Talk:Anomeric effect

Untitled

Hello, I am currently taking a class where one goal is to improve chemistry wikipedia pages for the general public. I will be editing this page over the course of the next month. I have read through the talk page and saw how passionate people are with this topic. My goal is to improve the page so more people will be able to understand anomeric effect and to provide more examples besides just the 6-member ring chair conformations. I am willing to take any other suggestions as to how to improve the page. Thank you! (Physorgchem13 (talk) 23:25, 21 October 2013 (UTC))

Question: Should that be "in the case of dimethoxymethane..." rather than "in the case of dimethoxyethane... "For example, a small molecule that exhibits the anomeric effect and that is often used for theoretical studies is dimethoxymethane. In the case of dimethoxyethane the gauche,gauche conformation is..." If not, maybe the jump from dimethoxymethane to dimethoxyethane... should be clarified? Catalyzer (talk) 15:31, 11 April 2011 (UTC)

Maybe Itub should add a paragraph summarizing the experimental data that supports his description of the last edit as "opinion". Vgsbox 20:04, 30 May 2007 (UTC)

A citation supporting the paragraph would suffice to bring it from "opinion" to "published opinion", and therefore make it notable enough to be included. DMacks 20:22, 30 May 2007 (UTC)

Contradictory statements?

This article states that "In the case of dimethoxyethane the trans,trans conformation is 3–5 kcal/mol about lower in energy (more stable) than the gauche,gauche conformations" whereas the article on dimethoxymethane states that "Due to the anomeric effect, dimethoxymetane has a preference toward the gauche conformation around the C–O bonds, instead of the anti conformation."

Can both of these statements be true? Ansuman 13:19, 6 June 2007 (UTC)

No, the statement in this article was wrong and I have corrected it. --Itub 13:25, 6 June 2007 (UTC)

Original research and conflict of interest

User:Vgsbox has been adding his original research and opinion to this article again, which goes against Wikipedia policies. It is also obvious that he has a conflict of interest, because he is citing his own work and giving it undue weight. I'm reverting the latest edit[1] for these reasons.

I'm not saying that the article is perfect, as it could certainly needs expansion. I'm not even saying that the "conventional" explanation for the anomeric effect is The Truth. However, we have to give more weight to the mainstream explanation according to Wikipedia policies. Also, according to the No Original Research policy, preference should be given to secondary and tertiary sources, which means that in this case it is preferable to cite reviews and monographs rather than original research articles. Original articles that have not been cited much in the secondary scientific literature, with theories that have not had enough discussion in the scientific community shouldn't be given as much weight as the reviews and monographs. If Box turns out to be correct, surely future reviews, monographs, and even textbooks will reflect that, and we should certainly update the Wikipedia article accordingly. But that has not happened yet, and Wikipedia is not a crystal ball, so I'm afraid we'll have to wait until that happens. --Itub 12:16, 13 June 2007 (UTC)

Chair conformations

Six chair conformations for a 6-membered ring? You take one, do a chair-flip to get another, that's all I've ever heard of. Is the article conflating ring conformations with conformations of the side-chains on that ring? Let's please be very clear with terminology here even as there are certainly issues involving side-chain conformations that are based on the same/similar principles as ring-confs themselves. DMacks 14:13, 14 June 2007 (UTC)

I think he is talking about rotation around the exocyclic C-O bond. You have 2 chair conformations and three rotamers around that bond, resulting in a total of 6. However, the argument he added is misleading for reasons that I'll add later when I have time... --Itub 14:30, 14 June 2007 (UTC)

Ok, I'm back. I will call the oxygens "endocyclic" and "exocyclic", which I think is more clear than O1 and O2. The issue is that the exocyclic C-O bond is free to rotate and can adopt three conformations. In two of those, the endocyclic C-O antibonding orbital can interact with a lone pair of the exocyclic oxygen, which is stabilizing according to the hyperconjugation model. But that has nothing to do with which of the two chair conformations is favored. Now, if you look at the endocyclic C-O bond, it has only two (rather than three) conformations available because of the constraint of being in a ring. Of these two conformations, only for the axial one can the exocyclic C-O antibonding orbital interact with a lone pair from the endocyclic oxygen. This is similar to the case of dimethoxymethane in that there are two generalized anomeric effect involved, one per each rotatable bond to an oxygen. But in the case of a sugar or similar molecule, when talking about the non-generalized anomeric effect (dealing only with axial vs equatorial), only one of these two matters. (This prose can be hard to parse, making a drawing or a model certainly helps...) --Itub 15:33, 14 June 2007 (UTC)

Yes, I certainly agree that there are two good chair conformations essentially independent of three exocyclic-bond rotations, and that only the former is relevant to the discussion. There are always lots of effects and many global conformations available obviously. But for the article here and as a teaching example (i.e., not research paper), I think it's best to discuss a single part well rather than only considering the whole picture. DMacks 16:37, 14 June 2007 (UTC)

As I pointed out in the paragraph that I added (tried to add) and that was removed only because it showed obvious flaws in the n-sigma* argument, there are 6 conformations that must be considered, comprised of two chairs (axial, equatorial) and three rotamers about the C-2 - O-2 bond. Of these 6 conformations, three are heavily populated, the axial exoanomeric conformer, and two of the equatorial conformers. ALL of these 3 conformers MUST show n-sigma* interactions involving the O-2 lone pair and the C-2 - O-1 bond. It is specious to argue that a single n-sigma* interaction only occurs in the axial exoanomeric conformer.

Itub's conformational analysis paragraph above is pitiful at best and grossly misleading. Ask one of your organic chemisty friends to comment on it if you don't wish to take my opinion (36 years of teaching organic chemistry) into account.

If you insist on doing this kind of ignorance, then the article will soon be realized for what it is, an attempt to push n-sigma* interactions theory even in the face of other conflicting data. Not all of the people are fools and many will see what you are trying to do. I really didn't think that I would see this level of ignorance in this discussion. Vgsbox

When you have some time, go read the very first page of the paper, published by M.J.S. Dewar, in which SAM1 is introduced. Dewar comments that there are lots of theoretical chemists that have NO knowledge of chemistry. Is this relevant here? Vgsbox 14:27, 20 June 2007 (UTC)

No, what's relevant are the Wikipedia policies that you keep ignoring: WP:NOR and WP:NPA. --Itub 14:54, 20 June 2007 (UTC)

Compromise proposal regarding the rotamers

Perhaps we've been oversimplifying the issue. Box says that the hyperconjugation model is wrong because it doesn't consider the exo contributions. DMacks and I said that what determines the chair conformation is the endo contribution. In reality, there is a combination of both, that has been recognized for a long time, and when put in less provocative terms might be acceptable to all. I'll quote from Juaristi's review on the topic (p. 5061):

"It may be appreciated that the endo anomeric effect is the souce of the driving force for a polar aglycon to adopt the axial orientation; i.e., 58 [the axial conformer] is the lower energy conformer. In the alpha-anomer 58 the two effects (exo and endo) compete for electron delocalization toward the anomeric carbon. Not surprisingly, structural data suggest that the exo anomeric effect is stronger for the beta-anomer in which such competition is absent.

"In this context, Praly and Lemieux stress that an anomeric effect must be considered as the difference between the sum of the endo- and exo-anomeric effects in the equatorial conformer and the same sum for the axial conformer. However, since the endo anomeric effect is absent in the equatorial isomer, it is stabilized exclusively by exo anomeric interactions.

Anomeric Effect = (exo-AE_eq) - (exo-AE_ax + endo-AE_ax)"

What happens is that in most cases the sum exo-AE_ax + endo-AE_ax is greater than exo-AE_eq alone. The simplification in the discussion above by DMacks and me was that we assumed that exo-AE_ax was equal to exo-AE_eq, or at least that the difference between them was much smaller than endo-AE_ax. However, there are some exceptions. --Itub 15:07, 20 June 2007 (UTC)

Before I begin to reply to Itub, above, please let it be known that in simple six membered ringed compounds, the chair conformer is always the most stable and that has nothing to do with hyperconjugation.

Firstly, by classical conformational theory, the equatorial conformer of any 2-alkoxytetrahydropyran ought to be the lower energied one. That is how the whole issue of the AE got started. Many simple sugars, like glucose derivatives, anomalously show the axial conformer as the lower energied, especially in low polarity solvents.

Secondly, Box did NOT say that "that the hyperconjugation model is wrong because it doesn't consider the exo contributions". The article said that there was only ONE contributor to the hyperconjugation model of the Anoemeric Effect (AE), and I disputed that.

Thirdly, if you ignore the equatorial conformer, how do you explain why glucose does NOT show the AE in water? In fact, many acetals do not show a pronounced AE in very polar solvents. The hyperconjugation model does NOT explain this variation of the size of the AE with solvent polarity.

Maybe we should begin to worry about the true value and academic worth of this article on the Anomeric Effect, if Itub keeps control of the published material. I wonder how my colleagues will react to this discussion? Vgsbox 16:18, 20 June 2007 (UTC)

Nobody controls this article. As you have been repeatly told (and should know from the world of scientific publication in general), gotta get through peer review, and the standard here is WP:RS. Period...there's no cult-of-personality or article-ownership here. We're all waiting/hoping you or your colleagues will add some well-sourced information that supports and clearly explains whatever-you're-interested-in-explaining. Many of us teach chemistry and know how hard it is to explain something based on many inter-related (and often competing) effects. The more clearly each one can be explained as well as how they balance in the "real world" is quite a feat worth doing! DMacks 16:31, 20 June 2007 (UTC)

Glucose does show the anomeric effect in water, as discussed (again) in the review by Juaristi. However, the effect is not strong enough to overcome the preference towards the axial conformer, just to reduce it. Glucose prefers the axial conformation in the gas phase. It is a case of a solvent effect, complicated by all the hydrogen-bonding groups in glucose, which is the reason most model studies use simpler molecules than glucose. I do agree that the dipolar model helps explain the solvent effects better; each model has its strengths and weaknesses, which should explain why we still have two major models instead of only one. If one model were perfect, it would be the only one! --Itub 16:50, 20 June 2007 (UTC)

Yet another idea

Obviously there are many issues with THPOH, at least in part because there are two anomeric-effect bonds to consider. The ring doesn't seem to simplify anything beyond dimethoxymethane, though it is probably a more common application for many readers. Maybe we should use a 2-haloTHP instead of 2-hydroxy: only one rotatable bond, so we can focus on the anomeric effect itself (dipole/dipole, hyperconjugation, other effects) without also having to consider complications from sidechain conformations, less important H-bonding to solvents, etc.? DMacks 16:46, 20 June 2007 (UTC)

Ease of reading

I wonder if is this could be easier to understand if it were introduced kind of like in http://www.scripps.edu/chem/baran/images/grpmtgpdf/Krawczuk_Nov_05.pdf This may provide some insight on how to make this topic easier to understand. Sion55 (talk) 14:41, 25 July 2011 (UTC)

Peer review and responses during the educational assignment in Fall 2013

Overall, I think you did a great job making the introduction more accessible to non-experts compared to the original article. However, there are a few areas in the introduction that are slightly confusing. First, because you removed the pictures depicting glucopyranose, I would also remove the sentence that talks about glucopyranose. Another option is to re-include the picture and keep the description in because it was a nice example from the original article. If you do this, I think it would be more effective after you talk about the general case (C-Y-C-X). That way you can start more general and move to a more specific example. The example you use in your general case is slightly confusing. You define Y as a heteroatom, but then in your drawing on the left Y is a carbon, which is not a heteroatom. Perhaps state that the drawing on the left does not exhibit the anomeric effect, while the drawing on the right with a heteroatom, Y, exhibits the anomeric effect. Also, it would be helpful if you explained why the effect is most common when Y= oxygen. Lastly, for the introduction I think you wrote “steroids” instead of “sterics” (In the cyclohexanol molecule on the left, the substituent prefers the equatorial position due to steroids.)

As you move into physical explanation and controversy there are some terms that could be defined to make the article more accessible to non-experts. A short sentence defining hyperconjugation would be helpful in addition to your link. Also, I suspect most non-experts will not know what antiperiplanar is or what a sigma* orbital is. A little more explanation would help clarify. The wording in your last paragraph for the hyperconjugation section is confusing. You can take out the two also’s and a few commas. It would be helpful if you explained what the inconsistency is between theory and experiments for acetal chemistry, instead of just stating that there is an inconsistency. A figure here might help clarify. For the section on dipole minimization, the example for the E/Z conformation of esters needs a reference. Lastly, the subsections are: Hyperconjugation, Dipole Minimization, then Hyperconjugation again. You can probably combine the two hyperconjugation sections.

I thought the influences on anomeric effect was well done. The one thing I would suggest is linking to “reverse anomeric effect” in your own article instead of saying “see below”. I think there is a way you can link to sections within your own article. Also, a picture for the reverse anomeric effect would be very helpful for non-experts.

Finally, I think the section on synthetic applications can be expanded. A picture depicting the Koenigs-Knorr Glycosidation and an explanation as to how the anomeric effect is applied in this case would help expand this section.

In general, I thought all of your examples were appropriate and not duplicative of any other content already on Wikipedia for the anomeric effect. Your figures are very well done, easy to read, and informative. Additional explanation in the text for a few of the figures (like the C-Y-C-X example) would be helpful for non-experts. You have a nice combination of journal sources and secondary sources, however, a source is missing for the example of the E/Z conformation of esters. --Iriidium (talk) 15:38, 2 November 2013 (UTC)

_______________________________________

General Remarks/Overall Presentation: I believe that you greatly improved the content of this article. The sections and subsections were organized in a coherent manner and, for the most part, were written using clear language. Both the figures and the examples enhance the article. The references came from a variety of sources. Most of my recommendations are relatively trivial and are listed in the following sections.

Content: In the Talk section of the original article, someone recommended using http://www.scripps.edu/baran/images/grpmtgpdf/Krawczuk_Nov_05.pdf to introduce the topic. This is one of the resources I used when preparing for this peer review and I found it to be an excellent primer. Your introduction might benefit from adopting some aspects of it, such as the first two figures in which they directly compare alkyl substituted cyclohexanes and alkyl substituted tetrahydropyrans.

The section on Synthetic Applications was a mere three sentences long. If I were you, I would either expand it or eliminate it. Otherwise, the sections were of an appropriate length.

I am sure there are some places in the “Influences on Anomeric Effect” where you could link to other topics on Wikipedia. There are currently no links.

I have two specific editing recommendations: First, in the heteroatom hyperconjugation section, you switch your syntax around when referring to the different types of conformations. At first, you refer to the “"trans", "trans"” conformation and the “"gauche", "gauche"” conformation. However, later in the section, you refer to it as the “trans,trans” conformation. I personally prefer the italicized version, but whichever one you choose, you need to be consistent. Also, I also might advise against using the Cy, THF, etc. abbreviations. If someone was only interested in reading the section on Solvent Effects, for example, they would not understand those abbreviations because they were introduced in the Substituent Effect section. It does not take too much effort to write out the words in full and doing so could save a great deal of confusion for a potential reader.

Figures: In the introduction, it might be worthwhile to have a figure explicitly labeling the anomeric carbon; currently, you say that it is C-1 but the general audience may not necessarily know what that means. In addition, I understood the concept you were trying to convey with your description of C-Y-C-X, however, I think it could be made even better by labeling on the figure which atoms are Y and which are X. This could be as simple as using an arrow to point to them. The current figure in the introduction seems a little fuzzy. Did you upload it as a .png file or a .jpg? I personally found that the file type made a difference in the clarity. The rest of the figures were crystal clear.

References: The original Wikipedia page on the Anomeric Effect had eight references. Your sandbox has 15. I did not go through and check if you had in fact added eight references and just eliminated some of the original references. If you haven’t added eight, you will want to do so. You had a good mixture of different kinds of sources: there were journal articles, an encyclopedia article, and books.

P org 2013 (talk) 19:11, 2 November 2013 (UTC)

_______________________________________

Content: There were some strong sections added and also a few that need a little work. The introduction was actually rather confusing. Considering the majority of the audience looking at this page will be upper lever chemists, they could figure it out, but I think it would be better and easier to just clarify a few things. I do find the last paragraph in the introduction to be rather confusing. I believe there are a few typos that made it confusing (steroids vs sterics, hydroxytetrahydrofuranose (I’m no sugar chemist, but I think the name is incorrect), and cyclohexanol (it’s not an alcohol)). I think if you are leaving the part about glucopyranose on the page you need pictures. The figure that was on the original page is clear so there really is no reason to remove it. It’s also much easier to look at the picture instead of trying to visualize it based on the provided description. In the heteroatom hyperconjugation section, I got rather confused again. I would just call the two structure in the figure trans and gauche though they are listed as trans, trans and gauche, gauche. This may be due to my own ignorance, but I didn’t think you could label a single bond more than one of these. If this confusion is due to my ignorance, it would be helpful to more clearly discuss these for the general chemist. Another part that I came to that I find unclear was the Solvent Effect section particularly the part about axial positions and electrostatic interactions. I tried to access the provided reference, though I am unable to as I am currently not on campus. It occurred to me that another concept could explain the items discussed in this section. To me, it seems like the equatorial position would have more interactions with the polar solvent and thus be more stabilizing due to dipole-dipole interactions. The final section that may need some work is the Reverse Anomeric Effect. The second sentence was rather confusing; it would be best to include a picture here or just utilize better naming. The sections are of good length except for the last part about synthetic applications. Only one is listed, though it says there are many applications in sugar chemistry. Maybe list a few others or don’t say there are many? It also would be nice to link to solvent effects in that section since it was only a brief explanation. Generally, the examples given are fine. I’m assuming other than the content that was originally on the page that most information was produced for the project since anomeric effect is a pretty unique topic.

Small grammatical issues that would really shine up this page:(1) Influences on the Anomeric Effect- sentence 1, effected to “affected”.(2) Solvent Effect- sentence 1, One often brought up problem to “One common problem”. (3) Solvent Effect- sentence 7, there is more electrostatic repulsions to ...”there are more”…

Figures: Overall, the figures are nice. They are accurate and clear enough to read (the first is a lot less clear than the others for some reason) and help clarify the text. I think it would be helpful to label them (ie: E vs Z, gauche conformation, the names of the molecules in the intro). The labeling would make it easier for people.

References: There appears to be enough references with a mix of journals and books. Surprisingly, some references were deleted from the original page and I can’t really see what content that was deleted. It appears most of the original content was retained with only some rewording.

Overall Presentation: Overall, I think the page is rather informative. The last paragraph in Introduction needs some work. There certainly needs to be more referencing (especially dipole minimization and overcoming the anomeric effect as there are currently no references for either section). The pictures are well drawn and easy to read. It would be helpful to label them. In general, the page would be helpful for anyone looking to learn a little more about the anomeric effect.

--5402013SD (talk) 15:26, 3 November 2013 (UTC)

Suggestions from ChemLibrarian (talk) 02:26, 5 November 2013 (UTC)

1. As other reviewers suggested, if you have deleted references cited in the original article but kept the original sentences, please add those references back.

2. At the end of the first paragraph under the Physical Explanation and Controversy section, you linked to a blog page to the word "settle". I would suggest making this webpage a reference for the whole sentence instead of a link to one word "settle". If you concern is not to cite a non-scholarly source, I think it's OK. The blog you are citing is a professional blog and you have enough other scholarly sources throughout the article.

3.I see your images have a mixed file types (.png, .tiff, and .jpeg). Actually, Wikipedia recommends "The basic choices are SVG for simple diagrams (especially those that need to be scaled), JPEG for photographic images, and PNG for everything else" as discussed on this page Wikipedia:Preparing images for upload. So, if you drew these diagrams in ChemDraw, it's better to save them as .png . If you are using other tools allowing saving as .svg, that would be the best.

Additional Comments

There have already been an extensive number of comments on this page so I'll refrain from adding too much more. The peer reviewers advice is good and should be listened to. The figures are a mix of old and new, and that is OK, but the formatting is not consistent. It would be better if it was. You can either re-format your figures, or make modified versions of the old ones. UMChemProfessor (talk) 20:25, 5 November 2013 (UTC)

Response to Reviewers

Thank you for all of your suggestions. We would like to comment on how we took your suggestions.

Citations: If we deleted citations from the original page it means we deleted the information. If you read the talk page from the original page you would find that an individual cites his/her own research, which is against wiki’s policy. We found broader information from secondary sources to take its place. References were also added in to the E/Z conformation and the overcoming the anomeric effect sections. The external link which was from the original article, was fixed so it cites the sentence and not linked to the word.

Figures: We have adjusted our figures for all of them to be in the same format. Further more we took the suggestions of making our figures clearer by labeling within the figure. For example, the E/Z conformation figure and sigma star orbital figure were adjusted with labels. We also added a few more figures (reverse anomeric effect and natural products) and returned the intro figure to help facilitate our explanations.

Content: In response to using the Baron group document we did use the document to start researching our topic and ended up finding more detailed information in other sources. We have edited the introduction to introduce our topic with clearer descriptions. For the C-Y-C-X explanation, we adjusted the figure and provided a more general description to aid the general publics understanding of it. Furthermore, we have added definitions of concepts through out the article and adjusted any grammatical errors that were pointed out. The organization of the physical explanation section was redone to combine the hyperconjugation sections. The synthetic application section was expanded and more examples were provided, to address the concerns that the section was too short. More links were also added within the influences on anomeric effect section. As far as editing the trans, trans and gauche, gauche areas, details were added to the paragraph for further explanation. Any abbreviations were eliminated and full words were used to eliminate any confusion in the article. A figure was added to the reverse anomeric effect section to help clarify any confusion. In general, all of the information that was added to the article came from the references cited. The explanations were summaries of others work and not our own new explanations for the phenomena. — Preceding unsigned comment added by Physorgchem13 (talk • contribs) 17:19, 9 November 2013 (UTC)