nice choice of project! The reaction equation looks odd (the starting material doesn't match the mechanism you've drawn). Also, not clear what you mean by "cis" (I think you mean the Ar with respect to the O). FOr the 13C spectra - you should have tried to quantify the difference between the calculated and experimental for the two isomers, to see which fits best. (I assume no data were given in the lit for 3d - pity). What technique would you suggest to definitively tell them apart?

Talk:Mod:tb12

2010-11-30T10:32:11Z

Alana:

Cp: Energies and structures fine. Why is the endo isomer kinetically preferred? Why is 3 strained?

NAD: Good

Taxol: Structure 10 OK, but your 9 has a trans-ring junction (rather than cis) and a boat conf. for the 6 ring. What structural features make the alkene "hyperstable"?

CCl2: Good

Mini-project: Interesting structures, and a nice choice of project! THe reaction equation looks odd (the starting material doesn't match the mechanism you've drawn). Also, not clear what you mean by "cis" (I think you mean the Ar with respect to the O). FOr the 13C spectra - you should have tried to quantify the difference between the calculated and experimental for the two isomers, to see which fits best. (I assume no data were given in the lit for 3d - pity). What technique would you suggest to definitively tell them apart?

Talk:Mod:tb12

2010-11-30T10:26:16Z

Alana:

Talk:Mod:tb12

2010-11-30T10:14:16Z

Alana:

Talk:Mod:tb12

2010-11-30T10:11:49Z

Alana:

Cp: Energies and structures fine. Why is the endo isomer kinetically preferred? Why is 3 strained?

NAD: Good

Taxol:

Talk:Mod:tb12

2010-11-30T10:09:37Z

Alana: New page: Cp: Energies and structures fine. Why is the endo isomer kinetically preferred? Why is 3 strained? NAD:

Cp: Energies and structures fine. Why is the endo isomer kinetically preferred? Why is 3 strained?

NAD:

Talk:Mod:jamesmac

2010-11-30T10:05:29Z

Alana:

Cp: Energies for 1 and 2 are OK; those for 3 and 4 are off slightly (although they are the right way round). Why is the endo-isomer kinetically preferred? What structural features cause the strain in 3? Note that getting the lowest energy product does NOT necessarily mean a reaction is under thermodynamic control - often, the same product is preferred both kinetically AND thermodynamically.

NAD: Discussion a bit hard to follow without being able to rotate your structures! For the second reaction, the amine attacks on the OPPOSITE side to the carbonyl...

Taxol: Energy for 9 is right; 10 is a bit too high - I can't see why without being able to rotate your structures, but I suspect the 6-ring might be a boat.

CCl2: HOMO looks a bit odd (partly because I'm not sure what orientation it's displayed in - can't see the structure underneath). Discussion of vibrations OK

Mini-project: Tricky choice because the molecules are conformationally flexible... However, nice discussion of the mechanism and predicted stereochemical outcome of the reaction (minor point: the stereocentre is badly drawn in the products!) Calcs of 13C seem fine - however, you should have tried to quantify how well each set fit with the experimental data. There are more peaks in the calculated spectrum because in the "real" one, conformational averaging of e.g. the two ortho-carbons on the Ph ring makes them equivalent. 1H J-values would only be useful if you knew the preferred conformations of the molecule (which modelling could help with, of course). COSY would not be useful as it doesn't tell the size of the couplings. NOESY can be used in conjuction with molecular modelling, which can indicate which protons are close together in space. You haven't gone into much detail as to how the authors used NMR to assign the stereochemistry (or how you think it would be done). Calculating the IR and UV was not necessary as they would not help in assigning stereochemistry.

Overall - good effort

Talk:Mod:jamesmac

2010-11-30T10:02:44Z

Alana:

Talk:Mod:jamesmac

2010-11-30T09:55:44Z

Alana:

Talk:Mod:jamesmac

2010-11-30T09:51:11Z

Alana:

Talk:Mod:jamesmac

2010-11-30T09:45:14Z

Alana:

Talk:Mod:jamesmac

2010-11-30T09:41:35Z

Alana:

Talk:Mod:jamesmac

2010-11-30T09:36:55Z

Alana: New page: Cp: Energies for 1 and 2 are OK; those for 3 and 4 are off slightly (although they are the right way round). Why is the endo-isomer kinetically preferred? What structural features cause t...

Talk:Mod123CLMAFC

2010-11-30T09:30:27Z

Alana:

Cp: Energies and structures all look fine. What structural features are responsible for the strain in 3?

NAD: Basic analysis seems OK, but you haven't shown your structures, so I can't check them.

Taxol: Again, no structures given, so I can't check them. Why is the alkene "hyperstable"?

CCl2: Orbitals are OK I think (hard to read, as they are on top of the Table, which also obscures some of the data in the Table!) You haven't discussed the difference between the two alkene C=C stretches, or the C-Cl stretch.

Mini-project: The formation of diastereomers (as here) is NOT the same as racemisation! Although you have listed the calculated and observed 13C data for the two isomers, you have not made any attempt to quantify how well they compare. Would it have been possible to tell them apart with confidence from these results? How else could they be distinguished?

Overall - a little more discussion would have been good in places. Also - you should pay attention to your English - a lot of the time, you don't write in sentences - you connect independent clauses with commas...

Talk:Mod123CLMAFC

2010-11-30T09:29:45Z

Alana:

Cp: Energies and structures all look fine. What structural features are responsible for the strain in 3?

NAD: Basic analysis seems OK, but you haven't shown your structures, so I can't check them.

Taxol: Again, no structures given, so I can't check them. Why is the alkene "hyperstable"?

CCl2: Orbitals are OK I think (hard to read, as they are on top of the Table, which also obscures some of the data in the Table!) You haven't discussed the difference between the two alkene C=C stretches, or the C-Cl stretch.

Mini-project: The formation of diastereomers (as here) is NOT the same as racemisation! ALthough you have listed the calculated and observed 13C data for the two isomers, you have not made any attempt to quantify how well they compare. Would it have been possible to tell them apart with confidence from these results? How else could they be distinguished?

Overall - a little more discussion would have been good in places. Also - you should pay attention to your English - a lot of the time, you don't write in sentences - you connect independent clauses with commas...

Talk:Mod123CLMAFC

2010-11-30T09:24:02Z

Alana:

Cp: Energies and structures all look fine. What structural features are responsible for the strain in 3?

NAD: Basic analysis seems OK, but you haven't shown your structures, so I can't check them.

Taxol: Again, no structures given.

CCl2: Orbitals are OK I think (hard to read, as they are on top of the Table, which also obscures some of the data in the Table!) You haven't discussed the difference between the two alkene C=C stretches, or the C-Cl stretch.

Mini-project:

Talk:Mod123CLMAFC

2010-11-30T09:20:16Z

Alana:

Talk:Mod123CLMAFC

2010-11-30T09:09:38Z

Alana: New page: Cp: Energies and structures all look fine. What structural features are responsible for the strain in 3?

Cp: Energies and structures all look fine. What structural features are responsible for the strain in 3?

Talk:Mod:tmlkmcd

2010-11-29T16:18:18Z

Alana:

Intro: you seem to be referring to molecular mechanics, not molecular modelling - the latter does include e.g. ab initio calculations!

Cp: Energies and structures look good. Your explanation for the exo-selectivity is not that clear (what's the "sterically unfavourable overlap"?) What causes the bending strain in 3?

NAD: Good

Taxol: Structures look good. Why is the energy for 10 different in the two tables? What kind of strain is there in the saturated system?

CCl2: Good

Mini-project: Interesting choice. How did they tell them apart in the lit? Apart from X-ray, any other ideas? Would be interesting to model the TSs to try to explain why the "endo" isomer is favoured.

Overall - generally good discussion, and well presented

Talk:Mod:tmlkmcd

2010-11-29T16:08:20Z

Alana:

Talk:Mod:tmlkmcd

2010-11-29T16:04:34Z

Alana:

Talk:Mod:tmlkmcd

2010-11-29T15:58:16Z

Alana:

Talk:Mod:tmlkmcd

2010-11-29T15:56:01Z

Alana:

Talk:Mod:tmlkmcd

2010-11-29T15:50:58Z

Alana:

Talk:Mod:tmlkmcd

2010-11-29T15:45:23Z

Alana: New page: Intro: you seem to be referring to molecular mechanics, not molecular modelling - the latter does include e.g. ab initio calculations! Cp:

Intro: you seem to be referring to molecular mechanics, not molecular modelling - the latter does include e.g. ab initio calculations!

Cp:

Talk:Mod1:axg2010autumn

2010-10-26T15:51:16Z

Alana:

Cp: Energies for the structures OK (although you've given too many dec. places). Note that it is perfectly possible for a product to be preferred kinetically AND thermodynamically - i.e. the kinetic product is not necessarily less stable. (The component values for 1 and 2 look a little strange - do they add up to the totals? I expect more difference in the bend energies).

NAD: Structure for 5 looks OK. FOr 7, I think there should be a lower energy structure in which the Me is not pseudoaxial (conclusions are OK though).

Taxol: Structures look good! Why exactly is the alkane more strained than the parent bridgehead alkene?

CCl2: You haven't made it clear which orbital matters for the reaction with the carbene. The vibration results look good, but again your exaplanations are not clear - why should a higher stretching frequency lead you to expect that a bond is "more reactive"? Did you look at the bond lengths?

Mini-project: The structures in Table 11 do not match the ones shown below Table 12 - some of the former have the ester in an (unstable) s-trans conformation (with respect to the C(O)-OEt bond). The IR calculation was a bit of a waste of time unless you had some reason to expect it to distinguish the isomers. In fact, you haven't addressed that key question - what WOULD be the best way to tell them apart in "real life"?

Talk:Mod1:axg2010autumn

2010-10-26T15:50:49Z

Alana:

Cp: Energies for the structures OK (although you've given too many dec. places). Note that it is perfectly possible for a product to be preferred kinetically AND thermodynamically - i.e. the kinetic product is not necessarily less stable. (The component values for 1 and 2 look a little strange - do they add up to the totals? I expect more difference in the bend energies).

NAD: Structure for 5 looks OK. FOr 7, I think there should be a lower energy structure in which the Me is not pseudoaxial (conclusions are OK though).

Taxol: Structures look good! Why exactly is the alkane more strained than the parent bridgehead alkene?

CCl2: You haven't made it clear which orbital matters for the reaction with the carbene. The vibration results look good, but again your exaplanations are not clear - why should a higher stretching frequency lead you to expect that a bond is "more reactive"? Did you look at the bond lengths?

Mini-project: The structures in Table 11 do not match the ones shown below the 13C results - some of the former have the ester in an (unstable) s-trans conformation (with respect to the C(O)-OEt bond). The IR calculation was a bit of a waste of time unless you had some reason to expect it to distinguish the isomers. In fact, you haven't addressed that key question - what WOULD be the best way to tell them apart in "real life"?

Talk:Mod1:axg2010autumn

2010-10-26T15:41:25Z

Alana:

Talk:Mod1:axg2010autumn

2010-10-26T15:34:57Z

Alana: New page: Cp: Energies for the structures OK (although you've given too many dec. places). Note that it is perfectly possible for a product to be preferred kinetically AND thermodynamically - i.e....

Talk:ModOne:hhlk2010

2010-10-26T15:22:01Z

Alana:

Cp: Structures, energies all OK (too many dec. places though!) Good explanation for endo-selectivity. Why exactly is the exo-isomer "less strained"?

NAD: Your lowest energy structure of 5 is good, but I hope you can see that the others have serious problems (wrong carbonyl bond angles!) They are anomalies of the forcefield... For 7, I think there should be another, lower energy structure with the carbonyl "down".

Taxol: Structure 10 is good. For 9, there is a lower energy form if you flip to the "other" chair form of the 6-ring (yours IS a chair, not a twist boat). Why is the alkane less stable than its parent bridgehead alkene?

CCl2: Your HOMO looks to be centred on the anti-alkene to me... Your stretching frequencies all look good. Your analysis is a little confused though...why would a higher stretching frequency be expected to make a bond more reactive? What about the bond lengths?

Mini-project: There is no point comparing MM2 results for 14 and 15 - they are not isomers. Similarly, you were meant to think about how you would distinguish 15 from the other product regioisomer (the lactone with the O on the other side of the carbonyl!) In fact, the regioselectivity of this reaction is quite interesting. Even for the one product 15 that you did calculate the 13C for, you should have tried to quantify the agreement between calculation and experiment. The values in the middle of the table are a LONG way out - there is something wrong. I suspect you have compared the wrong carbons.

Talk:ModOne:hhlk2010

2010-10-26T15:08:43Z

Alana: