|WikiProject Chemistry||(Rated C-class, Mid-importance)|
|This article is/was the subject of an educational assignment in Fall 2013. Further details are available on the course page.|
- 1 Merging with intermolecular interaction
- 2 New discussion on merge
- 3 Reason for Renaming Page
- 4 Peer Review #1
- 5 Peer Review #2
- 6 Additional Comments
- 7 Suggestions from ChemLibrarian (talk) 14:47, 5 November 2013 (UTC)
- 8 Peer review and responses during the educational assignment in Fall 2013
Merging with intermolecular interaction
(Copied over from User talk:Itub):
I'm puzzled by your [Sadi Carnot's] removal of the merge tag from non-covalent bonding with the reason "non-covalent bonding is important in the field of supramolecular chemistry according to Lehn". I'm not questioning the importance of non-covalent bonding. What I'm questioning is whether the Wikipedia articles currently titled non-covalent bonding and intermolecular interaction actually deal with different topics. My opinion is that they don't, and therefore having two articles is redundant. I don't have a strong preference regarding the title of the resulting article, though. --Itub 12:33, 12 March 2007 (UTC)
- While I appreciate your effort to organize, I have interest in supermolecular chemistry and although one could loosely merge these without to much difficulty, I reason that they should remain separate. Although I need to read more in this area, from what I understand so far Jean-Marie Lehn, the main founder of this field, who won the 1987 Nobel Prize for his work in SMC, defines “molecular chemistry”, as begun by Friedrich Wohler in 1828, as related to the making and breaking of covalent bonds. He contrasts this with the new field of “supramolecular chemistry” as related to the making and breaking of non-covalent bonds between supermolecules. Intermolecular forces, on the other had, is a more general term which may include the covalent bond if fashioned so. If you don’t believe me, look at this edit by User:V8rik, in which the intro definition of supramolecular chemistry is defined by the use of the term “noncovalent bonding. I hope this helps? --Sadi Carnot 00:26, 13 March 2007 (UTC)
- I'm still not convinced. The terms "noncovalent bonding" and "intermolecular interaction" are used synonymously (yet another synonym is "weak interactions/bond"). A good example is the reference you provide: it says "Supramolecular chemistry is a highly interdisciplinary field of science covering the chemical, physical, and biological features of chemical species of higher complexity, that are held together by means of intermolecular (noncovalent) binding interactions'" (emphasis mine). Intermolecular interactions conventionally never include the covalent bond; (I'd say it's because if you bind two molecules with a covalent bond you end up with one molecule, and the interaction is no longer considered intermolecular. This may seem in contradiction with the fact that the "intermolecular" forces also act intramolecularly, but the convention still is to call these forces "intermolecular" in general. The nature of the force does not depend on whether it is intermolecular or intramolecular.) My conclusion is still the same: the two articles are dealing with the same topic: hydrogen bonding, ionic and dipole interactions, and dispersion forces and should be merged. --Itub 08:50, 13 March 2007 (UTC)
- Also see Lehn's Nobel lecture , which begins with "Supramolecular chemistry is the chemistry of the intermolecular bond" and frequently alternates between intermolecular and non-covalent. --Itub 09:23, 13 March 2007 (UTC)
- Noncovalent bonding (671,000 hits)
- Intermolecular force (1,050,000 hits)
- Intermolecular interaction (1,140,000 hits)
Also, according to the McGraw Hill Encyclopedia of Chemistry (2004), Oxford Dictionary of Chemistry (2005), and the Essential Dictionary of Science (2004) only the term ‘intermolecular force’ is defined by each. A search on a definition for Supramolecular chemistry shows a lot terminology overlap. Oxford defines SMC as the study ‘of assemblies of molecules held together by intermolecular forces’, where as McGraw Hill defines SMC as the study of ‘complex chemical species held together and organized by means of intermolecular (noncovalent) bonding interactions.’ At this point I will remain ambivalent. If you find more support for your merge, I would only suggest a merge to “intermolecular force”, but not intermolecular interaction, which can either be “attractive” or “repulsive” and not necessarily qualify as a bond by itself; only combinations of intermolecular interactions may qualify as a chemical bond. --Sadi Carnot 13:06, 13 March 2007 (UTC)
- I am in favor of merge, the topics are indeed identical . The majority of merge proposals in wiki concern non-identical topics which I strongly oppose but this is not one of them. I am also in favor of adopting the name intermolecular interaction because then it will include repelling forces as well. My name was mentioned somewhere in this discussion but I am not sure why, perhaps in relation to the article dynamic covalent chemistry which should definitely NOT be merged for obvious reasons. V8rik 17:52, 13 March 2007 (UTC)
- Support merge to "intermolecular interaction", as the one with the largest number of hits and the broadest. This terms are indeed almost identical. Merges are appropriate if there is a large overlap of content. That is the case here. Of course, it should cover repulsive as well as attractive forces. “intermolecular forces” can also be repulsive in, for example, force fields in molecular mechanics. We have far too many chemistry articles that are almost about the same thing. --Bduke 22:08, 13 March 2007 (UTC)
Why not Noncovalent interaction, just to please everybody? :P I also note that there is space in Chemical bond to expand the section on "weak interactions" which is currently near the bottom of that article (v. short because I was getting tired when I got to the end of the rewrite 9 months ago!). I tend to dislike restricting the concept to "intermolecular", as they can also be intramolecular or interatomic (in the case of van der Waals forces). You can get xenon atoms to stick to protein molecules (handy for resolving the crystal structure) if you apply a little pressure. I myself have published papers on inter- and intramolecular van der Waals forces in simple coordination compounds, a far cry from supermolecular chemistry as Lehn (and the Nobel committee) sees it. In any case, something needs doing with these articles.... Physchim62 (talk) 03:12, 4 April 2007 (UTC)
- I’m still not really in favor of a merge. I’ve found this definition of noncovalent bonds in a standard textbook of molecular cell biology; and a second one in a standard biology textbook. I’ll add these to the article. I hope this helps? --Sadi Carnot 07:44, 9 April 2007 (UTC)
- After reading the link you provided, I still see no difference (and note that the link acknowledges that they are also known as "noncovalent interactions"). The article could be called "noncovalent bond" as far as I'm concerned, but there should only be one article. --Itub 09:18, 10 April 2007 (UTC)
New discussion on merge
Hi there, I'm a university lecturer in Physical Organic Chemistry with specialisation in the study of non-covalent interactions and have read the discussion on this page with much interest.
With regards to the spelling of non-covalent...the hyphenated version should be preferred, as in all correct English usage of the non- prefix
Also the term "non-covalent BOND", should be dropped entirely, as it is an inaccurate description. The phrase bond should be restricted to cases where electrons are shared between the orbitals of different interconnected atoms. A weak transient interaction between two function groups is exactly that, AN INTERACTION, there is no (or very little) sharing or swapping of electron obitals. At the extremes of non-covalent interactions, more orbital overlap might occur and one might regard such a state as a weak covalent, dative or ionic situation. Indeed such a continuum from non-covalent interactions at one end of the scale to ionic at the other seems reasonable.
One further point, is an interaction between two oppositely charged ions correctly described by the word bond? I would argue not, since ionic interactions tend not to be directional, unlike dative and covalent bonds that have directionality enforced by the geometry of the orbitals involved. Thus, I am firmly of the opinion that the usage of the word bond should be restricted to examples where electron sharing is occurring, i.e. covalent and dative circumstances only.
I agree with the comments on "intermolecular interactions vs noncovalent interactions"...'intermolecular interaction' is not as encompassing as an article on non-covalent interactions in general that includes intramolecular interactions that operate with the same underlying physical princples as intermolecular interactions. Referring to the discussion as to whether the topics non-covalent interactions, non-covalent bonds etc should be merged, well yes they should, there is no difference between these topics, apart from the fact that 'non-covalent interaction' is the most appropriate broad description of this phenomenon; as was correctly pointed out above 'non-covalent interaction' importantly includes repulsive interactions.
I also note that textbooks very rarely present the current state-of-the-art of understanding. I would especially frown upon using a biological textbook as primary source of information regarding this topic in *chemistry*.
I hope that these comments have clarified the situation for you and that other people out there agree and enforce the hopefully sensible reasoning that I have laid down here.
--fray_bentos 16:24, 8 May 2008 (UTC)
You make some good points. Let us hope that this revives the discussion on this matter. The previous discussion is quite a long time ago and involves an editor who is now indefinitely blocked for pushing his own theories. A new discussion without him may be more fruitful.
We have to follow sources, so while your view that bonds have to be directional has some merit, it is not supported by general usage and sources. the term "ionic bond" for example is well established in our text books and literature. The term "hydrogen bond" is also well established, although I am not clear whether you want to change that.
Is your suggestion that we rename this to non-covalent interactions, leaving intermolecular force alone (note that Intermolecular interaction redirects to the latter)? We would then need to clean up both articles and Chemical bond to make sure they are consistent and tie together properly. --Bduke (talk) 23:37, 8 May 2008 (UTC)
-- You make very good points about the naming of hydrogen bonds in particular! I think in cases where there is a choice of different names for a single phenomenon (or group of phenomena) then it makes sense to consistently take the most accurate description for the title (and have the other descriptions redirect to this page), which in this case would be "non-covalent interaction". In contrast hydrogen bonds have a long-established name that needs not be messed with, more of a naming convention, rather than a factual description of the underlying physics. For example, many authors have described H-bonds as occuring in cases where no hydrogen atom is even involved in the interaction! Indeed, exactly what consitutes a "hydrogen bond" is matter of debate. Much of the pedantics over nomenclature stems from the problems caused by people naming different "classes" of non-covalent interactions different things ("halogen bond" is a more modern perpetrator!). Thus, when we talk about a "hydrogen bond" or a "halogen bond" this is just a narrow view on the much broader phenomenon of non-covalent interactions. Our established definition of H-bonds is biased from our observations made in aqueous solution, i.e. stronger non-covalent interactions that are able to compete with water solvation. This is a particularly narrow view on the topic since water is a strong H-bond acceptor and donor, which washes out so-called "weak hydrogen bonds". Originally, people considered that orbital overlap was important in hydrogen bonds, but the modern view taken in physical organic chemistry is that orbital considerations are not especially important in hydrogen bonds, hence technically the "bond" part of the name may be inappropriate according to my discussion in my last post. Evidence for the lack of orbital considerations in hydrogen bonds is again given by the relatively weak directionality of so-called H-bond interactions. For example if you observe the distribution of interacting H-bond donors around a carbonyl group from experimental data, i.e. crystallographic databases, you see (counter to popular belief) very little preference for H-bonds formed in the direction of the lone pairs on the oxygen atom. Instead H-bond donors positions spread much more evenly over the surface of the oxygen atom, due to smearing of electron density across the van der Waals radius of the entire oxygen atom. This reflects the fact that electrostatics dominate the nature of non-interactions between polar functional groups. The very slight preference for H-bonds to the lone pair positions on the oxygen most likely originate from the slightly higher electron density near the lone pair obitals. Another good example is a published crystal structure obtained with THREE terminal alkyne C-H groups (very polar CH) pointed directly towards the oxygen atom of dimethylsuphoxide, clearly satisfaction of the orbital considerations are not very important. It is probably too late to destroy naming conventions like "Hydrogen bond" (but not too late for halogen bond!).
Again it is sensible to reinforce the idea that non-covalent interactions consitute a continuum of different strengths, but are phenomonologically driven by the same underlying physical principles. On these grounds it makes no sense to have three separate articles describing the same things. Chemists and biologists prefer interaction, expressed in units of energy whilst physicists think perhaps more purely in terms of forces (rather than a function of force over distance i.e. energy and interactions). The wikipedia entry "intermolecular force" is clearly written by a physicists/hardcore theoreticians. As a result the writing style is not suitable for an encyclopedic entry. Is not well-written and is overly complicated by (mostly experimentally-unproven) mathematical theory. The way it is written is inaccessible to the average reader, and even myself as a specialist experimental researcher in the field. For example there is no real description of the real physical basis of some of the theoretical concepts described in that article (possibly because it is not possible to deconvolute the mathemetical descriptions into distinct physical properties that can be observed experimentally!). For example, I have never been able to grasp the real physical meaning of the "exchange" component listed in the noncovalent forces article, I think I would simply call that "repulsion", but I am not sure... In my view it is appropriate to include DESCRIPTIONS of the individual components contributing to non-covalent interactions e.g. repulsion, electrostatics, induction, dispersion and some SIMPLE mathematical descriptions may also be suitable, e.g. to show how electrostatic interactions change with distance. It should be pointed out in the article that naming conventions such as "hydrogen bond" and "halogen bond" are governed by the same underlying physical principles, they are not distinct phenomological examples. I would like point you in the direction of this work (not my own):
"Molecular recognition events in solution are affected by many different factors that have hampered the development of an understanding of intermolecular interactions at a quantitative level. Our tendency is to partition these effects into discrete phenomenological fields that are classified, named, and divorced: aromatic interactions, cation- interactions, CHO hydrogen bonds, short strong hydrogen bonds, and hydrophobic interactions to name a few."
Furthermore, having separate "INTRAmolecular force", "INTERmolecular force", "INTRAmolecular interaction", "INTERmolecular interaction", "non-covalent bond" and "non-covalent interaction" entries serves no purpose except to clutter and confuse information, rather than to clarify and unite.
--fray_bentos 16:07, 9 May 2008 (UTC)
First, just to demonstrate how really confusing all this is, I have looked at the titles you use just above and summarized the situation. Note that the the first letter can be capital or small letters, but after that they are distinct. I have used capital letters for the first letter throughout. Also note that a lot of redirects are not a bad think if they are possible search terms. Some cases however are not good. Intramolecular force is not the same as Intramolecular forces. Induced-dipole attraction is not the same as Induced dipole interattraction
- Intramolecular force - note not the same as Intramolecular forces - see below.
- Intermolecular force has redirects from Intermolecular forces, Intermolecular Forces, Intermolecular bond, Intermolecular attraction, Intermolecular interaction, Intermolecular interactions, Intermolecular, Dipole-dipole bond, Dipole-dipole force, Dipole-dipole attraction, Dipole-dipole interaction, Instantaneous dipole attraction, Instantaneous-dipole induced-dipole attraction, Instantaneous dipole, Induced-dipole attraction, Interatomic force, Nonbonded interactions, Keesom force and Keesom force.
- Intramolecular interaction, is not an article or a redirect.
- Intermolecular interaction reditects to Intermolecular force
- Non-covalent bond redirects from Noncovalent bonding, which also has redirects from Non-covalent bonding, Noncovalent, Non-covalent, noncovalent bond, Intramolecular forces and Intramolecular Forces.
- Non-covalent interaction, is not an article or a redirect.
We also have:-
- Van der Waals force has redirects from Van der Waals forces, Van der Waal's force, Van der Waal's forces, Van der Waals' force, Van der Waals' forces, Van der Waals bond, Van der Waals bonding, Van der Waals potential, Van der Waals interaction, Van der Waals interactions, London force, London forces, London dispersion force, London dispersion forces, Hamaker Force Interactions and Induced dipole interaction.
fray_bentos, I think we would all welcome your views specifically on what articles should be here in this general area. Please take a look at the stuff above which says what we already have. You raise the point that an article is written overly from the point of view of physics. I think this is a general problem for a whole set of articles in the border area between physics and chemistry. If physics people extensively edit an article, the chemists find it difficult to understand. It may well be that the reverse is true, so I am not criticizing the physicists. When both groups edit an article, it tends to become unfocused. I really think that there is a problem here but I do not know the solution. I guess all we can do is politely try to get the introductory paragraph as clear and simple as possible and then perhaps try to get the physics and chemistry perspectives in different sections of an article. --Bduke (talk) 04:18, 10 May 2008 (UTC)
- @Bduke: I have eradicated the incorrect links to Waal's and Waals' (both spelling errors). I don't know if the redirects should be deleted or not.
Reason for Renaming Page
As discussed previously on this talk page, the name change for this page is reflecting a more accurate description of the page content. Future revisions that further reflect the more accurate description will be coming shortly.
Peer Review #1
The first paragraph try to define what is non-covalent interaction by contrasting the covalent bond interaction. Several hyperlink to internal wiki sources were also made for general public if they have difficulty understand it. I think people without specific chemical knowledge will still get general idea from the text.
I think the second paragraph include too much information that are repeated in the "Applications" part. In addition, the examples only focus on the biological aspects. Although the non-covalent interaction is very important in biology, it is also important in other field, for example, material sciences. Only focusing on biology will make the general public have wrong impression that the non-covalnet interaction only happened in biological system. This part can be shorten or add other example not related only to biology.
I think the content for each specific interactions listed is well written and link to every previous wiki page. Figures are also sufficient enough to make reader under stand the basic concepts.
However, I still have several concerns:
1) I am confused about the classification; I think that the Dipole-Dipole interaction should also be classified under "Electrostatic interaction". Because in the first sentence of the main text in Dipole-Dipole section also mention: "Dipole-dipole interactions are electrostatic interactions between permanent dipoles in molecules."
2) I think one of the non-covalent interactions is missing: the hydrophobic interaction, which should also be considered as a non-covalent interaction. This interaction should be one of the main classification (topic).
3) For the third interaction "π-effects". I think that this section should be referred to a main wiki page: Pi interaction which is not linked in the text. There are more "pi-effects", for example, Anion-π interactions, C-H-π interactions etc. and those pi-effects should also be mentioned.
The author provide sufficient figures to illustrate the example of the "applications". The text is well written and accessible for non-expert. If possible, I will suggest make one more figure to illustrate how to design a drug based on the possible non-bond interaction that can be formed in the receptor/enzyme active site in the "drug design" section.
My only concern is the title "Applications". I think only the "drug design" section could be regarded as an application using the concept of those interactions. Others like protein folding, protein structure should be considered as a natural phenomenal. I would suggest just use "examples" or other terms instead of Applications.
There is also a one link should be made to one existing wiki page in "Protein structure.
I think the reference includes several representative textbooks which is good for general public to look for reference in library or students who also take that course.
I think, in general, the authors did a good job in collecting some of the non-covalent interactions that are already well written in other wikipedia pages. The writing is fluent, no difficult to read for general public. Original and high-quality figures even animations were well prepared and informative to illustrate the basic principle of each interactions and applications mentioned in the text. Several non-journal references were also cited which is good for non-expert reader. I just made some minor suggestions to point out my concerns to make this article more perfect.
Peer Review #2
Bisoxo (Jacob Geri), reviewing Non Covalent Interactions
1. Is the introductory section accessible for non-experts? The introductory section is accessible to non-experts. The first paragraph contains an unnecessary unit conversion, however, which would only serve to distract readers. In addition, the last several sentences do not come across as authoritative; it would be better to say that non-covalent interactions are often broadly divided among the four different forces. Also notable is that all the examples in the introductory section relate to supermolecular chemistry, but non-covalent interactions are what give rise to the physical properties that nonexpert readers can relate to, such as the boiling point of liquids, solvent dissolving power, gecko’s ability to walk up glass windows, etc.
2. Do the contents of each section justify its length? Yes. The article as a whole is built as a top-level description of noncovalent interactions, and most subsections have sufficient but not excessive content. However, I think that the protein folding section is too long and that the protein structure section could be folded into the protein folding section. Similarly, “Drug Design” and “Enzymatic Function” should be combined and considerably shortened due to the considerable similarity in their topics.
3. Are all the important terms/concepts linked to their respective Wikipedia pages for further reference? Yes, the article is decorated with such intra-wiki links and most of the sections contain links to main pages. A main article link for Protein Structure and Drug Design would be nice.
4. Are the highlighted examples appropriate? This part of the peer review is broken into the article’s sections. Electrostatic/Ionic: In the first example, there is a clear typo in that fluoride is F- rather than F+. In the next example, the explanation of acetic acid as being “commonly known as vinegar” is unnecessary, and would be better served by an internal link. Generally speaking the purpose of this example is very confusing because the charge is not localized on a single atom at all, and is delocalized across the carbonate moiety. Perhaps an alkoxide would be a better example? Dipole: A major error in this section is the parenthetic of acetone as the former main ingredient in nail polish remover. It is still the main ingredient. The example is otherwise quite useful. The hydrogen bonding example is also quite good, but should mention that hydrogen bonds do contain a small covalent component; similarly, the halogen bond example is well chosen. Π-effects: This section has good examples as well, but some explanation of how π-stacking works is needed. Van der Waals: The explanation of how this works is completely wrong. The authors should read the associated article… electron-electron repulsion reduces intermolecular interaction. Applications: The examples in this section are well chosen, but are ALL from biochemistry. Some non-biochemical examples are warranted.
5. Is the content duplicative of any other content already on Wikipedia? Inasmuch as the article is in ways a high level article which collects other subjects covered by Wikipedia, it is duplicative. However, it provides a useful summary of that information and organizes it into a single jumping off point from which users can follow the included links to more detailed articles. Through this, the article offers considerable value to Wikipedia.
1. Are the figures original and of high quality? Yes. I have no problems with the figures included in the article, and especially like the efficient inclusion of nonoriginal figures from Wikimedia. I would note, however, that the figure titled Enzymatic Transition State Stabilization is quite confusing. Where does the new methyl group come from? I understand that the incoming CH3 group is implied by the dashed line, but the fate of all the reactants and products are not clearly shown.
2. Are the figures informative and add to the text? Yes. The figures inform the text and are relevant to the relative sections. All figures are directly referenced by the text of the article and the captions are informative for a reader skimming through the article.
3. Are the Chemdraw structures chemically accurate, aligned, and easy to read? Yes, but again the transition state stabilization figure is quite confusing. I strongly recommend that this be corrected. Also, a minor problem with the chemdraw figures is that they use the default settings; I would recommend using the template favored by ACS Catalysis, which is known for its insistence on beautiful chemical structures.
1. Are the references complete (≥8)? Yes, there are twelve references spread through the article.
2. Are the references inclusive of non-journal sources? Yes, the references include cited books and even links to freely available, open access book chapters from Wiley.
Overall, the article contains a sufficient amount of content to provide coverage of the topic. The figures are well chosen, and aside from the last figure are of sufficient quality; incorporation of well-chosen secondary figures was done with good taste. However, the article still needs work: major sections need to be combined or eliminated in the applications section, and there are many examples of confusing or unclear explanations outlined above. A more thorough treatment of dispersion forces is desperately needed, as these forces are very important but only one sentence describing the underlying physics is given. Applications from areas beyond biochemistry are also needed, as are explanations of how π interactions are actually exploited in practice (such as iron N2 model complexes, protein structure organization, etc.).
UMChemProfessor (talk) 02:21, 5 November 2013 (UTC) The peer reviewers make some excellent points. The figures need to be consistent throughout, same scaling, sizing, etc. For example, some benzene rings have 'inner circles' and others have the double/single bonds drawn in. Be consistent!
Suggestions from ChemLibrarian (talk) 14:47, 5 November 2013 (UTC)
- You often times use sentences like "To see the Wikipedia page on H-bonding, click here". I don't see they are necessary since you can just add the internal link when you mention the term like H-bonding. In Wikipedia, people used to this way of following internal references. You may want to delete those sentences and just make internal references.
- You added nice images but all of them are in thumbnail. For some places it's good but for most paragraphs, you probably want to enlarge the picture and place them at the center of the page so that people can read them without clicking on them and the whole page can flow better too. See this page Wikipedia:Picture tutorial for how to place the image at different places and adjust the size.
- I see your images have a mixed file types (.png 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.
Peer review and responses during the educational assignment in Fall 2013
Response: Peer Reviewer #1
The sandbox previously linked "covalent bond" in the opening sentence, and directly contrasted non-covalent interactions as not the sharing of electrons but rather an electromagnetic/electrostatic interaction that does not involve sharing. We feel that is an appropriate distinction between the two, and if readers desire to look more into the differences, they can study the link to covalent bonds.
To the applications part, we agree that there are not enough examples outside of biology. We also agree that many items that we state in the second half of our introduction are repeated in the applications section. We have modified the wording and added examples that are less biochemistry related, yet still easy to understand and relate to.
For the concern regarding dipole-dipole interactions, we did further research and decided to more accurately break up the categories into electrostatic and van der Waals forces, of which dipole-dipole fits into. We hope that this may be easier to understand organizationally, but realize that hydrogen bonding is now not associated with dipole-dipole interactions and is instead listed under electrostatic. This is due to the van der Waals force page listing it as the forces outside of electrostatic, hydrogen bonding, and covalent bonding. To stay consistent, as well as distinguish the relative strengths between H-bonding and other dipole-dipole interactions, we felt that this organization was appropriate.
Regarding the hydrophobic effect, this section was indeed added to our page. However, it was not discussed in great detail because a Wikipage has already been created for this effect. Since our page serves as a starting point for all of the non-covalent interactions, we feel that a brief summary is appropriate for this section, with a link to a more detailed description.
As for π-effects, we agree that the pi-interaction page should be linked, and has been added to our Wikipage.
In regards to Applications, the title has been changed to “Examples.”
A link to “protein structure” has been added, as suggested.
An image was created for the “Drug Design” section using a commonly used local anesthetic, indicating relevant non-covalent interactions as they pertain to various chemical moieties.
Response: Peer Reviewer #2
The unit conversion is simply to make more clear the amount of energy needed to break a non-covalent bond to readers with little chemistry knowledge. Since the “calorie” is more easily understood than “kcal/mol”, we feel this is still appropriate to leave in for readers with lesser chemistry knowledge.
We have added non-biochemistry and non-supermolecular chemistry examples.
As for using acetate as the example for ionic bonds, we will change the molecule to reduce any possible confusion.
To respond to your comment regarding acetone in nail polish remover, many companies have actually phased out acetone in nail polish removers due to its possible link to liver damage and replaced it with ethyl acetate. Since some acetone-containing nail polish removers still may exist, we have modified our statement. However, we don’t feel that this is a major flaw in our overall argument.
With regards to further explanation of π-stacking, we feel that the link to the pi interaction page is sufficient, and no further detail is needed on our page (since there is already a well-written page on the subject).
Protein folding: We agree that the page was a bit heavy on the biochemistry examples. As such, the enzymatic function section has been eliminated and the protein structure and folding sections were combined. The comment was made that the protein segment was a bit long, but we have elected to keep the majority of the section as an example showing the interplay between the various non-covalent interactions in biological systems. It is also designed as a jump-off point with several internal links to related concepts such as “hydrophobic collapse,” “sterics,” “strain,” and the various orders of protein structures which may be of interest to the novice chemist.
The confusing “enzyme catalysis” chemdraw image was also removed.
A section was added regarding the non-covalent interactions (intermolecular forces) and their associated effects on boiling point – a non-biological application. Additional figures were also included.
Response: Additional comments
We agree that consistency is needed in the ChemDraw structures of the benzene molecules, and as a result have changed them to be consistent. Thank you for your input!
Response to ChemLibrarian
We have modified pictures to be mainly .png and of appropriate sizes and locations to make it easier and clearer to read through. Your tutorial was very helpful in doing this! We have also changed the way that linking is organized throughout our page according to more common practices.