User talk:GoBlue18/sandbox

Response to Peer Reviews

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.

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 to 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.

Note: These changes and responses were made by both contributors - I have just pasted the externally compiled responses GoBlue18 (talk) 09:14, 11 November 2013 (UTC)

Peer Review #1

Introduction

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.

Classifications

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.

Applications

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.

Reference

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.

Overall Presentation

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.

Trcum (talk)

Peer Review #2

Bisoxo (Jacob Geri), reviewing Non Covalent Interactions

Content

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.

Figures

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.

References

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 Presentation

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.).

Bisoxo (talk) 20:07, 4 November 2013 (UTC)

Additional Comments

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)

1. 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.
2. 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.
3. 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.