Wikipedia talk:WikiProject Chemistry

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WikiProject Chemistry
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Discussion of the WikiProject Chemistry - Please add your comment and discussion here. Older discussions are archived.

This discussion page is about the Chemistry project itself, for detailed, in-depth discussions about specific topics, you'd be best served at the talk page of the specific subject, e.g., Chemicals, Chemical infoboxes, etc. There is also an image request page which might be of interest to you.

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[edit] Assessment please

Would someone please do an assessment for superheated water? Richard001 (talk) 21:52, 4 April 2008 (UTC)

  • Done, B/Mid. I left autogenerated comments on the talk page for further improvements. Actually, I think it should be assessed against Physics rather than Chemistry? Wim van Dorst (talk) 13:43, 5 April 2008 (UTC).

[edit] Template:Reqchemstructure

Any chance of you guys merging the features of Template:Reqchemstructure into Template:Chemical drawing needed to eliminate one of the templates? Thanks. GregManninLB (talk) 16:04, 7 April 2008 (UTC)

Since {{Reqchemstructure}} was only used on two pages, I have redirected it to {{Chemical drawing needed}}. Though Reqchemstructure has a name more consistent with other image request templates, so if anyone wants to migrate all the templates the other direction, feel free. -- Ed (Edgar181) 16:31, 7 April 2008 (UTC)

[edit] The Periodic table

Someone moved Periodic table to The Periodic table, which IMO makes no sense. Could one of our many admins move it back please? --Itub (talk) 18:03, 14 April 2008 (UTC)

It's a vandal account too. Will take a look. DMacks (talk) 18:08, 14 April 2008 (UTC) Fixed, modulo the probably zillion double-redirects in its wake...I think a bot will clear those shortly. DMacks (talk) 18:14, 14 April 2008 (UTC)

[edit] Chemical Polarity

Could some kind person do an assessment for chemical polarity? Also, the page needs quite a bit of updating... I've been wikifying it a little, but real attention is needed. Thanks in advance! Señor Lelandro 04:53, 15 April 2008 (UTC)

[edit] Cladinose

Cladinose is described as "hexose deoxy sugar" but it is rather something like a "methyl ether of a branched heptose dideoxy sugar" - what would be an appropriate description in the article? Icek (talk) 18:18, 17 April 2008 (UTC)

[edit] Hydrogen donor

The article looks like a wrong understanding of the concept of proton donor. Have a look!--Stone (talk) 09:05, 20 April 2008 (UTC)

[edit] Zeisel

Ziesel reaction or Ziesel determination whats the difference and why do I have the feeling that both are the same?-Stone (talk) 20:21, 21 April 2008 (UTC)

[edit] Useful biographical resource

I recently came across the Biographical Database of the British Chemical Community, 1880-1970, from the Open University. I see that it is used in several articles already, but as it has details on "some 4860 chemists", we could use it a lot more. Could someone please list the page somewhere where others will be able to find and use it. Thanks. Carcharoth (talk) 11:37, 27 April 2008 (UTC)

[edit] Open Access Wiki

There is a new wiki designed to coordinate information on Open Access starting up at http://oad.simmons.edu/oadwiki/Main_Page. It's organised by such OA luminaries as Peter Suber. This could be a useful resource for Wikipedians in general. Walkerma (talk) 17:53, 5 May 2008 (UTC)

Looks good. But is there a more permanent place to list stuff like this and the link I provided in the previous section? Over time, people will lose track of what has been said here. Does anyone ever go back though the talk page archives and pick out the important points and links and changes? Carcharoth (talk) 19:16, 5 May 2008 (UTC)

[edit] {{Reaction_mechanisms}}

New template, per request at my talk. Comments, please? --Rifleman 82 (talk) 19:14, 6 May 2008 (UTC)

Looks good. Why is E1 elimination a redlink though... :-) Carcharoth (talk) 22:33, 6 May 2008 (UTC)
There are so many mechanisms already on wikipedia, though, what would define their inclusion? Off the top of my head, there are more SN's: SRN1, ANRORC, Vicarious nucleophilic substitution, then there are electrofilic substututions - (EAS, including DOM), various cycloadditions (including the famous Diels-Alder) and sigmatropic rearrangements (odd, there is no article for haptotropics). And this is just o-chem! Inorganics has its share of fun - Trans effect, Inner sphere electron transfer, Outer sphere electron transfer, and I am sure there's more related topics. --Cubbi (talk) 23:14, 6 May 2008 (UTC)
Yes, there are. There are three choices:
  1. no navbox
  2. navbox containing the most basic articles
  3. navbox containing all articles
I was originally thinking of the second choice, but even so, it'll be a judgment call. Fortunately, whatever I did there is not cast in concrete, we can still change it to be better. That's the approach I took for {{Chiral synthesis}}, {{Organometallics}}, {{Distillation}}, etc. --Rifleman 82 (talk) 18:36, 7 May 2008 (UTC)
E1 and E2 are both covered at elimination reaction. An eventual split could be considered. See also Category:Reaction mechanisms. --Itub (talk) 06:17, 7 May 2008 (UTC)
Seems like a difficult task. It seems that organic chemists, who traditionaly most religiously bought into the classification business, are coming to grips with the messiness that comes with the other elements, as found in homogeneous and heterogeneous catalysis, electron transfer, and proton-coupled this and that. IMHO. And maybe my skepticism is misplaced.--Smokefoot (talk) 12:52, 7 May 2008 (UTC)
Re R-82 comment above, it is my view that having a basic template with the most basic reaction mechanisms would be useful. At the moment there is no linking structure at all between various reaction mechanisms, all you can do is pop around from one "see also" page to another. Trying to make a definitive template with every mechanism is more trouble than it is worth, and in the end the big picture is lost amongst all the noisy details i.e. the importance of the SN2 mechanism as a concept would be lost when next to all the more specific reaction mechanisms such as the 2+3 sigma anti-angio plastic boo-hippy zip lock reaction mechanisms (yes I made it up) – option 2 is the only sensible (and useful) way to go -- Quantockgoblin (talk) 19:59, 7 May 2008 (UTC)
Yes, #2 looks like a good choice - just the major mechanisms. This is a very helpful template for bringing together the world of mechanisms - thanks a lot, Rifleman! It's surprising we didn't do this ages ago! One thing - is it only going to cover organic mechanisms, and if so, should it indicate that in the title? There is a list of the basic mechanisms here that is worth reviewing. Thanks, Walkerma (talk) 02:07, 8 May 2008 (UTC)

[edit] Chemistry wikis

There has been a lot of discussion of late regarding the possibility of a chemistry wiki. Many organisations such as ChemSpider (WiChempedia) and Rich Apodeca's Chempedia. What should be our response? Should we set up our own chemistry wiki, where we can do all the chemistry things we can't do on Wikipedia? Should we try to fight it? Collaborate with it? We will have an IRC discussion covering this topic on #wikichem on Tuesday at 1600h UTC (noon US EDT). ChemSpiderMan expects to attend, so he can give the ChemSpider view. Walkerma (talk) 05:43, 11 May 2008 (UTC)

IRC meets can never please everyone. It will be 2.00 a.m. for me. Is this the place to discuss things before the IRC meet. If so, I have a few questions:-
  1. Do either of these wikis have a substantial editor base, sufficient to keep them self-sufficient?
  2. Do either of them allow things that are desirable, yet can not be added to Wikipedia as they are against WP policies?
  3. What sort of collaboration do you think is possible? --Bduke (talk) 05:56, 11 May 2008 (UTC)

I think there is a real need for a place to compile useful chemistry knowledge. I would prefer establishing wiki to place routine procedures or useful tables that are often difficult to find. There are so many things that I end up searching forever to find, eventually forget, and then need to find 3 years later. If the Wiki's you are referring address only individual chemicals then they seem redundant. M stone (talk) 12:36, 12 May 2008 (UTC)

See User:Rifleman_82/Proposal for some ideas a few of us have been throwing around on IRC. I must emphasize that these ideas are not set in stone; the proposed chemistry wiki is NOT intended to poach editors from WP. Rather, the point of this wiki is that WP guidelines on "encyclopedic" material restrict us from being a truly chemistry-centric repository. Where appropriate, work done at this wiki will be fed back into WP, and vice versa. --Rifleman 82 (talk) 15:48, 12 May 2008 (UTC)
I added a "NOT" into Rifleman's post above - I'm pretty sure that's what he meant! Walkerma (talk) 19:31, 12 May 2008 (UTC)

OK, the answers to my questions (2) and (3) are relatively clear. Let me return to question (1). I am also active in the Scouting WikiProject and there is a wiki called ScoutWiki (in fact 12 different language ones - curiously the French and Finnish ones are larger than the English one}. The differences between the English ScoutWiki and WP are very similar to what you suggest, although the content of course is quite different. ScoutWiki can take stuff like details of individual troops that WP can not and so on. However, it is virtually dead because there are so few editors, and this has been the case for months. A couple of us on WP are moving articles over, but progress is slow, and mainly confined to articles on WP that really should not be here, at least in their present form. Unless ChemWiki can attract a substantial number of editors, I fear Rifleman's roadmap will not be achieved. --Bduke (talk) 22:51, 12 May 2008 (UTC)

Sorry if this is slightly off-topic, but is there a Ph.D. thesis wiki/library, where if you were so inclined you could post your complete Ph.D. thesis. I'd would have to check with my old Ph.D. supervisor if he was happy for it to be published in this way (I think the most of the remaining publication have been squeezed out of it by now), but in principle I would consider publishing it in this way. I presume others would consider this also? The stable carbene article has large parts of it based on the introduction to my thesis (and which is now growing with new edits, which is nice to see). There are a few more bits and pieces in my thesis that I'm sure people in the stable carbene world might want to pick through, especially some of the gritty practical matters - another resource for the chemwiki? I'm shooting a little from the hip here so maybe this is one of the proposals, or even completely outside the scope of the project? regards -- Quantockgoblin (talk) 23:20, 12 May 2008 (UTC)
As a distant spectator, sadly, I have to agree with Bduke's comments - I worry that R82's ideas are ahead of their time. When I last checked, even most of the Chem-oriented blogs were undersubscribed or lame. Certain sets of data are versatile and valuable, but I use Hans Reich's physical organic lists: http://www.chem.wisc.edu/areas/organic/index-chem.htm. One approach, admittedly vague, would be to get "anchoring" very useful data on WE or the wikichem project (pKa's, solvent purification, heats of formation) and more authoritative than many assume for WE-chem, possibly protected. Ideally such anchoring data could be imported from some benevolent source, in the US, possibly NIST.--Smokefoot (talk) 23:42, 12 May 2008 (UTC)
To be fair to R-82, the whole wiki-experiment shows that with enough people working at the same goal even with small contributions at a time, quite a lot can be achieved. This seems to be an antidote to apathy. That said, I'm not too sure I have the time to really put lots of oophff into this idea, but it is good idea in principle. I guess the question is whether it is worth trying -- Quantockgoblin (talk) 23:58, 12 May 2008 (UTC)
This is an idea that many of us have tossed around for years, but we have reached a point where people are beginning to go off and set up sites anyway. One key reason is that chemists want a structure searching capability (such as at chempedia), which is unavailable at Wikipedia. My own opinion is that isolated wikis will almost certainly fail, but if the various interested people (including many outside this group) can work together - either on one wiki, or by sharing content between sites - then I think a critical mass could be reached. If we can get a good amount of real content up fairly quickly, that could also get things moving and bring in more contributors. I'd also like to see groups like ACS, RSC, IUPAC supporting such a venture to give it some "official" status. (This may sound like wishful thinking, but these groups are all VERY interested in wikis.) This idea can definitely work, but it would have to be done very carefully. I think such a site would actually bring contributors to WP. More important, it could have a huge effect on the world of chemical information. Walkerma (talk) 02:14, 13 May 2008 (UTC)

I'd like to clarify that while I believe every word of that proposal, it does not belong to me alone. Just in case anyone thought otherwise. That was written on a wiki, in the usual many-revisions by many people. Not that it matters much.

One of the ways we can generate content would be opportunistic. I was thinking of collecting detailed, in-depth procedures (c.f. Org/Inorg Synth) simply by interested chemists running reactions, either directly from the literature, or modified (benzyl instead of methyl). Secondly, when using new chemicals, I run its NMR, IR, etc spectra out of the bottle to create baseline data. Very quickly, our spectrum library will be populated. For example, I did the literature prep of menthone, and I couldn't find the NMR structure anywhere. The literature synthesis would be copyright by OrgSynth, and to post the whole (detailed) synthesis here, as well as the NMR structure here would be unencyclopedic. As a result, I stuck could only give the synthesis a brief mention here, and I gave Chemspider the 1H, 13H here.

The point is that by letting users add data in small steps, as a short detour out of their usual route, there is a lower activation energy, and you get many more edits. I've been editing here for a few years, and when I used to start new reactions, I'd wiki the reactants and that's how some of them got their images drawn, chemboxes filled out, etc. --Rifleman 82 (talk) 05:09, 13 May 2008 (UTC)

Having our own wiki would also let us relook the chembox issue - perhaps storing the data in a database format, which is transcluded into the article when needed. This allows the data to be more easily curated, and mined, compared with the way we do it now - as an entry in the article itself --Rifleman 82 (talk) 05:13, 13 May 2008 (UTC)
Sulfanilic acid is where I've been experimenting with doing that. DMacks (talk) 05:46, 13 May 2008 (UTC)

I've also thought about chemically-enabled wikis, but the question I always come back to is: Why? In other words, what exactly is missing from MediaWiki or Wikipedia itself that makes these tools less than what they could be for chemistry? The answer I always come back to is "handling chemical structures." A secondary answer is "handling special datatypes such as spectra."

A Wiki that knew what chemical structures were, how to show them, how to edit them, and how to query them would enable many interesting scenarios. One of them would be a low-cost chemical laboratory notebook.

When seen from this perspective, it might make sense to do everything possible to first build on Wikipedia and/or MediaWiki before attempting to implement a solution from scratch.

Chempedia is an attempt to put this philosophy into practice: just build a cheminformatics layer on top of Wikipedia - don't try to replicate anything that Wikipedia is already doing well. The result, although far from where I want it to be, nevertheless shows what can be done with some fairly simple tools. Chempedia (talk) 19:57, 10 June 2008 (UTC)

[edit] Anyone into macromolecular chemistry or some flavor of nanotechnology?

I'm thinking of journals like http://pubs.acs.org/journals/ancac3 or the FNANO conference (http://www.cs.duke.edu/~reif/FNANO/FNANO08/FNANO08fullschedule.html). This is a fairly hot field in North Carolina, and I could probably find content experts and collaborators if there are interested Wikipedes. - Dan Dank55 (talk)(mistakes) 18:08, 14 May 2008 (UTC)

[edit] Deletion of chemical images on Commons

Following the deletion of a perfectly good PNG skeletal formula on Commons, I have been discussing the issue with an admin there.

I think that (except in very simple, obvious cases) only chemists are fit to decide whether a chemical image is worth keeping or not, so I propose we draft a set of guidelines on the issue for all concerned.

Ben (talk) 21:10, 14 May 2008 (UTC)

Were the images in use on Wikipedia articles? Seems like before deleting a commons item, one would check whether other WP projects are using that item instead of deleting it out from under them. If it's in an article, then that article would be a place to learn (or at least ask) if that image really is superfluous or of such poor quality that it should be killed. I don't know the technical terminology on commons nor what mechanism was used to delete this items for this case, but on en.WP, one uses PROD or similar and tags the articles that use the image with {{Ifdc}} instead of using administrative fiat. DMacks (talk) 21:27, 14 May 2008 (UTC)

The image was in use at furosemide. The admin deleted the image, then put the SVG in its place at furosemide. No notification, no discussion.

Ben (talk) 21:38, 14 May 2008 (UTC)

Deletion of raster images superseded by SVGs has been suspended for ages. As the uploader, you should have been notified of deletion, no matter the process (discussion, speedy, etc.) or reason!
As an aside, I'd like to apologize for the terrible quality of that SVG (one of my first, from when I barely knew my way around Inkscape). Regardless of the outcome here, I'll overwrite it with a proper structure ASAP. Fvasconcellos (t·c) 22:15, 14 May 2008 (UTC)

This particular image isn't really of any concern. I thought it was worth raising here since many WP:CHEM editors commented on the deletion of superseded images on Commons previously, and this action seemed to go against the agreement reached there. Might be a good time to set down a few simple guidelines in a short, easy-to-read way that all admins at Commons can see and all users at Commons can refer to quickly.

Ben (talk) 22:36, 14 May 2008 (UTC)

Wow—how much clearer than Commons talk:Deletion requests/Superseded can it get? :) Fvasconcellos (t·c) 22:51, 14 May 2008 (UTC)
I'm not sure about what you exactly mean. The statment on Commons:Commons:Deletion requests/Superseded is very clear. However, looking at the talk page it is much less clear. While high quality PNG such as the ones by Ben or Edgar should definitifely been kept, I strongly support the deletion of low quality structures, especially for those in JPG or GIF format, if they are superseded by an SVG or PNG version. We don't have to keep every crap. --Leyo 23:16, 14 May 2008 (UTC)
I quite agree. But the image deleted here was not GIF or JPG, was hi-res, big etc. If admins at commons can't tell the difference, we've got a problem!
Ben (talk) 23:21, 14 May 2008 (UTC)
No, of course not; but the reason for deletion in such cases shouldn't simply be "superseded because there is an SVG". There should be a rationale for why the image was superseded in the first place—SVG is not inherently superior to PNG, which is why {{vector version available}} is not considered a "superseded" template anymore. Besides, there should be a discussion before a low-quality image is deleted. Fvasconcellos (t·c) 23:25, 14 May 2008 (UTC)

I'd also like to add that Fvasconcellos's SVGs really are excellent and I'm sure everyone here will join me in thanking him for his enormous contribution to illustrating chemistry across the various Wikimedia projects. Fvasconcellos, NEUROtiker, Leyo, Slashme, Su-no-G and a few others are responsible for the vast number of top-quality SVG chemistry diagrams and structural formulae out there.

Some other uploaders have uploaded lower-quality chemical SVGs (1, 2, 3, 4) that clearly do not supersede the best-quality chemical PNGs from uploaders such as Ed, Smokefoot and Rifleman 82. The most common problem that severely affects a chemical SVG is bonds and atom labels not lining up properly due to some issue in the WP SVG-rendering software.

It's also important not to scare away users who are uploading top quality PNGs. Without those PNGs, half the SVGs we have wouldn't have been made anyway, as many of them are conversions. Also, there's nothing wrong with a good PNG, they do most of the things SVGs do just as well, with the bonus of being much easier to create for many people.

Ben (talk) 22:36, 14 May 2008 (UTC)

Indeed. The greatest advantages of SVG in my very humble opinion are small filesize (rarely more than 5 KB for a single structure, and often far less) and ease of editing (e.g. if one wants to create structures of closely related compounds from a "master" SVG, which I've done on several occasions). Nevertheless, PNGs are much, much faster—a minute or so once you get the hang of it—and much easier to create. I see no reason why both shouldn't coexist harmoniously :) Fvasconcellos (t·c) 23:07, 14 May 2008 (UTC)
P.S. Thanks for the compliment. Fvasconcellos (t·c) 23:07, 14 May 2008 (UTC)

Just a few thoughts, as I am the admin in question: I was editing the article de:Furosemide on de:WP, when I looked for an image on Commons. In fact I found four of them, one svg, one jpg, and two pngs. Believing in my youthful naivety that svg automatically is better I deleted the others and replaced them in the projects where they were used with the svg-Version.
One might argue that I did not follow due process (whatever that is), but the fact remains that we do not need four versions of the same formula. I have asked NEUROtiker to create a "nicer" version and replace the current, and he kindly agreed to do so in the next few days. Then at least the issue of the "prettier" image should be resolved.
I am now aware (admittedly I wasn't at the time of deletion) that the "Superseded-policy" has been suspended, however I strongly believe that the issue lies different with chemical formulas, for several reasons:

  • One version per structure is sufficient.
  • pixel-graphic have no advantage over svg
  • However svg have several advantages over pixel-graphics, as they are scalable, smaller in size, and as previously pointed out, easily adapted to other structures
  • The actual "creative" input that goes into creating formulas is relatively small, and they are PD anyways, so there is no (legal) need to preserve the history (saying this I mean no disrespect for those having created formulas. I have done a few myself and I know how much work goes in there until they are presentable. Therefore I am hugely grateful for the work done by the uploaders of the countless structures)

Therefore I would propose a different policy for chemical structures on Commons, stating that a) only 1 version should be kept and b) assuming chemical correctness and accordance with the guidelines for chemical structures, SVGs should be given preference. Lennert B (talk) 23:49, 14 May 2008 (UTC) P.S.:Sorry for all the confusion. I promise to never again do anything hasty structure-wise. But if a consensus is found then at least some good should come of it.

I place my comment down here, even though it's a reply to "Besides, there should be a discussion before a low-quality image is deleted.": There are so many crap structural formulas on Commons (besides many good or excellent ones), that it is not feasible to discussion each of them seperately. For this reason, we have the templates Template:Low quality chem and Template:Disputed chem and the associated categories Category:Low quality chemical diagrams and Category:Disputed chemical diagrams. Images in these categories can be deleted after one month and no reaction (upload of a new version, discussion) by the uploader or other users. --Leyo 23:53, 14 May 2008 (UTC)

One version per structure may not be sufficient - different views of the same molecule, for example (e.g. 1, 2). If one was SVG and the other PNG, some admins might follow the one-image-per-structure rule and delete the PNG, even though both images were good and had different uses.
SVGs are fine for display on WP, but try and insert them into a Word document and you're stuck. You need special software to use and manipulate SVGs. PNGs are easier to make and easier to use, so it is not true to say that raster images have no advantages over SVG. It would make sense to have one good SVG version and one good PNG version of each structure.
Also, are structural formulae all automatically PD? This was the subject of debate on Commons a while ago.
Ben (talk) 00:08, 15 May 2008 (UTC)
Sorry, that was unclearly phrased. Of course I am not arguing for the deletion of two different views of the same structure.
Good point, however the Mediawiki-Software renders them anyways, so rightclicking and "Save image as" will yield a PNG.
Oh dear, that's an entire different can of worms. As far as I remember they are, but if there is any uncertainty about it I prefer to leave this out of the discussion rather than getting side-tracked.
Lennert B (talk) 00:32, 15 May 2008 (UTC)
This is all fine, then. It's good that we're discussing it, because it means we raise a load of issues, find a policy for each that we can all agree to, then write it down for others to refer to.
If we're going to put dodgy images into death-row categories, we should at the least inform the uploader on their talk page and give them a chance to argue against deletion. If no good reason to keep is forthcoming within a couple of weeks, fine, go ahead and kill it.
We should also to re-state our position that it is perfectly acceptable to create and upload chemical images as PNGs (as long as they meet all the other criteria) - don't want to discourage potential illustrators. If someone else subsequently uploads an SVG of the same thing, the original PNG author should be contacted, and given a chance to give their seal of approval to the SVG version before the PNG is deleted.
Finally, the benefits of SVG over PNG are not so great, and the pitfalls of PNG are not so bad, that it is not necessary to replace all chemical PNGs with SVGs. It's much more productive for SVG-capable editors to create new content, rather than SVGing old stuff that is raster but good quality.
Ben (talk) 00:40, 15 May 2008 (UTC)

I agree that crappy, faulty, or low resolution structures should be deleted sooner or later if there is a high quality replacement available. However, I do not agree that there is any inherent superiority of SVG over PNG. Compressed high-res b/w PNGs are extremely small and nobody will (or should!) edit SVG structures directly (a molecule editor with the correct settings should be used instead). Leaving ideological reasons aside, it does not matter which file format is used, it is the quality of the content that counts. And in my experience, the majority of SVG replacements of PNGs were of low and/or inferior quality, probably because they were made by chemistry-inexperienced users. In my opinion, the "should be SVG" templates did much more harm than good for chemical structure diagrams. A simple "superseeded by SVG" template should never be used as a reason for deletion if the original structure is of sufficient quality. Template:Low quality chem and Template:Disputed chem would be much better indicators. Cacycle 02:43, 15 May 2008 (UTC)

After a wiki-holiday that lasted about a year, I'm a little fearful of mentioning this topic again ... but ... wasn't there talk about getting a "wiki-style template" on ACD [ChemSketch] (a very good and freeware chem-drawing package), and having the ability to save these structures in both .png and .svg format ([best link?])?
The advantage of a set "wiki-style" as a set style in the software package would be that every image drawn with it would automatically comply with the chemistry drawing style guidelines ([best link?]). This would solve many of the consistency problems, and would allow these images to be saved straight into .png and preferably .svg format. I don’t believe any free software (or even non-free software) currently offer this .svg saving option. Chemdraw I believe offers .png saving option.
I think the stumbling block was that the wiki-users interested in the idea (me included) seemed to drag their feet when it came to signing a sort of non-disclosure policy with ACD-chemsketch to test this wiki-template. I guess such a non-disclosure policy does not really fit in well with the general wiki-ish spirit of doing things. As this template and program are not being routinely used by chemistry wiki-users, I suspect that the idea never quite took off. As useful as I believe such a template and saving option would be, at the moment I don't have the time to breath life into this beast (in fact, I really should be doing something else as we speak!!), but maybe there are other editors that would be interested in picking up the baton (and showering themselves in glory) by establishing such a definitive wiki-style in a software package which can be used by anyone (even quite novice users) who wants to draw images on wikipedia ... -- Quantockgoblin (talk) 00:16, 20 May 2008 (UTC)
I use ChemSketch. I lost the settings for wikipedia, but I found it easy to make good quality images by using ACS settings, and exporting directly to PNG at 300 to 480 dpi resolution (PNG available for ChemSketch 11). --Rifleman 82 (talk) 05:31, 20 May 2008 (UTC)
I use ChemDraw (created my own template, I think I just cloned & renamed ACS?), which does indeed save directly to PNG (no need to save and then convert, as...somewhere in the WP:CHEM guides...suggests). BKChem can save directly to SVG. DMacks (talk) 05:47, 20 May 2008 (UTC)
The fact that ChemSketch 11 has PNG export is a direct result of our discussions last year. You draw it with ACS settings, then export to PNG as Rifleman describes and you're ready for upload. The thing that did flounder was the InChI export, because reaction schemes were generating bizarre combination-InChIs. Then ACD got interested in InChIKeys, so we decided to wait & see before we did any more. My plan was to get in touch with them to test InChIKey generation this summer (my best time) - with a hope of getting that into ChemSketch 12 or 13. That would make our structures findable using Google.
As for open software, GChemPaint (runs under Unix) allows automatic PNG generation, as was used in this demo image (which supposedly has embedded InChI too), as discussed here. Meanwhile I think BKChem allows direct SVG export, as described here. Walkerma (talk) 05:54, 20 May 2008 (UTC)

On a related point, would people be interested in putting together a clear set of "quality criteria" for chemical images on Commons? I discussed this with some Commons people last year when we had the last bout of unhelpful PNG→SVG conversions, and the response was positive. We would need to coordinate with German WP on this, as they are also significant producers of chemical imagery. Physchim62 (talk) 13:04, 20 May 2008 (UTC)

Great sounds like good progress - just to conclude, would it be fair to say then that we can scrap the idea of a "wiki-chemical-structure template" as such, and simply state that the prefered wiki drawing settings are the same as the ACS drawing settings? Sounds like a simple solution, and no extra work required. -- Quantockgoblin (talk) 13:10, 20 May 2008 (UTC)
Yes, after a great deal of work by participants in the structure drawing workgroup, the conclusion was that ACS setting are at least as good as anything else proposed (and better than many structures currently on WMF projects). That's all most chemists need to know, but it might be useful to have some wider guidelines so that non-chemist admins can see that the details are important and have been discussed! Some of these are aleady in our style guidelines, but to put them on Commons we would need to format them and to check that other projects are OK with them. Physchim62 (talk) 15:27, 20 May 2008 (UTC)

[edit] Tetrazolium chloride

Reduction of triphenyltetrazolium to formazan
Reduction of triphenyltetrazolium to formazan

Hi. Can you please have a look at the structure in the middle? We discuss(ed) on de-WP, if this reaction is correct or not. I would say no, because the 4 orbitals of the nitrogen atom are already occupied by the bonds and there is no space left for the radical. What do you think? --Leyo 17:37, 15 May 2008 (UTC)

Yep, I think you're right. It has 9 electrons, which is one too many. I think what is currently a N=N double bond should be a single bond, and the upe on the nitrogen atom that then only has 7 electrons. Of course, given that there is a mirror plane in reality the electron is not going to be localised on any one nitrogen atom, but delocalised; probably over the N-C-N fragment of the ring (off the top of my head, so don't quote me on that!).Chris (talk) 21:11, 15 May 2008 (UTC)
It's hard to represent such radicals with conventional Lewis structures. In molecular orbital terms, the additional electron goes into an antibonding orbital, which results in "breaking half a bond". You can think about it in terms of three-electron bonds; Pauling used a notation with three dots in his famous book The Nature of the Chemical Bond, for molecules such as Cl2− and Ne2+ (ASCII art figure below).[1] --Itub (talk) 08:22, 16 May 2008 (UTC)
  ..   ..         ..   ..
[:Cl···Cl:]−    [:Ne···Ne:]+
  ..   ..         ..   ..
I agree with Itub here: there is no breach of the orbital requirements of nitrogen by forming the radical. The electron goes into a delocalised π*-orbital, which is probably very nearly non-bonding in such an extensive delocalised system, especially if the redox potential is such that tetrazolium chloride can be used as a redox indicator in bilogical systems. There is nothing particularly unusual about such delocalised radicals: a common example is the deep-blue radical anion of benzophenone, generated by reduction of the ketone with sodium in anhydrous solvent and widely used as an idicator of the dryness of solvents such as THF and toluene. As this anion is commonly drawn, it would appear to have nine electrons on the oxygen, but the extra electron is actually delocalised over the entire π-system. Physchim62 (talk) 10:38, 17 May 2008 (UTC)

I took the structure of the cation from Acta Cryst. (1997). B53, 451-456, and assumed the radical has the same structure. I put the structural data into Spartan and did a semi-empirical calculation of the relevant π MOs. If anyone wants to see the results, I can send them out or upload them somewhere.

Ben (talk) 13:02, 17 May 2008 (UTC)

Computational Chemistry Wiki used to exist for this sort of data, but it seems to have died. I will see if there's anywhere else that would be interested in your upload – I'm sure there's somewhere, even if WP isn't quite the place! Physchim62 (talk) 18:28, 19 May 2008 (UTC)

Oh, no, it's not worth all that! It's only a quick and dirty calculation. I just made it in case anyone wanted to look at the shape of the MOs, to see what the skeletal formula can't show. But no need.

Ben (talk) 20:50, 19 May 2008 (UTC)

Oh well, I would be interested in how the reduction reaction would have to be redrawn correctly. 84.75.152.187 (talk) 21:09, 21 May 2008 (UTC)

[edit] Cocamide TEA

I have listed cocamide TEA for deletion as triethanolamides such as a "cocamido triethanolamide" do not exist (at least not as stable compounds). A Beilstein database search did not give a single hit for any triethanolamide and only 5 suspect hits for trialkylamides in general. The confusion probably stems from listings were "cocamide" and "TEA" (triethanolamine) were listed subsequently as different chemicals. Please comment on Wikipedia:Articles_for_deletion/Cocamide_TEA. Thanks, Cacycle (talk) 17:42, 17 May 2008 (UTC)

[edit] Cold fusion

The Cold fusion article has seen a lot of argumentation in the two years since it lost "featured article" status. However, there was a recent mediation that ended in mid-April that seemed to go well, in which all parties agreed that the article should say that the issues aren't settled, and the cases for both sides should be presented briefly, with enough references for readers to follow up the subject on their own. I recently finished a review that ended in upgrading it to a Good Article. I did quite a lot of the editing myself, and I was quite happy with the article at the time of my last edit, 00:28, 29 May 2008. My hope was that this was going to be one of those articles that Wikipedia can be proud of, by virtue of the fact that we manage to treat a contentious subject much more productively than other encyclopedias do.

The problem is that the skeptics who participated in the mediation were largely uninvolved during the Good Article review, and they have continued to be uninvolved, even after the article has been changed to say that cold fusion has not only been demonstrated, but that some explanations of it conform to "textbook physics". (I must have been reading the wrong textbooks, the ones that don't mention coherent phenomena involving millions of atoms at ordinary temperatures.)

So, what do we do with this one? I made a request on the talk page of User:Seicer, since he was the mediator, and he replied "I'll try to get to this soon. I've been out of town a lot and I haven't been able to get too involved in anything as of late." But even with his help, future options are limited, unless there are people who are not proponents who are willing to take an interest in the page. I can't and don't want to maintain it myself, but I'm interested in the subject of what can be salvaged, and which version of the page Version 0.7 and Version 1.0 should be most interested in. - Dan Dank55 (talk)(mistakes) 17:56, 1 June 2008 (UTC)

The article on cold fusion risks emerging as another example of Wikipedia being exploited to legitimize pseudoscience. The non-involvement of prominent scientists in this area of research speaks volumes (who at MIT, Oxford, CalTech, Munich, Kyoto, etc has large programs focused on cold fusion?). We witness similar albeit smaller waves of editing on other topics. Advocates of marginalized perspectives are highly energetic editors whereas mainstream scientists are too busy to do battle with quacks and nutcases. If this trend continues, Wikipedia risks becoming a forum for folksy perspectives, with all POV's represented. Not a disaster, but not great either.--Smokefoot (talk) 18:43, 1 June 2008 (UTC)
Okay, thanks, we got enough participation (including from Smokefoot) that I felt comfortable editing the lead myself. - Dan Dank55 (talk)(mistakes) 18:16, 2 June 2008 (UTC)
One more thing: we need some help from someone comfortable with quantum chemistry or physics to insert a couple of sentences to balance the sentence in the lead that says that some consider cold fusion to be consistent with textbook physics. Volunteers are encouraged to leave a message either on the article talk page or my talk page. - Dan Dank55 (talk)(mistakes) 18:25, 5 June 2008 (UTC)

[edit] Suggested merger of Glyphosate and Roundup

Please take part in the discussion. As of now, the latter article is essentially a duplicate of the former, with a potential to become a POV-fork. Colchicum (talk) 17:14, 5 June 2008 (UTC)

[edit] Oxypnictide

The new article Oxypnictide needs a hand from a inorganic chemist! What I would say that all nitrat, nitrit, phosphates and arsenates are part of this group?--Stone (talk) 07:18, 6 June 2008 (UTC)

The name would suggest that nitrate is an oxypnictide, but apparently the it is actually used in practice, the pnictogen is nearly always As, sometimes P or Sb, and the compounds are not simple salts like sodium nitrate, but more complex materials such as LaOFeAs with interesting conducting properties. --Itub (talk) 08:25, 6 June 2008 (UTC)
As the article gave no good description I was sure that it is not as simple! --Stone (talk) 09:40, 6 June 2008 (UTC)
It is perhaps a bit of a neologism. I had never heard the term before. It produces zero google books hits and only 21 google scholar hits, most of which are from 2007 or later. The oldest are a couple from 1994, in the Journal of Solid State Chemistry. --Itub (talk) 10:19, 6 June 2008 (UTC)
All comes from the hype on the iron based superconductors and the name coined by these japanese guys who discovered the stuff back in 2006.--Stone (talk) 10:21, 6 June 2008 (UTC)

[edit] Arsenobetane vs Arsenobetain

The article on Arsenobetane, but I think it should be called Arsenobetain. The main arsenic compound in fisch, crabs and in marine sediments is Arsenobetain according to various papers. doi:10.1039/b312956j or doi:10.1007/BF02143584. Should we rename it add a image and add the references?--Stone (talk) 08:55, 10 June 2008 (UTC)

Betaine is Me3N+CH2CO2− so arsenobetaine must be Me3As+CH2CO2−.
Ben (talk) 09:02, 10 June 2008 (UTC)
Arsenobetaine is already in Organoarsenic compound, but does the person who created the article mean that or is it a simple typo?--Stone (talk) 09:26, 10 June 2008 (UTC)

It should be Arsenobetaine; I'll move it. Chris (talk) 11:39, 10 June 2008 (UTC)

I've done the move, and recategoriwed the article: however, it still has a deserved {{expand}} tag on it, if anyone is feeling bored and valient ;) Physchim62 (talk) 15:42, 10 June 2008 (UTC)