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Error in structural formula for Cimetidine; how to fix?

As discussed at Talk:Cimetidine § Structural formula, the structural formula displayed there disagrees with the ball-and-stick model at File:Cimetidine-xtal-3D-balls.png and its reference R. J. Cernik; A. K. Cheetham; C. K. Prout; D. J. Watkin; A. P. Wilkinson; B. T. M. Willis (June 1991). "The structure of cimetidine (C10H16N6S) solved from synchrotron-radiation X-ray powder diffraction data". Journal of Applied Crystallography. 24 (3): 222–226. doi:10.1107/S0021889890013486. Confirmed in a 2017 article The topological phase diagram of cimetidine: A case of overall monotropy.

How does one go about redrawing this? 104.153.72.218 (talk) 12:14, 27 July 2017 (UTC)

The structural formula shown is a tautomer of the form shown in the ball-and-stick diagram, and since tautomers interconvert and can co-exist (depending on their relative energies), the inconsistency is not as serious as it might at first appear. However, the crystal structure determination from 2014 – doi:10.5517/ccz4vsq – matches the ball-and-stick diagram. There have been investigations of the tautomers such as doi:10.1016/S0022-2860(02)00491-X (from 2003) and doi:10.1016/j.aca.2015.02.033 (from 2015) and also suitable book references, so it seems to me that the tautomer issue could be discussed in the article, but that the question of the dominant form as the ball-and-stick form is settled.
As to your question of an updated drawing, I know of at least four approaches:
  1. If you click on the structure, you can see it is hosted at Wikimedia Commons and was updated recently by Vaccinationist, who also posts here at the English Wikipedia... so you could ask him or her directly.
  2. You can post somewhere like here and ask for an editor with structure drawing software to provide an updated / corrected image.
  3. You can look at the file at Commons in the category where the image is hosted, and see if there is an alternative available, such as File:Cimetidine Structural Formula V.1.svg, File:Cimetidine structure.svg, File:Cimetidine-2D-skeletal.png, File:Cimetidine-xtal-2D-skeletal.png, or File:Cimetidine.png. The same category also hosts two images on the synthesis of cimetidine, File:Cimetidine synthesis 01.svg and File:Cimetidine synthesis.svg, which could also be used to improve our article.
  4. You can search online for a correct image... since structure diagrams are ineligible for copyright, you can take an image and upload a replacement yourself.
Hopefully this helps in the present case and for any future cases where you find such inconsistencies... and good job on noticing it! EdChem (talk) 13:34, 27 July 2017 (UTC)
@EdChem: Thank you, I'm quite aware of tautomers, but the commenter on the talk page linked above explained why the form shown in the structural formula (with the methyl group on the double-bonded nitrogen) is quite unlikely.
Of the two papers you mention, the first describes only tautomers of the imidazole ring (swapping the hydrogen between the two nitrogens) and doesn't discuss the guanidine group at all. The second includes both, considering two possible ring tautomers (X and Y) with six possible guanidine tautomers (1 through 6, covering three possible double bond positions and two possible chiralities). In their numbering, the structural formula currently shown is X6 (with X3 being its stereoisomer).
But those are only listed as theoretical possibilities; the tautomer they actually identify (21 kcal/mol less stable that the primary, with a high enough interconversion barrier to make it stable) is X2/X5, with the double bond pointing to the thioether.
So cimetidine does have stable tautomers, but the one currently shown in Wikipedia is not one of them.
On the subject of the redraw, I've taken your suggestion and tried to politely ask Vaccinationist on commons. And I'm abashed that I didn't think to look for an alternative such as the ones you pointed out. That could be even faster. 104.153.72.218 (talk) 17:56, 27 July 2017 (UTC)
@104.153.72.218: Communications like these are vulnerable to misinterpretation as they lack the contextual clues available in other modes. I did not intend to slight your knowledge of chemistry, and I apologise for any impression to the contrary. I haven't looked at your contributions and took your question as coming from someone inexperienced with Wikipedia, which is why I described alternative approaches rather than simply making a substitution of the image myself – and I do agree that it should be replaced with an image of the dominant tautomeric form.
I didn't look at the talk page discussion in any detail, looking more to the crystal structure determination showing the C=N bond pointing to the nitrile (as does the ball-and-stick model), which is also used by PubChem, other language Wikipedias, discussions of cimetidine, etc. I fully agree that the image should be replaced, and if I were you, I would go ahead and put into our article one of the other images available on Commons.
In commenting on the difference being tautomeric, I was thinking of mistakes that we see from time to time where images are missing functional groups, chain lengths are wrong, or bonds in the wrong position leading to definitively non-interconvertable structures (1-butene v. 2-butene, say). If you have read Watson's book on the discovery of the structure of DNA, it speaks of tautomerisation of the bases and how it was a revelation to them that the typically-drawn tautomers were not the dominant forms, something that was common knowledge to the organic chemists. In this context, someone with limited chemical knowledge might look at the structure in our article and think it fundamentally different from the dominant tautomer, when in fact the differences can be quite minor in some systems.
My intent, both then and now, was to be helpful, which I hope you can recognise and accept. Wikipedia can certainly use more chemically-knowledgeable editors, so I hope you will continue editing. Might I also suggest that registering for an account would be desirable, it makes it much easier to be recognised and to build a reputation and track record so that others have an idea of your knowledge and experience? Kind Regards, EdChem (talk) 01:14, 28 July 2017 (UTC)
@EdChem: Absolutely no need to apologize at length! You were being helpful, and if my response failed to acknowledge that, I'm the one who should apologize. You were pointing out some glaringly obvious things I had overlooked, so if I felt at all talked down to, that was my own fault for firing off a public message before doing the additional research you ended up doing for me. And I owe you a second apology for making you do the additional work of writing a long beginner-friendly reply rather than a brief "isn't that just an equally valid tautomer?"
(And yes I learned the word "tautomer" from exactly that book! It's been decades, but I recall him being told something like "the textbooks are littered with implausible tautomeric forms".)
You found a couple of very useful references on tautomers of cimetidine which I hadn't thought to look for. On wading through the papers, it appears that they actually support my point, but it takes some careful reading, and I don't fault you for not having done it. I confess to thinking a bit of "Ha!" when I figured that out, but if that private thought manifested itself as the tiniest bit of gloating tone, I sincerely apologize. I was just trying to summarize the salient points of the papers in enough detail that you and others wouldn't have to read them yourselves, or could easily check my interpretation if you did.
What's interesting is the "implausible tautomer" is found in several other drug databases, e.g. https://www.drugbank.ca/drugs/DB00501 and http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?tab=structure&ligandId=1231 . It may actually be worth a mention in the article. (I don't feel qualified to judge the argument on the talk page criticizing the cyanide group placement; does it make sense to you?}
While we're on the subject, I of course ended up reading tautomer and ended up making edits there. Would you be willing to double-check my edit there? I find the "swap a hydrogen and a double bond" mental model convenient, but did I explain it well?
104.153.72.218 (talk) 06:36, 28 July 2017 (UTC)
This user likes to remain an anonymous contributor and thus edits only from IP address and does not use an account. ±
@104.153.72.218: I find the same model useful, and it is based on the IUPAC Gold Book definition. I have commented on your edit below, FYI, but I think the tautomer article has bigger issues. I am glad to see that you have swapped the image in the cimetidine article, and I do wonder if something (perhaps a note) might be added to that article on tautomeric forms and the use of a minor form (based on energy differences) in some places.
As for our misunderstanding, don't worry about it.  :) Though communication online is open to misinterpretations of tone, between people of goodwill these can be resolved through discussion. EdChem (talk) 02:22, 30 July 2017 (UTC)

Deep Carbon Observatory wants to sponsor a Wikipedia Visiting Scholar

Of possible interest to WikiProject members:

The Deep Carbon Observatory (DCO) is looking to sponsor a Wikipedia Visiting Scholar.

DCO is an initiative involving about 1,000 chemists, physicists, geologists, and biologists collaborating to study various aspects of carbon deep within Earth. The project's Engagement Team, which is based at the University of Rhode Island (URI), would like to facilitate improving Wikipedia's coverage of topics related to deep carbon by providing an experienced Wikipedian with access to 9,000 deep carbon-related publications as well as full remote access to the URI library's online resources (databases, ebooks, etc.). The Visiting Scholar will also receive a $3,000 honorarium and, if convenient, will be invited to URI for a visit (expenses paid).

The Visiting Scholars program connects Wikipedians with educational institutions based on shared interest in a topic. Any editor in good standing is welcome to apply. Professional experience is not a requirement. For more information, see the Deep Carbon Observatory Visiting Scholars page. If you have questions, you can ping me here or leave a message on my talk page. --Ryan (Wiki Ed) (talk) 18:53, 24 June 2017 (UTC)

Updated. --Ryan (Wiki Ed) (talk) 20:06, 30 July 2017 (UTC)

Tautomers

Above, the IP editor 104.153.72.218 asked that I comment on these recent edits but I think there is a more fundamental issue with the tautomer article.

To address the IP's question, I am uncomfortable with examples like "H−O−C=CH ⇌ O=C−CH2" for two reasons:

  1. both carbon atoms appear to have only three bonds, and the associated images such as File:Tautomers.svg are thus preferable representations, whether the examples are taken as showing bonds to methyl groups or simply a fourth bond around the carbon centre; and,
  2. the examples are redundant to, and possible confuse readers given their inconsistency with, the illustrations.

More fundamentally, the article lacks a clear definition and this leads to questionable content. The IUPAC Gold Book definition makes clear that movement of a double bond is an essential aspect of tautomerism, yet we offer as the example in the lede the interchange of zwitterionic and charge-free forms of amino acids, in which there is no movement of a double bond, and which I am not even sure interconvert that readily. The article is written as if the shifted group must be a proton, which is inconsistent with the Gold Book.

There are certainly journal articles (like doi:10.1021/jp307391s and doi:10.1021/ja00141a024) and this Masters thesis that do treat amino acids's charge-free and zwitterionic forms as examples of tautomerism, which fits with some definitions online – like Merriam-Webster but not dictionary.com. There are also books (like this one) which take a broader approach to what is required for tautomerism, though books like March (my copy, anyway) keeps the definition in line with the Gold Book.

I think the tautomer article needs to be redrafted to express:

  • A basic definition in line with IUPAC
  • Examples of the standard cases first
  • Cases like 5-bond examples (in Gold Book definition) and non-proton
  • Coverage of atypical but sometimes used approaches like with amino acids, making clear that these are not included within the standard definition but are consistent with broader definitions used in some places

I am posting to seek input on this suggested approach, and on where consensus lies on what are / are not examples of tautomerism and what should be included. EdChem (talk) 02:16, 30 July 2017 (UTC)

You might check March or Vogel or a mainline textbook if you want to support an article on tautomers. IUPAC can be dogmatic and often seems to trying to overturn long traditions. --Smokefoot (talk) 02:36, 30 July 2017 (UTC)
I did check March, which is why I said "books like March (my copy, anyway) keeps the definition in line with the Gold Book." I do take your point on IUPAC dogmatism, though. Would you consider +
H
3NCH(R)CO−
2 ⇌ H
2NCH(R)COOH an example of tautomerism, Smokefoot? EdChem (talk) 08:05, 30 July 2017 (UTC)
Sorry I was not paying sufficient attention. --Smokefoot (talk) 13:17, 30 July 2017 (UTC)
@EdChem: Thank you for the detailed feedback! Yes, I was a bit uncomfortable with the missing bonds too, but I think there's great benefit in illustrating the generic form H−X−Y=Z ⇌ X=Y−Z−H stripped of as much irrelevant detail as possible. I couldn't figure out a way to recognize the additional bonds without damaging that clarity.
Options I'm considering are:
  1. Some additional introductory text saying that bonds not participating in the tautomerism are omitted. E.g. "the formulas here are not complete, as the intermediate atoms have additional bonds which are omitted for clarity."
  2. Adding "R" to the intermediate atoms, e.g. "H−NR−CR=O ⇌ NR=CR−O−H", "H−CR2−N=O ⇌ CR2=N−O−H"
  3. Adding a "free radical" dot, e.g. "H−N•−C•=O ⇌ N•=C•−O−H"
Another thing the article doesn't make clear is that the hydrogen doesn't actually move; it's exchanged with the surrounding solute, via an intermediate form with both (or neither) hydrogen.
As for the IUPAC definition, I generally like it (and I swear I invented the "H−X−Y=Z" notation independently!), but anything that excludes ketene–ynol is clearly too strict. And whether the glucose ring/chain isomerism is technically included or not, it requires discussion because it's so commonly called tautomerism.
We could start the article with the IUPAC definition and then describe other things as generalizations of it.
(I would definitely like an example where the group G is something other than a proton.)
104.153.72.218 (talk) 15:01, 31 July 2017 (UTC)
@104.153.72.218:: Having the generic form with X, Y, and Z largely avoids the missing bond problem, as who is to say how many bonds an X should have. The problems, as I see them, with your suggestions are: "omitted for clarity" is obvious to those who understand and confusing for those who don't, wondering what exactly is omitted; adding R's can be taken to mean they are all the same, adding R1, R2, R3, etc, just adds to cognitive load; free radicals confusing and extraneous. All up, I prefer a diagram with bonds to nowhere rather than text representations, or symbols unconnected to actual atoms. My thoughts on the article, at present:
  • Add a "Definitions" section immediately after the lede, starting from the IUPAC definition (generic) and perhaps that the keto-enol us the archetypal example. After that, add expanded definitions section covering ketene-ynol, amino acid awitterions etc (based on available sources).
  • A mechanism section could be added, explaining that direct 1,3-hydride shift is impossible, and then into comments on the actual mechanism (acid / base catalysed, solvent involvement, etc.) I think this should also make clear that this is unrelated to resonance as there are genuinely multiple interconverting forms. Also needed is that there can be (and usually is) a dominant form (maybe this acetamide example?).
  • A section of examples with links to all the standard cases under IUPAC and then broader definitions including ring-chain and the valence tautomerism.
  • Ignore the lede, I find it is much easier to write a summary once the main part is written.
  • A G ≠ H example would be good, certainly
Cheers, EdChem (talk) 15:38, 31 July 2017 (UTC)

World Science Photo Competition 2017

FYI Wikipedia_talk:WikiProject_Science#World_Science_Photo_Competition_2017--Alexmar983 (talk) 08:51, 6 August 2017 (UTC)

The article Precipitation (chemistry) needs attention.

It's of rather poor quality for such a important subject. OrganoMetallurgy (talk) 16:52, 7 August 2017 (UTC)

Yes the article is problematic. A diligent reader would come away with some idea of the concept. Some tweaking as you have done will help, but the real cure for the problem is WP:SECONDARY: textbook and reviews are the indispensable foundation for articles on such general topics.
It is helpful that you and all of us continue to highlight our problem articles.--Smokefoot (talk) 02:37, 8 August 2017 (UTC)

RfC: Colour group 12 as post-transition metals

I am seeking comments on a proposal to color code the group 12 elements as post-transition metals in the Wikipedia periodic table, rather than transition metals as they are currently color coded.

The RfC can be found here. Sandbh (talk) 23:04, 9 August 2017 (UTC)

Lattice constants of B12As2

Hello,

I found for the french page fr:Subarséniure de bore crystal space group is n° 166 on http://materials.springer.com/isp/crystallographic/docs/sd_0529519 but to see the lattice constants, it's necessary to have a login. Would any of you have a login on this site to give those constants, please ? --Titou (talk) 08:48, 10 August 2017 (UTC)

Instead of that page this is from Atom Work [1] which is free after registration
a = 0.53268 nm, b = 0.53268 nm, c = 0.53268 nm,
α = 70.504 °, β = 70.504 °, γ = 70.504 °
Cell volume 0.13004 nm3

or

a = 0.6149 nm, b = 0.6149 nm, c = 1.1914 nm,
α = 90 °, β = 90 °, γ = 120 °
Cell volume=0.3901 nm3
calculated Cell density -3.57 Mg m-3
Z=6

location of atoms in cell: 

                               symmetry x              y                z         
As 	As 	6 	c 	3m 	0 	        0 	        0.10019 	
B1 	B 	18 	h 	.m 	0.48417 	0.51583 	0.19513 	
B2 	B 	18 	h 	.m 	0.43623 	0.56377 	0.04777

also available are optical and electrical properties. Graeme Bartlett (talk) 09:25, 10 August 2017 (UTC)

Original source listed as "Mater. Res. Soc. Symp. Proc.,1987,97,,145-149,Morosin B., Aselage T.L., Feigelson R.S." if you can work out what that is. Graeme Bartlett (talk) 09:52, 10 August 2017 (UTC)
I'm guessing the first part is "materials research society symposium proceedings" OrganoMetallurgy (talk) 12:46, 10 August 2017 (UTC)
Found the source. Crystal Structure Refinements of Rhombohedral Symmetry Materials Containing Boron-Rich Icosahedra doi:10.1557/PROC-97-145.
Thanks a lot to all! --Titou (talk) 17:33, 10 August 2017 (UTC)

New letter on errors

I wanted to alert members of this WikiProject to a recently published letter to the editor in the Journal of Chemical Education, which outlines multiple errors in Wikipedia articles about chemistry topics, including Pfitzner–Moffatt oxidation and novobiocin. [2] Everymorning (talk) 17:41, 10 August 2017 (UTC)

I wrote to the editor to see if the journal would entertain a response. I think the idea is not to show bitterness from the Wikipedia side. Instead, the response could point out that Wikipedia-Chem is pretty good but knows it is imperfect. The response could also point out that it would have been easy for the author of that letter to correct the problem rather than publish such a criticism. Perhaps such a letter could encourage readers of J Chem Ed to contribute, if they can manage to do so without WP:COI, the perennial problem.--Smokefoot (talk) 18:23, 10 August 2017 (UTC)
@Everymorning:, the article was discussed here earlier and the previous discussion is located here in the archives. OrganoMetallurgy (talk)

Help with theoretical stuff

I'm working on a project involving theoretical elements, so I'm trying to make a reference page for it. Can someone here help me fill out the missing electrons per shell counts in this section? It starts with 122. I haven't done anything with chemistry for over 27 years. I appreciate any help. ···日本穣 · 投稿 · Talk to Nihonjoe · Join WP Japan! 03:11, 12 August 2017 (UTC)

Facto Post – Issue 3 – 11 August 2017

Facto Post – Issue 3 – 11 August 2017

Wikimania report

Interviewed by Facto Post at the hackathon, Lydia Pintscher of Wikidata said that the most significant recent development is that Wikidata now accounts for one third of Wikimedia edits. And the essential growth of human editing.

Internet-In-A-Box

Impressive development work on Internet-in-a-Box featured in the WikiMedFoundation annual conference on Thursday. Hardware is Raspberry Pi, running Linux and the Kiwix browser. It can operate as a wifi hotspot and support a local intranet in parts of the world lacking phone signal. The medical use case is for those delivering care, who have smartphones but have to function in clinics in just such areas with few reference resources. Wikipedia medical content can be served to their phones, and power supplied by standard lithium battery packages.

Yesterday Katherine Maher unveiled the draft Wikimedia 2030 strategy, featuring a picturesque metaphor, "roads, bridges and villages". Here "bridges" could do with illustration. Perhaps it stands for engineering round or over the obstacles to progress down the obvious highways. Internet-in-a-Box would then do fine as an example.

"Bridging the gap" explains a take on that same metaphor, with its human component. If you are at Wikimania, come talk to WikiFactMine at its stall in the Community Village, just by the 3D-printed display for Bassel Khartabil; come hear T Arrow talk at 3 pm today in Drummond West, Level 3.

  • Plaudit for the Medical Wikipedia app, content that is loaded into Internet-In-A-Box with other material, such as per-country documentation.
Editor Charles Matthews. Please leave feedback for him.
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MediaWiki message delivery (talk) 10:55, 12 August 2017 (UTC)

Should there be a hyphen in "Fourier-transform infrared spectroscopy"?

Somebody recently moved the page from Fourier transform infrared spectroscopy to Fourier-transform infrared spectroscopy (with a hyphen between "Fourier" and "transform"). If you have an opinion about which punctuation is better, please comment at Talk:Fourier-transform infrared spectroscopy#Propose to undo recent move. --Steve (talk) 12:23, 15 August 2017 (UTC)

Request for comment regarding the proposal to move Periodinane to Iodane

Please comment here Talk:Periodinane. OrganoMetallurgy (talk) 12:51, 15 August 2017 (UTC)

Template:Molar mass

Template:Molar mass

Just granpa (talk) 19:19, 17 August 2017 (UTC)

Interesting, but seems far surpassed by Module:MolarMass in scope/flexibility. DMacks (talk) 21:18, 20 August 2017 (UTC)

Are you a potential WikiFactMine collaborator?

I spent three days on a stall at Wikimania not long ago, and have been updating the WikiFactMine pages on Wikidata, to give a quite full view of the project. It applies fact mining to recent open access papers downloaded from Europe PubMed Central. Custom sets of search terms called "dictionaries" are used, and recently we have almost completely switched over to Wikidata and SPARQL queries to generate these dictionaries. With a new tool to convert a query into a dictionary, the process can be quite slick, though typically data work is needed also.

If you are interested in trying out our highly-parallel search technology, I'd be glad to help you. So far we have concentrated on plants, diseases and drugs. I'd be particularly interested in increasing what we do in fields of chemistry, where I have worked recently on alloys and terpenoids, and food science.

Let me know on my User talk page if you'd like to know more. Charles Matthews (talk) 16:44, 23 August 2017 (UTC)

Best matching between WP article and WD item

We manually curate data in WD by comparing some identifiers present in the WP:en infoboxes about chemicals with those available in WD. One of our big challenges is to identify the subject of the articles of WP:en because in some cases an article of WP:en corresponds to several items in WD due to the fact that WP articles often mix different subjects. In some cases, the WP:en article is not connected to the correct item according to data found in the infobox.

Just take the article about acetate. The first sentence of the article speaks about salt, the second sentence about ion and latter in the article we have a chapter about acetate esters. The current WD item linked to this article is the item about the family of acetate ester but the infobox is about the acetate ion. One possibility to match the identifiers in the infobox with the ones in the item about acetate ion, we can change the link of the article to the item about the ion.

Nothing is wrong, so nothing has to be changed, but here comes the questions: what is the best way to link an WP article with an WD item ?

If I take the example of anion, often in WP:en, the article aims for the ion AND for the family of compounds where the anion is present. WD split the 2 subjects so what is the best solution according to your opinions ? If we have a clear response from your side, we will adopt an uniform solution when we will encouter a similar case, simplifying our curation job. Please add your vote in the following part and only the solution for the majority of agreement will be applied by WD curation team. Thanks for your help. Snipre (talk) 21:17, 20 August 2017 (UTC)

Case 1

  • When an WP article speaks about one ion and the family of salts containing this ion,
    • the WP:en article has to be linked to the WD item about the ion
      • ...
    • the WP:en article has to be linked to the WD item about the family of salts
      • ...
    • the WP:en article has to be linked to the WD item about the chemical described by the infobox
      • ...
    • WP:en is the only responsible of the choice of the WD item linked to the article
      • ...

Case 2

  • When an WP article speaks about one chemical and a mixture of chemical containing the chemical,
    • the WP:en article has to be linked to the WD item about the chemical
      • ...
    • the WP:en article has to be linked to the WD item about the mixture of chemicals
      • ...
    • the WP:en article has to be linked to the WD item about the chemical described by the infobox
      • ...
    • WP:en is the only responsible of the choice of the WD item linked to the article
      • ...

Remarks

@Snipre: I don't know much about wikidata, but why can't one article be linked to multiple WD items? OrganoMetallurgy (talk) 01:56, 22 August 2017 (UTC)
@OrganoMetallurgy: It's a featur of the system: one item can only be linked to one article per wikipedia. I am not an expert of WD but if I can propose an explanation, I think it is a question of cache: when opening an article some data of the connected item are charged in the cache, allowing a faster access to these data. Perhaps I am wrong but definitively the restriction of one item = one article avoid any confusion when retrieving a value using the properties. Snipre (talk) 19:27, 23 August 2017 (UTC)

Facto Post – Issue 2 – 13 July 2017

Facto Post – Issue 2 – 13 July 2017

Editorial: Core models and topics

Wikimedians interest themselves in everything under the sun — and then some. Discussion on "core topics" may, oddly, be a fringe activity, and was popular here a decade ago.

The situation on Wikidata today does resemble the halcyon days of 2006 of the English Wikipedia. The growth is there, and the reliability and stylistic issues are not yet pressing in on the project. Its Berlin conference at the end of October will have five years of achievement to celebrate. Think Wikimania Frankfurt 2005.

Progress must be made, however, on referencing "core facts". This has two parts: replacing "imported from Wikipedia" in referencing by external authorities; and picking out statements, such as dates and family relationships, that must not only be reliable but be seen to be reliable.

In addition, there are many properties on Wikidata lacking a clear data model. An emerging consensus may push to the front key sourcing and biomedical properties as requiring urgent attention. Wikidata's "manual of style" is currently distributed over thousands of discussions. To make it coalesce, work on such a core is needed.


Editor Charles Matthews. Please leave feedback for him.
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4-Pyrazolone

4-Pyrazolone apparently...

Could someone with access to Scifinder please do a quick look-up on 4-pyrazolone for me? Commons currently gives the structure on the right (I'm guessing because ChemSpider does) but I really doubt it's correct. My access to journals is pretty limited these days. --Project Osprey (talk) 23:54, 29 July 2017 (UTC)

Cool idea in view of the discussion above.
  • The hydroxypyrazole: 4843-98-5 48 hits
  • The aminoiminoketo tautomer 27662-65-3 10 hits
  • The ChemSpider tautomer: zero hits. Not sure whether ChemSpider is just a poor search tool, or my search technique is flawed, but I entered your structure and SciFinder gave me back the two alternative tautomers.
most cited (non-med chem) paper on the first: "A theoretical treatment of solvent effects on the tautomeric equilibria of five-membered rings with two heteroatoms"

Karel'son, M. M.; Katritzky, Alan R.; Szafran, Miroslaw; Zerner, Michael C. Journal of the Chemical Society, Perkin Transactions 2:  Physical Organic Chemistry (1972-1999) (1990), (1), 195-201.--Smokefoot (talk) 01:27, 30 July 2017 (UTC)

Cheers. I'm trying to improve Pyrazolone at the moment, despite its exotic feel the group is ancient and has definable applications. Trying to unpick the tautomerisation issue is tricky, there are many papers spread across the decades but no reviews that I can find. Sufficed to say its tautomers appear to be expansive, especially when you start including zwitterions. The chemspider form clearly isn't a tautomer as the keto group has shifted (I think its a pyrazol-4-one and someone has gotten there naming systems in a spin). The hydroxypyrazole would be the logical form but I just wanted to check. --Project Osprey (talk) 08:42, 30 July 2017 (UTC)
What you have here appears to be a dihydropyrazolone, the kekule ring structure needs two double bonds not one. Plasmic Physics (talk) 19:47, 17 August 2017 (UTC)
I've proceded to fix the file name. The SMILES for pyrazol-4-one is as follows: O=C1C=NN=C1 . Plasmic Physics (talk) 05:51, 24 August 2017 (UTC)

National Nanotechnology Day

National Nanotechnology Day is coming up on October 9 (because nano is 10^-9, of course). DNA nanotechnology is planned for TFA that day, and it would be great to have some DYKs as well. A lot of nanoparticles by composition articles are missing or short and are good targets for DYKs. Shockingly, there's no Gold nanoparticle article—it redirects to Colloidal gold, which is an overlapping but different subject. Similarly, there are a lot of chemical reactions involving nanomaterials that could be created or expanded; some sections of Fullerene chemistry, Carbon nanotube chemistry, and Selective chemistry of single-walled nanotubes could be split out into new articles. I'm happy to collaborate on nanotechnology articles; please ping me if you're interested. John P. Sadowski (NIOSH) (talk) 04:41, 29 August 2017 (UTC)

There are many nations. Are you referring to the US? --Leyo 08:15, 29 August 2017 (UTC)
Yes, it is a U.S. initiative. Here's a link. John P. Sadowski (NIOSH) (talk) 18:54, 29 August 2017 (UTC)
Leyo: welcome to US-think, a recurring issue in en.wikipedia. Getting back to the suggested activity, my recommended first step is to just move almost all content from Colloidal gold to Gold nanoparticle. --Smokefoot (talk) 19:15, 29 August 2017 (UTC)

ISO 4 redirects help!

{{Infobox journal}} now features ISO 4 redirect detection to help with the creation and maintenance of these redirects, and will populate Category:Articles with missing ISO 4 abbreviation redirects. ISO 4 redirects help readers find journal articles based on their official ISO abbreviations (e.g. J. Phys. A → Journal of Physics A), and also help with compilations like WP:JCW and WP:JCW/TAR. The category is populated by the |abbreviation= parameter of {{Infobox journal}}. If you're interested in creating missing ISO 4 redirects:

  • Load up an article from the category (or only check for e.g. Chemistry journals).
  • One or more maintenance templates should be at the top of page, with links to create the relevant redirects and verify the abbreviations.
  • VERIFY THAT THE ABBREVIATION IN |abbreviation= IS CORRECT FIRST
  • There are links in the maintenance templates to facilitate this. See full detailed instructions at Category:Articles with missing ISO 4 abbreviation redirects.
  • |abbreviation= should contain dotted, title cased versions of the abbreviations (e.g. J. Phys., not J Phys or J. phys.). Also verify that the dots are appropriate.
  • If you cannot determine the correct abbreviation, or aren't sure, leave a message at WT:JOURNALS and someone will help you.
  • Use the link in the maintenance template to create the redirects and automatically tag them with {{R from ISO 4}}.
  • WP:NULL/WP:PURGE the original article to remove the maintenance templates.

Thanks! Headbomb {t · c · p · b} 12:47, 31 August 2017 (UTC)

Requesting reinforcements

Hi all, I am surprised by the low quality of the QM/MM article considering the importance of the topic, before some of you run away as this is not your field of expertise ;) please could I get help on things such as WP:GNOME work as well. I have also included a todo list on the articles talk page please take a look (fix it if need be first time I have ever added one). The reviews I have referenced should be quite accessible to anyone with a chemistry background even if they are not specialists in theoretical/computational chem. Thanks EvilxFish (talk) 18:51, 7 September 2017 (UTC)

RfC: Replace categories of poly/diatomic nonmetal with less active/active nonmetal

I am seeking comments on a proposal to change the name and composition of two of the colour categories appearing on our periodic table, as follows:

From Polyatomic nonmetal
C, P, S, Se		 Diatomic nonmetal
H, N, O, F, Cl, Br, I
To Less active nonmetal
H, C, N, P, S, Se		 Active nonmetal
O, F, Cl, Br, I

The RfC can be found here. Sandbh (talk) 23:49, 9 September 2017 (UTC)

Thank you for bringing this to our attention. EvilxFish (talk) 11:20, 10 September 2017 (UTC)

User:Theislikerice/chemistry

I thought I should bring this to the attention of the chemistry experts here.—Anne Delong (talk) 01:21, 12 September 2017 (UTC)

Electroless nickel vs. Electroless nickel plating

Does it make sense to have articles for Electroless nickel and Electroless nickel plating? Or should they rather get merged? --Leyo 07:37, 13 September 2017 (UTC)

Method of style

Hi everyone. I think that it is time we have a look at the method of style regarding how we treat complex compounds in articles, specifically, complexes featuring neutral ligands. We need to set out some guidelines as to when and where it is appropriate to treat a hydrate as an aqua complex in name, formula and discussion; and when and where it is appropriate to omit the hydrate. Should lability of the neutral ligand, or the ability to dehydrate the compound by heating, or homolepticity be taken into account? As a point of discussion, I'd like to refer to copper(II) sulfate, where both cases are used interchangeably. Plasmic Physics (talk) 02:47, 17 September 2017 (UTC)

Facto Post – Issue 4 – 18 September 2017

Facto Post – Issue 4 – 18 September 2017

Editorial: Conservation data

The IUCN Red List update of 14 September led with a threat to North American ash trees. The International Union for Conservation of Nature produces authoritative species listings that are peer-reviewed. Examples used as metonyms for loss of species and biodiversity, and discussion of extinction rates, are the usual topics covered in the media to inform us about this area. But actual data matters.

Dorstenia elata, a critically endangered South American herb, contained in Moraceae, the family of figs and mulberries

Clearly, conservation work depends on decisions about what should be done, and where. While animals, particularly mammals, are photogenic, species numbers run into millions. Plant species lie at the base of typical land-based food chains, and vegetation is key to the habitats of most animals.

ContentMine dictionaries, for example as tabulated at d:Wikidata:WikiFactMine/Dictionary list, enable detailed control of queries about endangered species, in their taxonomic context. To target conservation measures properly, species listings running into the thousands are not what is needed: range maps showing current distribution are. Between the will to act, and effective steps taken, the services of data handling are required. There is now no reason at all why Wikidata should not take up the burden.

Editor Charles Matthews. Please leave feedback for him.
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MediaWiki message delivery (talk) 14:46, 18 September 2017 (UTC)

Iodometry

Can someone please edit the Iodometry article? There are some sentences which sound were basically fused by mistake, like - To a known volume of sample, an excess but known amount of iodide is added, which the oxidizing agents oxidizes iodide to iodine. 93.142.92.50 (talk) 16:49, 21 September 2017 (UTC)

I did a quick cleanup - I hope that's a bit better now. Others are welcome to rework it some more. Thanks for reporting it! Walkerma (talk) 05:29, 22 September 2017 (UTC)

{{Chembox}} name change

Proposal: {{Chembox}} → {{Infobox chemical}}. See Template_talk. -DePiep (talk) 11:21, 1 October 2017 (UTC)

Article creation experiment

FYI you may like to read Science Is Shaped by Wikipedia: Evidence from a Randomized Control Trial. The articles were posted by Carolineneil (talk · contribs · deleted contribs · logs · filter log · block user · block log) and may require attention. SmartSE (talk) 10:07, 4 October 2017 (UTC)

See also Wikipedia:Administrators' noticeboard/IncidentArchive965#Single purpose account for mass adding articles by a number of PhD students for paid experiment on Wikipedia. DMacks (talk) 13:47, 4 October 2017 (UTC)

Can we agree to eradicate RCOOH (vs RCO2H)?

This question is about one of those very unimportant issues that bug some (me) chemists: the formula for carboxylic acids. I suspect that RCOOH is archaic, but I am unsure. If we can agree on my proposal, maybe we can enter this into our MOS. --Smokefoot (talk) 17:50, 1 September 2017 (UTC)

I do strongly prefer RCOOH. In a chemical structure, however, I prefer having the carboxylic acid drawn explicitly (i.e. not to condense it to –COOH). --Leyo 19:31, 1 September 2017 (UTC)
I oppose, the proposed formula suggests that the bonding types of the two oxygen atoms are identical. Plasmic Physics (talk) 09:35, 2 September 2017 (UTC)
I suspect the trouble with this is that we will have a large group of people who will come in and be annoyed by RCOOH, considering it to have been superseded in common usage by RCO2H, and we will also have a large group of people and be annoyed by RCO2H, considering it to have been superseded in common usage by RCOOH. A brief look at the multitude of basic chemistry texts I have suggests that they are both right about their preferred form being common, and both wrong about the other one having become archaic, perhaps even in their particular text or syllabus. The most reasonable course is surely to keep both in free variation, since people are going to have to be familiar with both anyway. Double sharp (talk) 15:30, 2 September 2017 (UTC)
I'd like to hear from more chemists. My annoyance is minor. It is just one of those things. No journal or textbook that I consult seems to use this construction, but maybe I am not looking in the right places. I wonder if Leyo or other adherents could cite some prominent source. Agreed that RCOOH was common many decades ago. My grandfather's books on dyes use it, for example. It's not a big deal. --Smokefoot (talk) 18:57, 2 September 2017 (UTC)
IUPAC Blue Book appears to use COOH in both the 1993 version[3] and 2004 draft[4]. In some areas--admitedly rare cases unless you're discussing organic oxidants--using CO2H is clearer to the reader when trying to distinguish among acid, peroxyacid, and higher analogs (acyl tri/tetraoxides); CAS# 958758-62-8 is the pathological case. DMacks (talk) 19:14, 2 September 2017 (UTC)
And thinking of ambiguoity or that CO2H implies both O are equivalent, COOH could imply both O are consecutive in the structure rather than the first being a carbonyl. Hydroperoxycarbenes are an interesting area of study. But then CO2H could also be a dioxirane if you want to push into corner cases. DMacks (talk) 19:22, 2 September 2017 (UTC)
@DMacks: CO2H Does not imply they are equivalent. There are plenty of instances of a molecular formula having multiple of a particular atom that are coordinated differently. One example is Methanium (which is actually drawn wrong on the article and I should fix at some point :D ). EvilxFish (talk) 20:32, 3 September 2017 (UTC)
Georginho's way is the best: RC(=O)OH. Peace!
(I would go with what IUPAC uses in their books.)
Georginho (talk) 19:16, 3 September 2017 (UTC)
Whereas perhaps a standard should be set in order to create uniformity across all wikipedia articles I am personally more familiar with RCOOH, that being said we should probably adopt the IUPAC standard (if there is one). In reality as you said it isn't that big a deal. EvilxFish (talk) 20:18, 3 September 2017 (UTC)
I am chastened! Even March uses RCOOH. Sigh.--Smokefoot (talk) 21:55, 3 September 2017 (UTC)
The IUPAC Blue Book 2013 uses only COOH (543 hits vs 0 hits for „CO2H” doing pdf search), but in structure drawings neither COOH nor CO2H is acceptable or preferred (Graphical Representation Standards for Chemical Structure Diagrams (IUPAC Recommendations 2008); from the examples of esters, I think acceptable are C(O)OH and C(=O)OH, and preferred is File:Carboxylic-acid-skeletal.svg). Wostr (talk) 14:31, 5 September 2017 (UTC)
Check out JACS or ACIE or JOC or Org Lett etc etc. --Smokefoot (talk) 17:08, 5 September 2017

(UTC)

Every publisher or even journal has its own preferred system. I accidentally saw this discussion where nobody mentioned the newest Blue Book or IUPAC recommendations about chemical structure drawing and I thought that pointing the fact that „CO2H” is not used there may be helpful. If it's not, you can ignore my comment, as I'm not en.wiki editor and it's really not my concern. Wostr (talk) 13:38, 7 September 2017 (UTC)
I can't recall when I've ever seen it written as RCO
2H. Plasmic Physics (talk) 20:05, 5 September 2017 (UTC)
My organic chemistry textbook (published in 2013) uses both...GalobtterTalk to me! 07:40, 5 October 2017 (UTC)

An offline app for Chemistry

Hello everyone,

The Kiwix people are working on an offline version of several Wikipedia subsets (based on this Foundation report). It basically would be like the Wikimed App (see here for the Android light version; iOS is in beta, DM me if interested), and the readership would likely be in the Global South (if Wikimed is any indication): people with little to no access to a decent internet connexion but who still would greatly benefit from our content.

What we do is take a snapshot at day D of all articles tagged by the project (minus Biographies) and package it into a compressed zim file that people can access anytime locally (ie once downloaded, no refresh needed). We also do a specific landing page that is more mobile-friendly, and that's when I need your quick input:

  1. Would it be okay for you if it were hosted as a subpage of the Wikiproject (e.g. WikiProject Chemistry/Offline)? Not that anyone should notice or care, but I'd rather notify & ask
  2. Any breakdown of very top-level topics that you'd recommend? (see Wikipedia:WikiProject_Medicine/Open_Textbook_of_Medicine2 for what we're looking at in terms of simplicity) Usually people use the search function anyway, but a totally empty landing page isn't too useful either. Alternatively, if you guys use the Book: sorting, that can be helpful.

Thanks for your feedback! Stephane (Kiwix) (talk) 12:28, 10 October 2017 (UTC)

Valid criticism

See Wikipedia’s Science Articles Are Elitist for a valid criticism of Wiki science. Far too often the articles are written for other science specialists with little thought to the general reader who might want to learn a bit, but is driven away by sci nerds talking/showing off to other sci nerds. Thoughts? Vsmith (talk) 18:23, 13 October 2017 (UTC)

Clearly at least the lead sentence and preferably the whole lead should be written in a way so that it can be understood by a wide audience. It also depends on how specialized the topic is. There is a hierarchy of articles from the general to the more specialized. More general articles should be written in a more accessible style. The linked critique above gives a couple of examples. Graphene (growing technological importance; rated high importance) and Electroweak interaction (Nobel prize; rated high importance) in my opinion fall in the more general category while nonribosomal peptide (rated low importance) is more specialized. Boghog (talk) 20:27, 13 October 2017 (UTC)
Timely article. There are various issues, to expand on Boghog:
  • stuff for specialists only. Many articles are not written for general readers. I recently wrote about zirconium acetylacetonate. About 2200 papers/patents mention it, which suggests that the topic will appeal to other specialists, but not to Joe Sixpack.
  • intermediate cases. Many thousands of chemical compounds are on ingredient lists. And many thousands of processes are intrinsically chemical. Think cooking, cleaning, fuels, cosmetics, clothing. These are areas where chemistry editors can more readily help readers. And we can remind them that they live in a chemical world (and therefore need to employ more of us). One challenge is to find good sources.
  • Final point: WP:NOTTEXTBOOK, to quote: "The purpose of Wikipedia is to present facts, not to teach subject matter."

--Smokefoot (talk) 22:16, 13 October 2017 (UTC)

There's some validity to the argument - but at the same time I don't think its as easy as the article makes out. The article you cite is a blog and as such is free to adopt a conversational tone when discussing things, this can be very helpful for explaining entirely new concepts. Wikipedia however tries to keep to an encyclopedic tone and that language can make technical concepts sound even more technical. That's not to say that its impossible to have an article that is technical, encyclopedic and easily understood; but it is hard. In terms of where to begin with this, to me the obvious place to start would be most popular pages in Chemistry. --Project Osprey (talk) 01:06, 14 October 2017 (UTC)
Agree w/ project osprey. Not always the easiest to balance having explanations with conciseness. But honestly even as a science nerd I found the lead sentence in graphene absolutely horrible at explaining what graphene is. So I've rewritten it. Galobtter (talk) 15:46, 14 October 2017 (UTC)

Article in need of attention

Hello all. Could someone more knowledgeable than me take a look at F number (chemistry)? I don't think I recall the concept from my organic chemistry (which was some time ago). I stumbled upon it because it has been listed as an orphan for 8.5 years. Any efforts to beef it up or deorphan it would be much appreciated! Happy editing! Ajpolino (talk) 02:13, 21 September 2017 (UTC)

I can't find any other refs which use F number in this way on GBooks, and it doesn't show up in my old chemistry textbook. I've PRODed the article. If this is a notable topic and I'm just missing it please remove the PROD tag and add references or point me in a direction where I might find some. Thanks! Happy editing! Ajpolino (talk) 23:36, 14 October 2017 (UTC)
It seems to be used and referenced in a few dozen liquid chromatography primary research papers. But I cannot see any reviews. You could probably get some information on its effects, can calculated values for several substances. Graeme Bartlett (talk) 01:39, 15 October 2017 (UTC)
Good find! I'd missed those before (got swamped out by the optical "F-number" articles). I don't see anything from the last 20 years, does anyone know if this term is still used? If it's totally outdated and only a few primary papers every reference it, perhaps we should just merge to polycyclic aromatic hydrocarbon? Thoughts? Ajpolino (talk) 02:18, 15 October 2017 (UTC)
This is my search: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=R.J.+Hurtubise+%22F+number%22&btnG= A merge sounds like a good idea, as although it may scrape past notability, there is not much written about the number. Graeme Bartlett (talk) 02:26, 15 October 2017 (UTC)
I added some details to the article, including the usefulness/application of it (rather than just measuring it) for chromatography. I found refs from multiple research groups and up through 2005, so I de-PRODed. DMacks (talk) 03:07, 15 October 2017 (UTC)
Great! Thanks! Ajpolino (talk) 05:18, 15 October 2017 (UTC)

Article for Creation

Why don't we have a dedicated article to cover the topic of metallisation - the phase transition that occurs under pressurisation of a solid that most importantly results in the delocalisation of electrons leading to the appearance of metallic characteristics in the solid? I thought that this would be a relatively important article to have. Plasmic Physics (talk) 23:49, 13 October 2017 (UTC)

@Plasmic Physics: I certainly plan to make one eventually (under the title Metal-insulator transition), but it may take years before I get around to it. You should try asking about it on the Wikiproject Physics talk page since it's more of a physics topic than a chemisty topic. OrganoMetallurgy (talk) 00:24, 14 October 2017 (UTC)
I may take on the challenge, that way you can add to it in pieces when have time. The only problem is that I know very little about it. I could also post a notification at Physics, although I believe that this is a interdisciplinary topic, relating to both chemistry and physics. Plasmic Physics (talk) 00:39, 14 October 2017 (UTC)
@Plasmic Physics: I'm rather embarrassed to point out that the page Metal–insulator transition already exists and has existed for about a decade. I really ought to have checked to see if it already existed before posting my initial response. OrganoMetallurgy (talk) 19:19, 15 October 2017 (UTC)

Facto Post – Issue 5 – 17 October 2017

Facto Post – Issue 5 – 17 October 2017

Editorial: Annotations

Annotation is nothing new. The glossators of medieval Europe annotated between the lines, or in the margins of legal manuscripts of texts going back to Roman times, and created a new discipline. In the form of web annotation, the idea is back, with texts being marked up inline, or with a stand-off system. Where could it lead?

1495 print version of the Digesta of Justinian, with the annotations of the glossator Accursius from the 13th century

ContentMine operates in the field of text and data mining (TDM), where annotation, simply put, can add value to mined text. It now sees annotation as a possible advance in semi-automation, the use of human judgement assisted by bot editing, which now plays a large part in Wikidata tools. While a human judgement call of yes/no, on the addition of a statement to Wikidata, is usually taken as decisive, it need not be. The human assent may be passed into an annotation system, and stored: this idea is standard on Wikisource, for example, where text is considered "validated" only when two different accounts have stated that the proof-reading is correct. A typical application would be to require more than one person to agree that what is said in the reference translates correctly into the formal Wikidata statement. Rejections are also potentially useful to record, for machine learning.

As a contribution to data integrity on Wikidata, annotation has much to offer. Some "hard cases" on importing data are much more difficult than average. There are for example biographical puzzles: whether person A in one context is really identical with person B, of the same name, in another context. In science, clinical medicine require special attention to sourcing (WP:MEDRS), and is challenging in terms of connecting findings with the methodology employed. Currently decisions in areas such as these, on Wikipedia and Wikidata, are often made ad hoc. In particular there may be no audit trail for those who want to check what is decided.

Annotations are subject to a World Wide Web Consortium standard, and behind the terminology constitute a simple JSON data structure. What WikiFactMine proposes to do with them is to implement the MEDRS guideline, as a formal algorithm, on bibliographical and methodological data. The structure will integrate with those inputs the human decisions on the interpretation of scientific papers that underlie claims on Wikidata. What is added to Wikidata will therefore be supported by a transparent and rigorous system that documents decisions.

An example of the possible future scope of annotation, for medical content, is in the first link below. That sort of detailed abstract of a publication can be a target for TDM, adds great value, and could be presented in machine-readable form. You are invited to discuss the detailed proposal on Wikidata, via its talk page.

Editor Charles Matthews. Please leave feedback for him.
If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Opted-out of message delivery to your user talk page.
Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 08:46, 17 October 2017 (UTC)

Short interview for the Wikipedia Facebook page about your work

Hello,

My name is Melody and I work on the Foundation's blog and social team. We elevate our community's work and help people better understand the facts they see on Wikipedia. As you may know, October 23 is "Mole Day," an unofficial holiday celebrated by chemists to honor Avogadro's Number. We would love to use this day as a way to help people better understand the mole, learn some facts related to the mole, and (if there's interest here) let them know about WikiProject Chemistry. If you are interested in helping with this effort or have feedback, please let me know. This is an experiment, and I'm looking forward to discussing further. (And if this doesn't work out, given the short notice, I'd love to think about a way to amplify your work in a different way.) Thank you!

MKramer (WMF) (talk) 14:05, 19 October 2017 (UTC)

The underlying idea is pretty simple "I have 10g of water, I wonder how many molecules that is?" the sticking point for most people is getting your head around how big that number actually is. A mole of pennies is more money that exists in the world, a mole of marbles would cover the Earth to a depth of 50 miles, there are plenty of analogies on Google. Such analogies don't appear in our articles as they're not exactly encyclopedic but they might be a good way of engaging a new audience, a la XKCD.
On a separate note, how did we end up with separate articles on Avogadro constant and Mole (unit)? I would have thought them fairly indivisible! --Project Osprey (talk) 14:53, 19 October 2017 (UTC)
By extension, those sorts of analogies can convey just how small a molecule is. Those marbles covering the Earth 50 miles deep? That's how many molecules are in a little over a tablespoon of water. DMacks (talk) 17:46, 19 October 2017 (UTC)
Yes, show and illustrate order of magnitude. Don't even try to describe ;-) , and surely without math formulae ... For example, physics is about the size range 10−20 – 10+20. Even recent: the InTheNews gravitational wave is about Neutron stars that "a teaspoon full weighs as much as ...". Unfortunately I'm not sure I can help this specific OP question. -DePiep (talk) 20:11, 19 October 2017 (UTC)
Definitely interested though I am not available on the 23rd, I have some great ways of representing the concept of a mole though from when I was at school years ago. EvilxFish (talk) 07:31, 20 October 2017 (UTC)

Facto Post – Issue 5 – 17 October 2017

Facto Post – Issue 5 – 17 October 2017

Editorial: Annotations

Annotation is nothing new. The glossators of medieval Europe annotated between the lines, or in the margins of legal manuscripts of texts going back to Roman times, and created a new discipline. In the form of web annotation, the idea is back, with texts being marked up inline, or with a stand-off system. Where could it lead?

1495 print version of the Digesta of Justinian, with the annotations of the glossator Accursius from the 13th century

ContentMine operates in the field of text and data mining (TDM), where annotation, simply put, can add value to mined text. It now sees annotation as a possible advance in semi-automation, the use of human judgement assisted by bot editing, which now plays a large part in Wikidata tools. While a human judgement call of yes/no, on the addition of a statement to Wikidata, is usually taken as decisive, it need not be. The human assent may be passed into an annotation system, and stored: this idea is standard on Wikisource, for example, where text is considered "validated" only when two different accounts have stated that the proof-reading is correct. A typical application would be to require more than one person to agree that what is said in the reference translates correctly into the formal Wikidata statement. Rejections are also potentially useful to record, for machine learning.

As a contribution to data integrity on Wikidata, annotation has much to offer. Some "hard cases" on importing data are much more difficult than average. There are for example biographical puzzles: whether person A in one context is really identical with person B, of the same name, in another context. In science, clinical medicine require special attention to sourcing (WP:MEDRS), and is challenging in terms of connecting findings with the methodology employed. Currently decisions in areas such as these, on Wikipedia and Wikidata, are often made ad hoc. In particular there may be no audit trail for those who want to check what is decided.

Annotations are subject to a World Wide Web Consortium standard, and behind the terminology constitute a simple JSON data structure. What WikiFactMine proposes to do with them is to implement the MEDRS guideline, as a formal algorithm, on bibliographical and methodological data. The structure will integrate with those inputs the human decisions on the interpretation of scientific papers that underlie claims on Wikidata. What is added to Wikidata will therefore be supported by a transparent and rigorous system that documents decisions.

An example of the possible future scope of annotation, for medical content, is in the first link below. That sort of detailed abstract of a publication can be a target for TDM, adds great value, and could be presented in machine-readable form. You are invited to discuss the detailed proposal on Wikidata, via its talk page.

Editor Charles Matthews. Please leave feedback for him.
If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Opted-out of message delivery to your user talk page.
Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 08:46, 17 October 2017 (UTC)

Short interview for the Wikipedia Facebook page about your work

Hello,

My name is Melody and I work on the Foundation's blog and social team. We elevate our community's work and help people better understand the facts they see on Wikipedia. As you may know, October 23 is "Mole Day," an unofficial holiday celebrated by chemists to honor Avogadro's Number. We would love to use this day as a way to help people better understand the mole, learn some facts related to the mole, and (if there's interest here) let them know about WikiProject Chemistry. If you are interested in helping with this effort or have feedback, please let me know. This is an experiment, and I'm looking forward to discussing further. (And if this doesn't work out, given the short notice, I'd love to think about a way to amplify your work in a different way.) Thank you!

MKramer (WMF) (talk) 14:05, 19 October 2017 (UTC)

The underlying idea is pretty simple "I have 10g of water, I wonder how many molecules that is?" the sticking point for most people is getting your head around how big that number actually is. A mole of pennies is more money that exists in the world, a mole of marbles would cover the Earth to a depth of 50 miles, there are plenty of analogies on Google. Such analogies don't appear in our articles as they're not exactly encyclopedic but they might be a good way of engaging a new audience, a la XKCD.
On a separate note, how did we end up with separate articles on Avogadro constant and Mole (unit)? I would have thought them fairly indivisible! --Project Osprey (talk) 14:53, 19 October 2017 (UTC)
By extension, those sorts of analogies can convey just how small a molecule is. Those marbles covering the Earth 50 miles deep? That's how many molecules are in a little over a tablespoon of water. DMacks (talk) 17:46, 19 October 2017 (UTC)
Yes, show and illustrate order of magnitude. Don't even try to describe ;-) , and surely without math formulae ... For example, physics is about the size range 10−20 – 10+20. Even recent: the InTheNews gravitational wave is about Neutron stars that "a teaspoon full weighs as much as ...". Unfortunately I'm not sure I can help this specific OP question. -DePiep (talk) 20:11, 19 October 2017 (UTC)
Definitely interested though I am not available on the 23rd, I have some great ways of representing the concept of a mole though from when I was at school years ago. EvilxFish (talk) 07:31, 20 October 2017 (UTC)

Women in Red November contest open to all


Announcing Women in Red's November 2017 prize-winning world contest

Contest details: create biographical articles for women of any country or occupation in the world: November 2017 WiR Contest

Read more about how Women in Red is overcoming the gender gap: WikiProject Women in Red

(To subscribe: Women in Red/English language mailing list and Women in Red/international list. Unsubscribe: Women in Red/Opt-out list)

--Ipigott (talk) 07:36, 23 October 2017 (UTC)

Gibbs–Duhem equation

Gibbs–Duhem equation (edit | talk | history | protect | delete | links | watch | logs | views)

An IP editor has attempted to add some information here, but the mathematical notation (as well as some of the later attempted explanation/reasoning) makes no sense (I've reverted it a few times on these grounds, but they seem fairly adamant). Unfortunately, I know very little about chemistry, so I thought I'd ask for some extra eyes here. There also appears to be a mild English issue which is making things more difficult. See also some discussion at WP:RD/MA#Equivalence_between_differential_expressions. Thanks! --Deacon Vorbis (talk) 14:10, 25 October 2017 (UTC)

Gilbert Stork, 1921-2017

It appears that Gilbert Stork has sadly died at 95. Our current article on him is pretty paltry and while biographies aren't exactly my thing I'll be having a go at improving it over the coming days. Help, particularly from those of you with an organic background, would be appreciated. Here's a nice (open access) paper of amusing anecdotes about him doi:10.1002/anie.201200033 (and the fact that Angewandte would publish such a thing says enough about him). --Project Osprey (talk) 13:12, 24 October 2017 (UTC)

Not a synthesis guy but will help out. Would appreciate it if you checked my work as well. Kind regards EvilxFish (talk) 14:01, 24 October 2017 (UTC)
Also are you sure he is dead? The only evidence I can find is a blog post. EvilxFish (talk) 14:06, 24 October 2017 (UTC)
Aside from Derek Lowe's blog post, I don't see it announced in the news yet either. I would generally consider Lowe a reliable source though. -- Ed (Edgar181) 14:11, 24 October 2017 (UTC)
It's up now on the Columbia website: https://chem.columbia.edu/news/gilbert-stork-1921-2017/.
I'm too old for organic chemistry. I didn't know that his wife is also a synthetic chemist!
Georginho (talk) 19:05, 25 October 2017 (UTC)

Peroxide reorg

I wonder if we should not reorganize peroxide, which is a collection of information on H2O2, [O2]2-, organic hydroperoxides (ROOH), diorganic peroxides.

A proposal:

  • make peroxide exclusively about inorganic peroxides (Na2O2, etc), guiding readers from the get-go to related articles. One slight problem is that in the US, "peroxide" means hydrogen peroxide to nonchemists.
  • hydrogen peroxide could/should absorb content from peroxide that is about H2O2.
  • Peroxy acid (about both inorganic and organic) seems to be ok.
  • split organic peroxide into
    • hydroperoxides, currently a redirect to peroxide, should be stand-alone. They are fairly common. I might need admin help and advice on making that move vs copy-paste.
    • diorganoperoxides (ROOR, not exactly sure what they should be called), but they are topical because of interest in acetone peroxide and the like. Would possibly include dibenzoy peroxide.

Suggestions welcome. --Smokefoot (talk) 17:53, 11 November 2017 (UTC)

I wouldn't say inorganic peroxides are what I'd expect to find at peroxide. Does peroxide usually mean inorganic peroxide to chemists? Could create the article Inorganic peroxide and make peroxide the disambiguation..  Galobtter (talk) 18:23, 11 November 2017 (UTC)
Those ideas are excellent. They solve a lot of problems.--Smokefoot (talk) 18:59, 11 November 2017 (UTC)
I think that Peroxide should cover the organic and covalently bound molecules exclusively. We should split off an article called Peroxide ion, which obviously covers the ion itself, the hydroperoxide ion, and salts containing these ion. I believe that Peroxide should only discuss covalent compounds which are covered in their own articles in the context of ROOR chemitry. In other words, if a comparisson isn't made, it does not belong on this article. Plasmic Physics (talk) 20:09, 11 November 2017 (UTC)
I think Smokefoot's "slight problem" is actually a pretty serious one. We're not a chemistry encyclopedia, but an everyone encyclopedia. I don't think people outside of science are likely to know or care about anything except "the thing most people call peroxide, that is H2O2". And maybe they know about the bleaching agent for hair or fabric. But among science people, there are multiple other meanings (the ion, the organic class, etc.). I don't support having the simple "peroxide"-named page be a specialized article when the layperson meaning is not that, assuming a specialized WP:COMMONNAME case. Instead, I support following WP:CONCEPTDAB and having peroxide be a general top-level article with summaries of the meanings and links to each one's page. That's pretty much what Galobtter said, except I think it might be possible to write a concise intro and bit about each meaning as an article rather than just a DAB list-of-links. DMacks (talk) 20:29, 11 November 2017 (UTC)
Yes, I'd think that'd be quite a bit more useful than a simple DAB. Agree that meanings should be clear to everyone since we're an everyone encyclopaedia. Galobtter (talk) 04:48, 12 November 2017 (UTC)
Summary of action:
I will continue to refine as I locate further secondary and tertiary sources. Thank you for the advice, --Smokefoot (talk) 18:53, 12 November 2017 (UTC)
Oh dear I just took a look at the (now old) peroxide article and it didn't really contain a summary of the different peroxides. Pretty awful article - just a random mishmash of various information. Galobtter (talk) 19:08, 12 November 2017 (UTC)
Okay, I made Inorganic peroxide redirect to metal peroxide and also added a few plural redirects. Currently hydroperoxide redirects back to peroxide.. Galobtter (talk) 05:00, 13 November 2017 (UTC) I made hydroperoxide redirect to organic peroxide, which seems to make more sense.... Galobtter (talk) 05:05, 13 November 2017 (UTC)

Facto Post – Issue 6 – 15 November 2017

Facto Post – Issue 6 – 15 November 2017

WikidataCon Berlin 28–9 October 2017

WikidataCon 2017 group photo

Under the heading rerum causas cognescere, the first ever Wikidata conference got under way in the Tagesspiegel building with two keynotes, One was on YAGO, about how a knowledge base conceived ten years ago if you assume automatic compilation from Wikipedia. The other was from manager Lydia Pintscher, on the "state of the data". Interesting rumours flourished: the mix'n'match tool and its 600+ datasets, mostly in digital humanities, to be taken off the hands of its author Magnus Manske by the WMF; a Wikibase incubator site is on its way. Announcements came in talks: structured data on Wikimedia Commons is scheduled to make substantive progress by 2019. The lexeme development on Wikidata is now not expected to make the Wiktionary sites redundant, but may facilitate automated compilation of dictionaries.

WD-FIST explained

And so it went, with five strands of talks and workshops, through to 11 pm on Saturday. Wikidata applies to GLAM work via metadata. It may be used in education, raises issues such as author disambiguation, and lends itself to different types of graphical display and reuse. Many millions of SPARQL queries are run on the site every day. Over the summer a large open science bibliography has come into existence there.

Wikidata's fifth birthday party on the Sunday brought matters to a close. See a dozen and more reports by other hands.

Editor Charles Matthews. Please leave feedback for him.
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MediaWiki message delivery (talk) 10:02, 15 November 2017 (UTC)

Scientific images from WSC2017

Please take a look in here about newly uploaded scientific images on commons during Wiki Science Competitions 2017.--Alexmar983 (talk) 06:29, 17 November 2017 (UTC)

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