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Review request for QM/MM article

Hi all, I have recently added a lot of changes to the QM/MM article. I would appreciate it if these changes are reviewed for accuracy, clarity and general English/formatting. EvilxFish (talk) 14:01, 14 November 2018 (UTC)

@EvilxFish: Just stumbled across this request from ages ago. From someone with a lot of experience with traditional MD simulations but not much with QM/MM: your additions look good, though I'd split up the last equation, it's too long for one line. I think the article could use more context-setting and explanation of the types of systems the method is usually used to study - right now this is limited to a sentence in the lead without any further discussion in the body of the article. Personally, I'd move the stuff about scaling and efficiency into its own body section, use the lead to explain a bit further what kinds of systems lend themselves to QM/MM treatment, and add a new body section (maybe even with a diagram) discussing common use cases in more detail. (I'm a bio person so using a QM description of the active site to explore enzyme reaction mechanisms is the only one I know much about.) Also, the material currently in the second paragraph of the lead could use some updates, e.g. PME isn't really "recent". Opabinia regalis (talk) 05:19, 16 January 2019 (UTC)
@Opabinia regalis: Thank you for your feedback, much appreciated, I will dig up my references when I get time and make the suggested changes. Many thanks EvilxFish (talk) 09:18, 16 January 2019 (UTC)

Deletion discussion, 23 Jan 2019 : Combined gas law

There is currently a discussion to delete the Combined gas law article. For some reason it does not appear on this project page's deletion alerts, so could probably do with some chemistry experts to comment on the merits of that proposal. See Wikipedia:Articles for deletion/Combined gas law. Thank you. Nick Moyes (talk) 11:48, 29 January 2019 (UTC)

Facto Post – Issue 20 – 31 January 2019

Facto Post – Issue 20 – 31 January 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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Everything flows (and certainly data does)

Recently Jimmy Wales has made the point that computer home assistants take much of their data from Wikipedia, one way or another. So as well as getting Spotify to play Frosty the Snowman for you, they may be able to answer the question "is the Pope Catholic?" Possibly by asking for disambiguation (Coptic?).

Amazon Echo device using the Amazon Alexa service in voice search showdown with the Google rival on an Android phone

Headlines about data breaches are now familiar, but the unannounced circulation of information raises other issues. One of those is Gresham's law stated as "bad data drives out good". Wikipedia and now Wikidata have been criticised on related grounds: what if their content, unattributed, is taken to have a higher standing than Wikimedians themselves would grant it? See Wikiquote on a misattribution to Bismarck for the usual quip about "law and sausages", and why one shouldn't watch them in the making.

Wikipedia has now turned 18, so should act like as adult, as well as being treated like one. The Web itself turns 30 some time between March and November this year, per Tim Berners-Lee. If the Knowledge Graph by Google exemplifies Heraclitean Web technology gaining authority, contra GIGO, Wikimedians still have a role in its critique. But not just with the teenage skill of detecting phoniness.

There is more to beating Gresham than exposing the factoid and urban myth, where WP:V does do a great job. Placeholders must be detected, and working with Wikidata is a good way to understand how having one statement as data can blind us to replacing it by a more accurate one. An example that is important to open access is that, firstly, the term itself needs considerable unpacking, because just being able to read material online is a poor relation of "open"; and secondly, trying to get Creative Commons license information into Wikidata shows up issues with classes of license (such as CC-BY) standing for the actual license in major repositories. Detailed investigation shows that "everything flows" exacerbates the issue. But Wikidata can solve it.

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MediaWiki message delivery (talk) 10:53, 31 January 2019 (UTC)

Isotope analysis

Isotope analysis says it is about the analysis of stable isotopes, without a hatnote. This seems odd to me, since radioactive isotope analysis is also a something that occurs. This seems to need a hatnote for a more general article, or possibly be renamed -- 70.51.201.106 (talk) 06:28, 17 January 2019 (UTC)

Well, Stable isotope analysis, Analysis of stable isotopes and Stable isotopic analysis are at least redirects to this article. --Leyo 00:02, 8 February 2019 (UTC)

Formation of triphenylene

According to our article on the Wurtz–Fittig reaction, the reaction of chlorobenzene with sodium produces triphenylene (C
18H
12) via a side reaction (citing doi:10.1021/ja01407a038). An editor has produced File:Formation_of_triphenylene.png as an image of this process, but the image is clearly flawed. It shows the mechanism:

2 C6H5· → C6H5− + C6H6
3 C6H5− → C18H12

This conserves neither mass nor charge. Can someone draw a reasonable (radical) mechanism for the production of triphenylene from the phenyl radical? Thanks, EdChem (talk) 12:06, 25 January 2019 (UTC)

In the meantime, that kind of flawed artwork should be removed, which I did. --Smokefoot (talk) 12:55, 25 January 2019 (UTC)
I also noticed that our benzyne article is almost exclusively about the ortho isomer.--Smokefoot (talk) 13:09, 25 January 2019 (UTC)
You are right, of course, Smokefoot. I started out looking at the image and trying to figure it out, then in writing the mechanism here recognised just how flawed it was, but did not go and remove it from the article. I was actually thinking more about notifying the uploader, to be honest. Thanks for removing the image. Cheers, EdChem (talk) 13:34, 25 January 2019 (UTC) PS: I have commented out the associated text that is consistent with the flawed image that has already been removed. EdChem (talk) 13:38, 25 January 2019 (UTC)
I have nominated the image for deletion: w:Commons:Commons:Deletion requests/File:Formation of triphenylene.png. -- Ed (Edgar181) 13:44, 29 January 2019 (UTC)
The images was deleted yesterday. BTW: The images in the de.wikipedia article are technically better. Some of them might be used to replace the lower quality images in the en.wikipedia article. --Leyo 00:10, 8 February 2019 (UTC)

Would the likely mechanism be disproportionation of the phenyl radical to produce benzene and benzyne followed by cyclotrimerization of benzyne? EdChem (talk) 12:43, 26 January 2019 (UTC)

The Phosphaethynolate Anion

And yet another new article. I can evaluate based on copyvio, citations, grammar, etc... but the guts of the article need expert input. Onel5969 TT me 13:36, 29 November 2018 (UTC)

I renamed it to Phosphaethynolate. I am more concerned about Herbalism and Biotechnology which just seems to be about two very separate topics. Graeme Bartlett (talk) 21:35, 29 November 2018 (UTC)
Is there a reason not to delete the redirect The Phosphaethynolate Anion? --Leyo 10:53, 12 February 2019 (UTC)
You could tag it as an unlikely redirect for speedy deletion. RFD is possible too. I usually leave the harmless redirects after renames, so that the writer can easily find the correct page. In this case they have done more editing after the rename, so they have found it. The education dashboard refers to this name, so it would be a good idea to change it there (not at Wikipedia:Wiki Ed/MIT/Main Group Chemistry (Fall 2018) though]]) if the redirect is to get the chop. Graeme Bartlett (talk) 20:19, 12 February 2019 (UTC)
OK, I deleted the redirect. --Leyo 22:03, 12 February 2019 (UTC)

Removed text from Bodenhausen's article

Hi what do you think about this removal from a one-edit user . I ping User:TovarishB but I am not sure he/she will see that, sometimes this type of user just disappear for months after the first edit that's why I am here.

Now it is true that my sandbox was moved by another user were it was not ready (I told him he should have informed me before doing so, but I just received very generic comments). this is a very technical description so it should have waited for more consistency and sources but again, it was not my choice to move it to ns0. In any case, it is sourced material about his research activities so i don't understand why it was removed from that paragraph.--Alexmar983 (talk) 13:36, 14 February 2019 (UTC)

Beta amino acid and Gamma amino acid.

I think that we should create seperate articles for these amino acids. Do you have an opinion about best article name? We have three choices. 1) Beta-amino acid. 2) Beta amino acid. 3) β-amino acid. At least we have to make Wikidata pages for these acids. --Sharouser (talk) 13:23, 15 February 2019 (UTC)

Agreed. SciFinder does not distinguish beta amino acid from beta-amino acid. 4521 references, 249 reviews.
Top cited reviews:
  • The Direct Catalytic Asymmetric Mannich Reaction By Cordova, Armando From Accounts of Chemical Research (2004), 37(2), 102-112.
  • Asymmetric synthesis of β-amino acids and α-substituted β-amino acids By Cardillo, Giuliana; Tomasini, Claudia From Chemical Society Reviews (1996), 25(2), 117-128.
  • β-Peptidic peptidomimetics By Seebach, Dieter; Gardiner, James From Accounts of Chemical Research (2008), 41(10), 1366-1375.
Recent reviews:
  • Highly functionalized cyclic β-amino acid moieties as promising scaffolds in peptide research and drug design.By Kiss, Lorand; Mandity, Istvan M.; Fulop, FerencFrom Amino Acids (2017), 49(9), 1441-1455.
  • Using β-Amino Acids and β-Peptide Templates to Create Bioactive Ligands and Biomaterials Del Borgo, Mark P.; Kulkarni, Ketav; Aguilar, Marie-IsabelFrom Current Pharmaceutical Design (2017), 23(26), 3772-3785.
--Smokefoot (talk) 13:35, 15 February 2019 (UTC)
There are categories in French Wikipedia and Wikimedia Commons. Alpha, Beta, Gamma, Delta --Sharouser (talk) 06:17, 16 February 2019 (UTC)

Tropolone and isomers

There are three tropolone isomers. Some wikipedias have articles about the isomeric class. d:Q416558

Should we create an article for d:Q416558? I think that most of English sources uses the word tropolone as α-Tropolone. So we don't need to move Tropolone to another title such as α-Tropolone. The title for d:Q416558 in English Wikipedia can be Hydroxytropone or Tropolones. --Sharouser (talk) 01:49, 18 February 2019 (UTC)

I would leave the situation alone. The scorecard from Chem Abs:
  • 533-75-5 1691 hits (2-isomer)
  • 3324-76-3 31 hits (3-isomer) (the most highly cited article has 20 some hits)
  • 4636-39-9 38 hits (4-isomer)
My threshold for notability is usually a couple hundred hits.--Smokefoot (talk) 02:37, 18 February 2019 (UTC)

Phosphoryl group

Phosphorylation is currently defined as the 'attachment of a phosphoryl group' - but what is a phosphoryl group? The current page has a prominent image of the --PO3H2 radical, but I'm pretty sure that's a phosphonate radical (phosphonyl). I've found mention of phosphoryl as anything that's O=PX3 where the phosphorous is P(V) but thus far I've got nothing I'd be happy using to change the definition of the functional group. --Project Osprey (talk) 11:52, 18 February 2019 (UTC)

Those articles would be useful to revise. IUPAC has nothing I could find on phosphoryl, but has this for phosphorylation: "A process (catalysed by enzymes) involving the transfer of a phosphate group from a donor to a suitable acceptor; in general, an ester linkage is formed, for example:

ATP + alcohol-->ADP + phosphate ester" So IUPAC is sticking to the traditional biochem usage, converting alcohols to phosphate esters.

To me and, I think, most chemists, in synthetic organic chemistry phosphoryl = P(O)(OR)2, usually introduced as an electrophile such as ClP(O)(OR)2, pyrophosphate, and even P4O10. It would be convenient to find a source.--Smokefoot (talk) 13:30, 18 February 2019 (UTC)
So... all phosphonyls are phosphoryls but not all phosphoryls are phosphonyls?... Not for the fist time I find myself wishing that organophosphorus chemistry contained a greater range of spellings. --Project Osprey (talk) 14:33, 18 February 2019 (UTC)
Well IUPAC says "phosphono: A prefix indicating the presence of the group –P(=O)(OH)2." IUPAC often advocates nomenclature that no practicing chemist uses. I have never encountered any phosphono compound, knowingly. Aldrich's online catalogue however illustrates usage of phosphono. The 2001 Chemical Reviews dedicated to (bio)phosphorylation focuses on replacement of active H's with PO3H2 (or its conj base). It follows that attachment of PO(OR)2 (R ≠ H) is part of the definition. We'd need a subsection on phosphorylating agents, including many nerve gases.--Smokefoot (talk) 14:54, 18 February 2019 (UTC)
I was thinking more in terms of hydrophosphonylation, before today I would never have through that a type of phosphorylation reaction but I would be hard-pressed to assert that it is not in-light of our current phosphoryl group article. --Project Osprey (talk) 15:21, 18 February 2019 (UTC)

Common term for nitric acid and N2O4 when used as oxidizers in rockets

There is a proposal under discussion in Talk:Nitric acid to merge the two articles red fuming nitric acid and white fuming nitric acid into a broader article about the use of nitric acid and nitrogen tetroxide as oxidizers for rocket propulsion. The first problem is, how should that article be named? Would "nitric oxidizers" be an acceptable name for both compounds? --Jorge Stolfi (talk) 19:05, 19 February 2019 (UTC)

Plumbylene

The plumbylene article was written by a student (Wltoh) as part of an assignment. Wltoh edited between 30 November and 9 December 2018 only, so presumably won't be returning. It has a few errors that I think we need to address:

  1. File:(2,4,6-(CF3)3C6H2)2Pb agostic chemdraw.png appears in the article but the trifluoromethyl substituents on C4 of the phenyl groups are missing. Could someone prepare and upload a replacement?
  2. The section on agostic interactions refers to a species [(R(CH3)2Si){(CH3)2P(BH3)}CH]2Pb with R being methyl or phenyl but the accompanying diagram File:Agostic_interactions_between_B-H_bonds_and_vacant_6p_orbital_of_Pb_(2).png seems to me to show [(R(CH3)2Si){(CH3)2PH(BH2)}CH]2Pb (differences in red). At first, I thought the diagram was correct, with a 5 coordinate P and 3 coordinate B centre, rather than both being 4 coordinate, but the source paper (doi:10.1021/om900614q) supports the latter formulation, as do the accompanying crystal structure images. Am I missing something, or is this diagram also wrong and in need of correction / replacement?
  3. I've fixed the references and added ndashes for bonds and nbsps between values and units, but it could use a proper copyedit and it's not an area where I've read up on the chemistry, so I'm leaving that for someone with greater knowledge.

Thanks, EdChem (talk) 15:43, 12 February 2019 (UTC)

For 1, I added the missing CF3 groups (image is now at File:(2,4,6-(CF3)3C6H2)2Pb skeletal.png) and also rolled File:(2,4,6-(CF3)3C6H2)2Pb coordinate complex.png. I'd love to improve the File:(2,4,6-(CF3)3C6H2)2Pb X-ray.png X-ray diagram of that molecule because it is not clear what direction each Pb–F bond comes off the Pb. For example, which 7-coordinate molecular geometry is lead? But when I examined the coordinates from the supporting info of doi:10.1021/om00047a014, I get about 20% difference in the bond-lengths and angles than that same ref reports. Could someone else check and see if I'm crazy here? DMacks (talk) 06:22, 13 February 2019 (UTC)
DMacks, thanks for the new images with the trifluoromethyl groups added. Any view on point 2, the H in the image v. the formula? Regarding the x-ray diagram, a proper image would be great but I don't know about the coordination geometry question you raised – sorry, hopefully someone else will comment. EdChem (talk) 00:32, 22 February 2019 (UTC)

Unreliable sources?

Hello there, I was just about to create Takashi Takahashi based on this. However, through lateral reading, I have found out that Allied Academies is "reportedly fraudulent", and I opted not to follow the source. I am just here for confirmation. Thanks. THE NEW ImmortalWizard(chat) 19:00, 21 February 2019 (UTC)

ImmortalWizard, even if I assume that source to be utmost reliable; how does the subject pass WP:ANYBIO or WP:GNG or WP:NACADEMIC? ∯WBGconverse 09:13, 24 February 2019 (UTC)
@Winged Blades of Godric: That is something O would have considered before creating the article. I just questioned about the source. THE NEW ImmortalWizard(chat) 09:53, 24 February 2019 (UTC)
Your poser contained I was just about to create Takashi Takahashi based on this. And, you would do well to bring a cease to your passive-aggressive communication style; Tony et al have been quite lenient, I won't be.
See this, this, this as to the wholesale unreliability of Allied Academics. ∯WBGconverse 10:13, 24 February 2019 (UTC)
@Winged Blades of Godric:This is not something to be enraged to and has nothing to do with my past issues. THE NEW ImmortalWizard(chat) 10:40, 24 February 2019 (UTC)

FYI: "New" template Minus

I (re)created {{minus}} because when fixing/writing formulas, where "-" should be replaced with "−", I always have to search for the minus sign "−" (like now). Just type {{subst:minus}} to get the sign. Christian75 (talk) 12:23, 24 February 2019 (UTC)

I added this nice solution to MOS:MATH. DMacks (talk) 12:40, 24 February 2019 (UTC)

RfC on thermal degradation

I've started an RfC on the terminology used for thermal degradation processes in some heavily-marketed tobacco products. It's at Talk:Electric smoking system#RfC on solid tobacco heated using external heat sources. We are discussion charring, smoke, destructive distillation, oxidative combustion, and so forth. I'd welcome your comments. Thank you! HLHJ (talk) 05:23, 25 February 2019 (UTC)

The page "nickel compounds" is too long

I think moving the tables in nickel compounds to a new page list of nickel compounds may be better. --Leiem (talk) 03:39, 19 February 2019 (UTC)

Maybe the community should discuss goals for such articles. Otherwise "it" (= nickel compounds as well as list of nickel compounds) is an endless meandering task because many compounds exist, with super obscure items get blended with notable compounds. Such projects begin with noble intentions, but they are naive. I recall that there is a wiki guideline against an indiscriminate listings, and that is what this thing is headed toward. --Smokefoot (talk) 12:57, 19 February 2019 (UTC)
The article is enormous. My first thought is to shatter it into a number of more manageable pages. Binary compounds of Nickle seems like a natural page but I'm not so sure about the huge sections detailing 'simple salts' and 'double salts', we don't have articles like that for any other elements - may require consensus. --Project Osprey (talk) 14:22, 19 February 2019 (UTC)
There is an article list of yttrium compounds. --Leiem (talk) 15:19, 19 February 2019 (UTC)
Many of us have created articles that later need to be reshaped. Some options:

--Smokefoot (talk) 00:41, 20 February 2019 (UTC)

  • I have been reducing the size by forking off based on sections. Traditionally the textbooks will start with halides and then move to chalcogenides, pnictides, other binary compounds, hydroxides and then other oxosalts. The halides (and their solvate variations) could make a separate article, but at this point there is not enough there to be worth forking off. Graeme Bartlett (talk) 12:43, 25 February 2019 (UTC)

Article title of hachimoji DNA base P

2-Aminoimidazo[1,2-a][1,3,5]triazin-4(1H)-one is a standard IUPAC name of this chemical. However, this exact name did not used in scientific articles. In scientific articles, this compound was called as various synonyms such as 2-Aminoimidazo[1,2-a][1,3,5]triazin-4(1H)-one, 2-Aminoimidazo[1,2a]-s-triazin-one or 5-Aza-7-deazaguanine.

In my view, the most appropriate article title is 5-Aza-7-deazaguanine. It does not contain any brackets. It avoids Wikipedia:Naming conventions (technical restrictions) --Sharouser (talk) 15:05, 24 February 2019 (UTC)

I did not redlink your name because of those restrictions. Graeme Bartlett (talk) 12:45, 25 February 2019 (UTC)

Template:Cite ChemRxiv

See Template:Citation Style 1 and Module:Citation/CS1. I made Template:Cite ChemRxiv. However it doesn't work now. --Sharouser (talk) 09:40, 27 February 2019 (UTC)

Facto Post – Issue 21 – 28 February 2019

Facto Post – Issue 21 – 28 February 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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Back numbers are here.
What is a systematic review?

Systematic reviews are basic building blocks of evidence-based medicine, surveys of existing literature devoted typically to a definite question that aim to bring out scientific conclusions. They are principled in a way Wikipedians can appreciate, taking a critical view of their sources.

PRISMA flow diagram for a systematic review

Ben Goldacre in 2014 wrote (link below) "[...] : the "information architecture" of evidence based medicine (if you can tolerate such a phrase) is a chaotic, ad hoc, poorly connected ecosystem of legacy projects. In some respects the whole show is still run on paper, like it's the 19th century." Is there a Wikidatan in the house? Wouldn't some machine-readable content that is structured data help?

File:Schittny, Facing East, 2011, Legacy Projects.jpg
2011 photograph by Bernard Schittny of the "Legacy Projects" group

Most likely it would, but the arcana of systematic reviews and how they add value would still need formal handling. The PRISMA standard dates from 2009, with an update started in 2018. The concerns there include the corpus of papers used: how selected and filtered? Now that Wikidata has a 20.9 million item bibliography, one can at least pose questions. Each systematic review is a tagging opportunity for a bibliography. Could that tagging be reproduced by a query, in principle? Can it even be second-guessed by a query (i.e. simulated by a protocol which translates into SPARQL)? Homing in on the arcana, do the inclusion and filtering criteria translate into metadata? At some level they must, but are these metadata explicitly expressed in the articles themselves? The answer to that is surely "no" at this point, but can TDM find them? Again "no", right now. Automatic identification doesn't just happen.

Actually these questions lack originality. It should be noted though that WP:MEDRS, the reliable sources guideline used here for health information, hinges on the assumption that the usefully systematic reviews of biomedical literature can be recognised. Its nutshell summary, normally the part of a guideline with the highest density of common sense, allows literature reviews in general validity, but WP:MEDASSESS qualifies that indication heavily. Process wonkery about systematic reviews definitely has merit.

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MediaWiki message delivery (talk) 10:02, 28 February 2019 (UTC)

COI editor needs advice

There's a guy who works for Thieme Medical Publishers who posted on Wikipedia:Conflict of interest/Noticeboard#Creating new drafts although a possible COI exists? after I advised him to do so, but nobody's offered him any advice yet. As a COI and spam specialist, I hold the view that he should hang it up and rest assured that if their journals deserve that much in-depth coverage on this encyclopedia they'll eventually get it, but he hasn't really responded to that. Is there anybody over here at this chemistry project who thinks he deserves some assistance and is willing to provide it? – Athaenara ✉ 14:24, 28 February 2019 (UTC)

Isostere

There is another meaning(d:Q1674534) of isostere. In meteorology and physics, isostere is a contour line that connects points on a map or chart that have the same gas density. dictionary example --Sharouser (talk) 02:03, 9 March 2019 (UTC)

Phosphorus oxyacid and oxyanion merge discussion

I've just created a merge discussion at Talk:Phosphoric acids and phosphates#Merge discussion, as I'm not even sure what the target page should be. Please provide feedback about what the target should be there. Care to differ or discuss with me? The Nth User 23:32, 9 March 2019 (UTC)

Facto Post – Issue 22 – 28 March 2019

Facto Post – Issue 22 – 28 March 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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Back numbers are here.
When in the cloud, do as the APIs do

Half a century ago, it was the era of the mainframe computer, with its air-conditioned room, twitching tape-drives, and appearance in the title of a spy novel Billion-Dollar Brain then made into a Hollywood film. Now we have the cloud, with server farms and the client–server model as quotidian: this text is being typed on a Chromebook.

File:Cloud-API-Logo.svg
Logo of Cloud API on Google Cloud Platform

The term Applications Programming Interface or API is 50 years old, and refers to a type of software library as well as the interface to its use. While a compiler is what you need to get high-level code executed by a mainframe, an API out in the cloud somewhere offers a chance to perform operations on a remote server. For example, the multifarious bots active on Wikipedia have owners who exploit the MediaWiki API.

APIs (called RESTful) that allow for the GET HTTP request are fundamental for what could colloquially be called "moving data around the Web"; from which Wikidata benefits 24/7. So the fact that the Wikidata SPARQL endpoint at query.wikidata.org has a RESTful API means that, in lay terms, Wikidata content can be GOT from it. The programming involved, besides the SPARQL language, could be in Python, younger by a few months than the Web.

Magic words, such as occur in fantasy stories, are wishful (rather than RESTful) solutions to gaining access. You may need to be a linguist to enter Ali Baba's cave or the western door of Moria (French in the case of "Open Sesame", in fact, and Sindarin being the respective languages). Talking to an API requires a bigger toolkit, which first means you have to recognise the tools in terms of what they can do. On the way to the wikt:impactful or polymathic modern handling of facts, one must perhaps take only tactful notice of tech's endemic problem with documentation, and absorb the insightful point that the code in APIs does articulate the customary procedures now in place on the cloud for getting information. As Owl explained to Winnie-the-Pooh, it tells you The Thing to Do.

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MediaWiki message delivery (talk) 11:46, 28 March 2019 (UTC)

Mass removals

JzG (talk · contribs) is currently mass removing references in chemistry articles without having a knowledge in the field of chemistry and without replacing the removed references with alternatives. This includes, among others, subpages of the Compendium of Pesticide Common Names. The owner of this website has been a member for several years of the BSI/ISO committee that assigns common names to pesticides. This website has been cited for many years by several users including Edgar181.
Thoughts? --Leyo 23:52, 22 January 2019 (UTC)

It's nothing to do with having a knowledge of the field of chemistry (though in fact my wife is a chemist). The issue is very simple: there's no evidence that Alan Wood's personal website has editorial oversight or any of the other indica of WP:RS. A quick glance at my user page will show that reliable sources is my thing. See also WP:SPS. Oh, and this doesn't come close to a mass removal. I have removed ten of thousand of references to predatory journals, and at least a thousand to one spam source. Guy (Help!) 00:06, 23 January 2019 (UTC)
I have read your opinion before. I am interested in opinions of other users. Your expertise is clearly insufficient to perform mass removals and thus to destroy information without having a short discussion on the affected websites before. The PAN Pesticide Database is another example of your mass removal of content. --Leyo 00:14, 23 January 2019 (UTC)
I am astonished that you do not understand how Wikipedia works after this much time. If you post your interpretation of something, you have no control over who else posts, and you are not the audience for this discussion anyway. And in any case the correct venue is WP:RSN. Guy (Help!) 00:21, 23 January 2019 (UTC)
Please do not distract. You failed to post your intentions on WP:RSN. --Leyo 00:24, 23 January 2019 (UTC)
I dont have to. There's no requirement for prior review of removal of a personal website. Guy (Help!) 00:28, 23 January 2019 (UTC)
I have used alanwood.net as a source of information for the most basic non-controverisal facts about identity, classification, and uses of pesticides. I have found it to be an entirely accurate database (much more so than sources such as, for example, the PubChem database which is much more widely used on Wikipedia chemistry articles). I have used it mainly out of convenience because it is so easy to source this basic information. I have no objection if someone wants to replace it with a different source, but I object to the simple blanket deletion of all references citing this source. -- Ed (Edgar181) 01:28, 23 January 2019 (UTC)
  • Note: I have started a discussion at RSN. Any and all comments / thoughts / etc welcome. I suggest that discussion on the issue of what is an acceptable source take place there. Thanks. EdChem (talk) 02:18, 23 January 2019 (UTC)
  • These sorts of mass removals are problematic. Yes, Alanwood.net and pesticideinfo.org may not standup to WP:RS, but a questionable source is better than no source at all. Better to tag with an appropriate sourcing template (like "questionable source" or "medical source needed" or whatever) than to have no source at all. This is especially true when the information being sourced is not in dispute and the existing source, like pesticideinfo.org, provides the references to more authoritative and WP-compliant sources. In other words, pesticideinfo.org provides citations to reliable sources for just about everything it says. So rather than completely removing the citation to pesticideinfo.org it would be better to change the citation to whatever pesticideinfo.org is citing. But that's a lot of work. If you are not willing to do it yourself, at least give others to opportunity to by leaving the citation to pesticideinfo.org in, and adding a tag. Nothing is gained by leaving things unsourced. (At least when we're talking about facts that no one disputes. I agree that more aggressive removals are called for if there's an actual content dispute.) Yilloslime (talk) 01:01, 25 January 2019 (UTC)
???
The discussion has continued here, as was noted above. Please do not split talks this way. Your contribution here might very well be ignored or missed. -DePiep (talk) 01:07, 25 January 2019 (UTC)
I guess you are referring to {{Additional citation needed}} or {{Better source}}. --Leyo 01:17, 25 January 2019 (UTC)
Yes thouse would do! Yilloslime (talk) 15:55, 25 January 2019 (UTC)

The thread at WP:RSN was archived. So what are we going to do in the cases of the removed references to

  • alanwood.net?
  • pesticideinfo.org?

--Leyo 21:30, 6 February 2019 (UTC)

The default is to leave removed since there was no consensus for reliability, but you can reopen alanwood if you want (pesticideinfo is an obvious no-hoper, as it's an anti-pesticide pressure group). Guy (Help!) 00:26, 7 February 2019 (UTC)
That's not how read the discussion, which petered out without reaching consensus or/and being formally closed. Interested editors can decide for themselves; here's the archived discussion: Wikipedia:Reliable_sources/Noticeboard/Archive_257#Compendium_of_Pesticide_Common_Names. Yilloslime (talk) 01:12, 7 February 2019 (UTC)
Initially, I purposely didn't want to do the evaluation myself, but would have expected the same from JzG …
I concur with Yilloslime. AFAIS the following chemistry experts have argued against blanket removal of refs to alanwood.net from Wikipedia articles, at least unless they are replaced with another source: Georginho, Graeme Bartlett, Yilloslime, Edgar181, DePiep, EdChem, myself. In his statements, Smokefoot focussed on PAN.
Based on the experts' opinions I see the following options:
  1. Simply reverting the removal edits.
  2. Reverting the removal edits and adding {{Additional citation needed}}.
  3. Reverting the removal edits and adding {{Better source}}.
Opinions on which of the options are favored? --Leyo 23:55, 7 February 2019 (UTC)
I think the links to alanwood.net should be restored, option 1. If anyone wants to replace them instead with better source that equivalently verifies the information, or if anyone wants to also tag the restored links with {{Additional citation needed}} or with {{Better source}}, I have no objection to that. -- Ed (Edgar181) 13:09, 8 February 2019 (UTC)
Alan Wood's site has absolutely zero evidence to show it is a reliable source, and Wood contacted me to tell me that he's not actually allowed to include the information that you all seem to think "everybody" should know. Obviously you will all form a voting bloc in any discussion about the site, but it is clear why any Wikipedian experienced in sourcing would remove it. Guy (Help!) 21:53, 8 February 2019 (UTC)
I have not seen this discussion before. I am a chemist but with no knowledge of pesticides. I agree with the 3rd option - Reverting the removal edits and adding {{Better source}}. A possible poor reference is better than no reference. --Bduke (talk) 22:04, 8 February 2019 (UTC)
In the discussion, I offered to contact people in academics and industries to ask their opinions about Wood's compendium. Alas, I received no response until the discussion was archived. I provided links to articles and even a patent to show the compendium's credibility. And I'm going to provide another one here: EPA used it as a source in a chapter in a review book in 2012. I'm inclined to simple reverting, but I'm fine with all the options. I just want to stress that the (active) chemistry Wikipedians seem all to agree that the compendium is a reliable source.
Georginho (talk) 22:33, 8 February 2019 (UTC)
See, that's the problem. We are not supposed to do primary research to establish a source is reliable we like it. Guy (Help!) 20:16, 10 February 2019 (UTC)

JzG, you ignored questions directed at you during the RSN discussion and your disdain for the notion that chemists might know more about chemistry is evident, but do you think you could at least pretend to WP:AGF? Regarding the pesticide network, you were pointed to www.pesticideinfo.org/Docs/data.html#AccuracyofData which describes the sources of data and fact checking / review. These references are then included with the database, so in removing the links rather than tagging them with "better source", you removed pointers to the actual (likely more acceptable to you) sources – hardly a valuable service to readers. You remove a lot of references, many to predatory journals and other flawed sources, which is valuable, but which also makes finding the cases where you over-react difficult. We are not talking about contentious data nor has any evidence of inaccuracy been shown, to my knowledge. Is it not possible for you to work with a group of dedicated Wikipedians who share your goals rather than treating us as ignorant / incompetent ("it is clear why any Wikipedian experienced in sourcing would remove it") and basically as one step above deliberate vandals? EdChem (talk) 01:58, 9 February 2019 (UTC)

Pesticideinfo is run by anti-pesticide activists and has no indicia of reliability, so is unacceptable.
Alan Wood tells me that he is an authority but can't say so on his site, everyone else says the same, so I have no further interest in this, other than th generic point that it is a terrible ides to decide a site is reliable when there is no independent verification of that.
Alan Wood reinserted at least some of these links himself. That's not good. He seems very keen to promote his work. Guy (Help!) 20:16, 10 February 2019 (UTC)

JzG Every time we get a comment or question in our talk page, we always engage in discussions in good faith. We expect the same from you.
You've been complaining about the reliability of Wood's compendium. From Wikipedia's policy of what constitutes a reliable source, I've gone great lengths to prove that the compendium is one. It was cited in an article, a patent by the biggest pesticide-producing company in the world, and even by the EPA itself. This is an independent verification. And I did this without using proprietary scientific search engines like SciFinder, Scopus, or Web of Science.
The question in the beginning of this discussion is whether or not the compendium is a reliable source per Wikipedia's definition. We opened a broader discussion, which has been archived now. We come back here to decide, and we keep the door open for your feedback. But we can't go anywhere fruitful with your belittling attitude.
If you want other proves for the compendium's reliability, I'll see what I can do to help. If you're not interested anymore, please say so so that we can go for a consensus or a vote.
Georginho (talk) 21:43, 10 February 2019 (UTC)

Concerning "Pesticideinfo … has no indicia of reliability, so is unacceptable.":

--Leyo 00:16, 11 February 2019 (UTC)

One week has passed without further comments. I say we continue with the current consensus.
Georginho (talk) 13:29, 18 February 2019 (UTC)

I think so, yes. As the evidence for reliability concerning pesticideinfo.org provided above has not been disputed, I'd suggest also reverting those removal edits and adding {{Additional citation needed}} or {{Better source}} for now. --Leyo 21:19, 18 February 2019 (UTC)
Anyone has a preference among those two options? --Leyo 21:28, 29 March 2019 (UTC)

Gas-evolving upward arrow

Is the Wiki-Chem editing community agreed that we want upward arrows for gas evolution? Example from potassium oxide:

  • I oppose this convention. My rationale: (i) This notation isn't used in journals, (ii) it is jargon that complicates the main message of an equation (stoichiometry). Its not a big deal. --Smokefoot (talk) 13:36, 11 March 2019 (UTC)
  • This convention seems common in textbooks, up through college-freshman gen-chem or so. I generally oppose its use (even down to that level when I deal with schools) for the reasons Smokefoot mentions. I do support using it in the limited case where "a gas evolves" is actually the point I'm trying to make (driving an equilibrium or collecting and measuring the gas as a product). DMacks (talk) 14:02, 11 March 2019 (UTC)
  • What about using (g) instead, perhaps more explicitly (gas)? OrganoMetallurgy (talk) 14:23, 24 March 2019 (UTC)
It seems that DMacks formulated a decent guideline: when it matters: where "a gas evolves" is actually the point of the supporting statement (driving an equilibrium or collecting and measuring the gas as a product). Usually either of the competing notations is unnecessary or causes more confusion than good.--Smokefoot (talk) 15:07, 24 March 2019 (UTC)

Figure numbers and MOS

I wonder if we (the Wiki-Chem project) should discourage (not ban) the use of figure numbers. Figure numbers make editing more complicated because they rigidify the article layout, preventing new layouts. One advantage to numbering is that a figure can be cited in the text, which can be very helpful. In the same spirit, I get the feeling that most editors agree that compounds should not be numbered in graphics for similar reasons. --Smokefoot (talk) 21:29, 3 March 2019 (UTC)

  • Smokefoot: Intra-article references -- to other parts of the same article, such as equations and figures by number, sections by number or name -- are bad style in Wikipedia generally. The reason is the one you mention: editors often make localized edits, and often want to insert, delete, or reorder equations, figures, an sections. If the article has intra-article references, a single change of that sort would require editing most figure/equation numbers and their references. Editors will often fail to do these fixes, leaving readers and other editors thoroughly confused.
    Usually one can make do with references limited to inline items to the immediate vicinity, as in "This reaction yields..." (just below a centered reaction diagram) or "The value can be computed by the following formula", or "the following graph shows ..." (just above a centered graph).
    Other cases can be handled by giving the item a "natural name", e.g. "the first step in the Tutankhamon reaction is" (just above the reaction diagram), and then later one can say "The first step of the Tutankhamon reaction can also use thiotimoline instead of porcupine...". Even if someone deletes the first picture, the reference to it will still make sense.
    In any case, one should never refer in the text to figures with "left" or "right" alignment, much less number them. Those figures often have to be moved or deleted for space limitations. And vice-versa: the caption of those figures may be too terse to make sense without the text, but it must not refer explicitly to the text, e.g. as "See section X" or "The colors are explained in the text."
    Anyway, this is what I have inferred from seeing and editing thousands of articles in many different areas...
    All the best, --Jorge Stolfi (talk) 02:10, 4 March 2019 (UTC)
The MOS suggests using image captions to refer to images in the text. See MOS:SEEIMAGE. --{{u|Mark viking}} {Talk} 03:40, 4 March 2019 (UTC)
I strongly oppose the practice of numbering figures (to the extent I would !vote for banning altogether), for the reason Smokefoot mentions. I can't think of a strong reason to do it, but only lots of difficulties down the road for both editors and readers. DMacks (talk) 04:23, 4 March 2019 (UTC)
It just was raised by someone from an entirely different topic-area at Wikipedia talk:Manual of Style#Labeling images as "Figures" in captions. DMacks (talk) 06:47, 3 April 2019 (UTC)

A new newsletter directory is out!

A new Newsletter directory has been created to replace the old, out-of-date one. If your WikiProject and its taskforces have newsletters (even inactive ones), or if you know of a missing newsletter (including from sister projects like WikiSpecies), please include it in the directory! The template can be a bit tricky, so if you need help, just post the newsletter on the template's talk page and someone will add it for you.

– Sent on behalf of Headbomb. 03:11, 11 April 2019 (UTC)

The Pauson/Kealy synthesis of ferrocene

Our ferrocene article includes the following graphic showing Pauson and Kealy's synthesis. I confess I was the editor who added it. I had reason to look at it again, and I think the stoichiometry is wrong... so I am asking for comment / input and possibly a replacement.

The top line, showing what they were trying to do in seeking fulvalene, appears to me to suggest:

  1. 2:1 combination of cyclopentadienyl magnesium bromide and iron(III) chloride to produce 2 equivalents of the cyclopentadienyl radical
  2. iron-containing product not identified
  3. Radical-radical recombination of the cyclopentadienyl radicals to yield dihydrofulvalene
  4. Oxidation of dihydrofulvalene to fulvalene with iron(III) chloride, yielding hydrogen gas

Step 1 has incorrect stoichiometry, it should be 1:1

C
5H
5MgBr   +   FeCl
3   →   C
5H
5   +   FeCl
2   +   MgBrCl

Step 4 will only produce hydrogen if the iron(III) chloride is a catalyst, but it being an oxidant seems more likely to me. That is:

C
5H
5–C
5H
5   +   2 FeCl
3   →   C
5H
4=C
5H
4   +   2 FeCl
2   +   2 HCl

rather than

C
5H
5–C
5H
5     C
5H
4=C
5H
4   +   H
2

The overall stoichiometry of Steps 1 and 2 are:

2 C
5H
5MgBr   +   2 FeCl
3   →   C
5H
5–C
5H
5   +   2 FeCl
2   +   2 MgBrCl

And for the whole process (assuming FeCl
3 is not a catalyst in step 4) is:

2 C
5H
5MgBr   +   4 FeCl
3   →   C
5H
4=C
5H
4   +   4 FeCl
2   +   2 MgBrCl   +   2 HCl

The bottom line, showing what actually occurred, appears to me to suggest:

  1. 2:1 combination of cyclopentadienyl magnesium bromide and iron(III) chloride to produce a 1:1:3 mixture of ferrocene, dihydrofulvalene, and magnesium bromide chloride equivalents of the cyclopentadienyl radical
  2. only iron-containing product identified is ferrocene, which is a problem as it is the production of iron(II) chloride from the above process that then reacts with the Grignard

The stoichiometry is clearly flawed as a 1:1 ferrocene to dihydrofulvalene mixture requires four cyclopentadienyl moieties, and every Grignard will lead to a magnesium ion. From above, we have:

2 C
5H
5MgBr   +   2 FeCl
3   →   C
5H
5–C
5H
5   +   2 FeCl
2   +   2 MgBrCl

The ferrocene is then formed by:

2 C
5H
5MgBr   +   FeCl
2   →   Fe(C
5H
5)
2   +   2 MgBrCl

For an overall stoichiometry:

6 C
5H
5MgBr   +   2 FeCl
3   →   C
5H
5–C
5H
5   +   2 Fe(C
5H
5)
2   +   6 MgBrCl

We can see that the actual process has cyclopentadienyl magnesium bromide to iron(III) chloride (shown as 2:1) is 3:1 for the actual process, 1:1 in the process sought. The products dihydrofulvalene to ferrocene to magnesium bromide chloride are produced in 1:2:6 ratio, but shown as 1:1:3. The hydrogen suggested in the planned sequence would suggest that iron(II) chloride would react with acid to produce iron(III) chloride and hydrogen gas, but that is not consistent with standard redox results.

Assuming my analysis is correct, I think we need a replacement for this diagram. Thoughts? EdChem (talk) 02:53, 7 April 2019 (UTC)

As the uploader of the diagram: EdChem evaluation about stoichiometry is right. It has been quite a while since I uploaded the graph and since then I had access to more literature so we can refine the picture.
In Nature 1951(168) p. 1039–1040, doi:10.1038/1681039b0 Kealy and Pauson described the synthesis with 4 grams (0.163 mol) magnesium and 18 grams (0.165 mol) ethyl bromide (to form the first Grignard reagent), 11 grams (0.166 mol) cyclopentadiene and 9.1 grams (0.055 mol) iron chloride. Pauson confirmed in J. Organomet. Chem. 2001 (637–639) p. 3–6: "Ferrocene—how it all began" (PDF; 103 kB) that iron(III) chloride, not iron(II) chloride was used in the mixture, so stoichiometry was as follows:
3 C
5H
5MgBr   +   FeCl
3   →   (A0)
According to Nature article the aim was to form C5H5-radicals which recombines to H5C5-C5H5 equivalent to follows reaction:
6 RMgBr   +   2 FeCl
3   →   3 R–R   +   2 Fe   +   3 MgBr
2   +   3 MgCl
2  (A)
The H5C5-C5H5 should be oxidised to fulvalene in the next step.
The formation of the resulting iron complex described Kealy and Pauson in Nature by following reaction:
2 C
5H
5MgBr   +  FeCl
2   →   C
5H
5–Fe–C
5H
5   +  MgBr
2  +  MgCl
2 (A1)
As described by EdChem above first intermediate step is the reduction of FeCl3 to FeCl2
C
5H
5MgBr   +   FeCl
3   →   C
5H
5   +   FeCl
2   +   MgBrCl (C)
So overall reaction would be
6 C
5H
5MgBr   +   2 FeCl
3   →   2 C
5H
5–Fe–C
5H
5   +   C
5H
5–C
5H
5   +  3 MgBr
2   +   3 MgCl
2 (B)
Which is very similar to the target reaction (A), just with side reaction driven by high stability of Ferrocene:
4 C
5H
5   +   2 Fe   →   2 C
5H
5–Fe–C
5H
5
Unless anyone disagrees with this analysis, I will redraw the file:Kealy Ferrocen Synthese.svg accordingly. Thanks to EdChem to bring this to my attention. Regards --Bert (talk) 10:54, 7 April 2019 (UTC)
Interesting conversation but I worry about WP:UNDUE (unimportant) and OR. Do we really want to dilute this article with guesses about stoichiometry dreamed up by (clever) Wikipedia editors? I recommend that the article note the Pauson/Kealy precursors and note the products Pauson/Kealy id'd. Those were primitive times. My two cents. --Smokefoot (talk) 13:19, 7 April 2019 (UTC)
Reactions above are cited from original literature, (A) and (A1) are copies from the Nature article by Kealy and Pauson, (A0) is simply the stoichiometry in the original experiment. Reaction (C) is required step to get Fe(II) chloride used by Kealy and Pauson in (A1). Reaction (B) is nothing else than sum of step (C) and (A1). So in fact there is really nothing added to experiments and findings from Kealy and Pauson. Regards --Bert (talk) 14:26, 7 April 2019 (UTC)
Bert.Kilanowski's equation B is identical to my "actual process" equation. Equation A may be what Pauson and Kealy were trying, but it seems odd to me that they expected reduction of iron(III) to elemental iron, and it omits the further oxidation of dihydrofulvalene to fulvalene. I think my suggested proposal of
2 C
5H
5MgBr   +   4 FeCl
3   →   C
5H
4=C
5H
4   +   4 FeCl
2   +   2 MgBrCl   +   2 HCl
is much more likely. Having said that, Smokefoot's point that OR stoichiometry is not appropriate for the article – and that is why I think we need a new diagram. The current one suggests that dihydrofulvalene is not produced, but it is actually the oxidation to fulvalene that does not occur. Even ignoring the stoichiometry, it is misleading. I will propose a replacement shortly. EdChem (talk) 01:39, 8 April 2019 (UTC)

I propose the following replacement:

It shows that the reaction of cyclopentadienyl magnesium bromide with iron(III) chloride is a redox process in which the cyclopentadienyl anion is oxidised to the cyclopentadienyl radical while reduction produces iron(II) chloride. Magnesium bromide chloride is a by-product. The radical forms dihydrofulvalene, as K and P anticipated, but further oxidation by iron(III) to fulvalene (hypothesised to be an aromatic system and thus providing a driving force for the reaction) does not occur. The iron(II) chloride produced with the radical reacts with the Grignard reagent, yielding ferrocene. The reactions shown as 1:1 (in A + B format) are, in fact, 1:1. Stoichiometry that is not 1:1 is indicated in the form A D, which does not imply any particular stoichiometry. I agree with Smokefoot that a focus on stoichiometry would by WP:UNDUE, so long as what is present does not imply something that is untrue / inaccurate. Smokefoot and Bert.Kilanowski (and anyone else), what do you think of this diagram? Thanks. EdChem (talk) 02:01, 8 April 2019 (UTC)

Another possibility might be to have an arrow coming down from cyclopentadienyl magnesium bromide and then across, joining the arrow coming down from iron(II) chloride, and continuing on to ferrocene. I'd then add "− MgBrCl" below the join. This would make it clear that the C
5H
5MgBr formula is the same as the structural formula drawn at the start (for the non-chemists) and also perhaps better imply the one-pot / in situ process is giving both the dihydrofulvalene and ferrocene products. Ultimately, if this (or something like it) is used, it'll need re-drawing to .svg format. EdChem (talk) 02:07, 8 April 2019 (UTC)
EdChem, do you have access to the Nature article? What Kealy and Pauson expected to achieve is reaction (A) this formula is written explicitly in the text. Accordingly, stoichiometry was as shown in (A0). So, this needs to be the starting point of the equation. I will update my original file based on these findings, but it may need a few days. --Bert (talk) 06:14, 8 April 2019 (UTC)
Bert.Kilanowski, A might have been what they expected, but that doesn't make it chemically reasonable. Consider that the oxidation of the cyclopentadienyl anion to the radical is a one-electron process, matching the one-electron reduction of iron(III) to iron(II). Consider further Pauson's words in the 2001 paper, which make it absolutely clear that a one-pot synthesis of fulvalene (not of dihydrofulvalene, the R–R in A) was being attempted with iron(III) as the oxidant. If A went to completion, there would be no iron(III) to form fulvalene. We also know that iron(II) is produced as it is the source of ferrocene. Coupled with the basic redox chemistry that shows reduction of Fe3+
 to Fe2+
 is comparatively easy but the reduction of Fe2+
 to elemental iron is much more difficult, it is clear that whatever Pauson and Kealy might have anticipated, what actually happened was:
  • A one-electron oxidation of the cyclopentadienyl anion to its radical, with the associated reduction of Fe3+
     to Fe2+
  • Radical-radical recombination of the cyclopentadienyl radicals to form the dimer dihydrofulvalene
  • Reaction of the Fe2+
     with the Grignard to yield ferrocene
  • No further oxidation of dihydrofulvalene to fulvalene with Fe3+
We need a diagram showing what actual chemistry takes place, not what chemistry Pauson and Kealy might have expected. EdChem (talk) 01:47, 9 April 2019 (UTC)
  • A new proposed replacement:

Thoughts / Comments? EdChem (talk) 05:57, 11 April 2019 (UTC)

Proposal of creating CAS number redirects to the corresponding chemical substances

Each substance has its unique CAS number. Sometimes it is easier to type CAS number to find a chemical (67410-64-4 → 5-Aza-7-deazaguanine). --Leiem (talk) 08:33, 20 April 2019 (UTC)

The search function finds the page even if it does not jump straight to it. Would you or anyone else actually use a CASNo redirect? I would not use it myself. Graeme Bartlett (talk) 21:10, 20 April 2019 (UTC)
The search should do it, not a redirect. -DePiep (talk) 21:42, 22 April 2019 (UTC)
The search is currently not available to link a CASNo to a chemical (e.g. 109-06-8 → 2-methylpyridine). I also hope that the search can do it. --Leiem (talk) 01:52, 23 April 2019 (UTC)
I just used WP's search box to look for that CASNo: "109-06-8" gave me that target article. It's also visible to google search. DMacks (talk) 03:09, 23 April 2019 (UTC)
FYI, recently some CAS-redirects survived a RfD (Wikipedia:Redirects_for_discussion/Log/2019_January_28#7440-22-4) - but consensus can change). Christian75 (talk) 22:14, 22 April 2019 (UTC)
Oops, I even !voted to "keep" in there (detail: they were chem elements only). May I repeat saying: 100K CAS numbers a redirect? No. -DePiep (talk) 22:21, 22 April 2019 (UTC)
I oppose also. I can't envision a case where I would want to wikilink to it, and the chemical articles already appear as hits when searching both using Wikipedia's own search and google. Redirects are cheap but pointless redirect creation is pointless. DMacks (talk) 03:09, 23 April 2019 (UTC)

Facto Post – Issue 23 – 30 April 2019

Facto Post – Issue 23 – 30 April 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer.
Back numbers are here.
Completely clouded?
Cloud computing logo

Talk of cloud computing draws a veil over hardware, but also, less obviously but more importantly, obscures such intellectual distinction as matters most in its use. Wikidata begins to allow tasks to be undertaken that were out of easy reach. The facility should not be taken as the real point.

Coming in from another angle, the "executive decision" is more glamorous; but the "administrative decision" should be admired for its command of facts. Think of the attitudes ad fontes, so prevalent here on Wikipedia as "can you give me a source for that?", and being prepared to deal with complicated analyses into specified subcases. Impatience expressed as a disdain for such pedantry is quite understandable, but neither dirty data nor false dichotomies are at all good to have around.

Issue 13 and Issue 21, respectively on WP:MEDRS and systematic reviews, talk about biomedical literature and computing tasks that would be of higher quality if they could be made more "administrative". For example, it is desirable that the decisions involved be consistent, explicable, and reproducible by non-experts from specified inputs.

What gets clouded out is not impossibly hard to understand. You do need to put together the insights of functional programming, which is a doctrinaire and purist but clearcut approach, with the practicality of office software. Loopless computation can be conceived of as a seamless forward march of spreadsheet columns, each determined by the content of previous ones. Very well: to do a backward audit, when now we are talking about Wikidata, we rely on integrity of data and its scrupulous sourcing: and clearcut case analyses. The MEDRS example forces attention on purge attempts such as Beall's list.

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MediaWiki message delivery (talk) 11:27, 30 April 2019 (UTC)

Facto Post – Issue 24 – 17 May 2019

Facto Post – Issue 24 – 17 May 2019
Text mining display of noun phrases from the US Presidential Election 2012
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer.
Back numbers are here.
Semantic Web and TDM – a ContentMine view

Two dozen issues, and this may be the last, a valediction at least for a while.

It's time for a two-year summation of ContentMine projects involving TDM (text and data mining).

Wikidata and now Structured Data on Commons represent the overlap of Wikimedia with the Semantic Web. This common ground is helping to convert an engineering concept into a movement. TDM generally has little enough connection with the Semantic Web, being instead in the orbit of machine learning which is no respecter of the semantic. Don't break a taboo by asking bots "and what do you mean by that?"

The ScienceSource project innovates in TDM, by storing its text mining results in a Wikibase site. It strives for compliance of its fact mining, on drug treatments of diseases, with an automated form of the relevant Wikipedia referencing guideline MEDRS. Where WikiFactMine set up an API for reuse of its results, ScienceSource has a SPARQL query service, with look-and-feel exactly that of Wikidata's at query.wikidata.org. It also now has a custom front end, and its content can be federated, in other words used in data mashups: it is one of over 50 sites that can federate with Wikidata.

The human factor comes to bear through the front end, which combines a link to the HTML version of a paper, text mining results organised in drug and disease columns, and a SPARQL display of nearby drug and disease terms. Much software to develop and explain, so little time! Rather than telling the tale, Facto Post brings you ScienceSource links, starting from the how-to video, lower right.

ScienceSourceReview, introductory video: but you need run it from the original upload file on Commons
Links for participation

The review tool requires a log in on sciencesource.wmflabs.org, and an OAuth permission (bottom of a review page) to operate. It can be used in simple and more advanced workflows. Examples of queries for the latter are at d:Wikidata_talk:ScienceSource project/Queries#SS_disease_list and d:Wikidata_talk:ScienceSource_project/Queries#NDF-RT issue.

Please be aware that this is a research project in development, and may have outages for planned maintenance. That will apply for the next few days, at least. The ScienceSource wiki main page carries information on practical matters. Email is not enabled on the wiki: use site mail here to Charles Matthews in case of difficulty, or if you need support. Further explanatory videos will be put into commons:Category:ContentMine videos.

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MediaWiki message delivery (talk) 18:52, 17 May 2019 (UTC)

MfD nomination of Portal:Organic chemistry

Portal:Organic chemistry, a page which you created or substantially contributed to, has been nominated for deletion. Your opinions on the matter are welcome; you may participate in the discussion by adding your comments at Wikipedia:Miscellany for deletion/Portal:Organic chemistry and please be sure to sign your comments with four tildes (~~~~). You are free to edit the content of Portal:Organic chemistry during the discussion but should not remove the miscellany for deletion template from the top of the page; such a removal will not end the deletion discussion. Thank you. UnitedStatesian (talk) 17:25, 20 May 2019 (UTC)

A possible Science/STEM User Group

There's a discussion about a possible User Group for STEM over at Meta:Talk:STEM_Wiki_User_Group. The idea would be to help coordinate, collaborate and network cross-subject, cross-wiki and cross-language to share experience and resources that may be valuable to the relevant wikiprojects. Current discussion includes preferred scope and structure. T.Shafee(Evo&Evo)talk 02:55, 26 May 2019 (UTC)

Lead Processing Plan Occupational Safety/Environmental Health Discussion at Doe Run Company

There is a discussion over at Doe Run Company that might interest people in this wikiproject about the safety, health, and environmental impacts of lead processing facilities. -Furicorn (talk) 21:40, 29 May 2019 (UTC)

Nomination of Portal:Fire for deletion

A discussion is taking place as to whether Portal:Fire is suitable for inclusion in Wikipedia according to Wikipedia's policies and guidelines or whether it should be deleted.

The page will be discussed at Wikipedia:Miscellany for deletion/Portal:Fire until a consensus is reached, and anyone is welcome to contribute to the discussion. The nomination will explain the policies and guidelines which are of concern. The discussion focuses on high-quality evidence and our policies and guidelines.

Users may edit the page during the discussion, including to improve the page to address concerns raised in the discussion. However, do not remove the deletion notice from the top of the page. North America1000 23:35, 2 June 2019 (UTC)

I found some missing chemicals.

Bowlane, Alkaplane and Octaplane. --Sharouser (talk) 07:44, 25 May 2019 (UTC)

In general, chemical compounds should meet the general notability guideline to be included in Wikipedia. Are there sufficient reliable sources about these compounds to support their notability? -- Ed (Edgar181) 18:35, 25 May 2019 (UTC)
see Draft:Octaplane and please add to it. There appear to be at least three book references with several pages each on octaplane. There is also a little on bowlane in these too. Graeme Bartlett (talk) 13:32, 3 June 2019 (UTC)

Glyphosate synthesis

The scheme below is currently shown in the synthesis section for glyphosate - Commons shows that its being used on several different wiki's. The first step makes no sense to me and I'm very sure its wrong. I'm guessing that it's supposed to be chloroacetic acid and ammonia with Ca(OH)2? I don't currently have any editing software, would anyone be able to overwrite the commons image with a corrected one? --Project Osprey (talk) 12:15, 3 June 2019 (UTC)

If you mix chloroacetic acid and ammonia, you likely get an acid–base reaction to form ammonium chloroacetate in situ. The WP article notes that this mixing is what is done (and comparable to ammonium acetate it seems like one could start with that salt?). However, the ref explicitly says this is not the order of mixing ("chloroacetic acid is added to a solution of NH3 and Ca(OH)2"). The whole process descriptionin the article is convoluted, and the discusion of the synthesis of iminodiacetic acid should be offloaded to that article's page since it does not matter how it is formed (and the ref says there are many ways). Although the ref does say "The production of IDA is often part of the integrated glyphosate process." so at least having its synthesis-equation here also might be reasonable? But the ref doesn't support this specific IDA method as being especially popular, so I think it's not best to have this synthesis-equation if we were to have any. Which brings me back to "omit it". DMacks (talk) 16:42, 3 June 2019 (UTC)
For now, I replaced that image with just the second equation from it:
And adjusted the article content accordingly. Anyone is welcome to create some "synthesis of IDA" diagrams...especially for the Iminodiacetic acid that currently has zero content or images for any of its synthetic routes. The cited ref by Dill (free PDF) has some good details. DMacks (talk) 17:05, 3 June 2019 (UTC)

A proposal for WikiJournals to become a new sister project

Over the last few years, the WikiJournal User Group has been building and testing a set of peer reviewed academic journals on a mediawiki platform. The main types of articles are:

  • Existing Wikipedia articles submitted for external review and feedback (example)
  • From-scratch articles that, after review, are imported to Wikipedia (example)
  • Original research articles that are not imported to Wikipedia (example)

Proposal: WikiJournals as a new sister project

From a Wikipedian point of view, this is a complementary system to Featured article review, but bridging the gap with external experts, implementing established scholarly practices, and generating citable, doi-linked publications.

Please take a look and support/oppose/comment! T.Shafee(Evo&Evo)talk 11:26, 5 June 2019 (UTC)

I oppose this idea, but sense that the horse is out of the barn. If you want to publish, then do so as an adult and deal with other adults. If you want to be a pretend scholar, join the boy scouts and earn merit badges. Next "wiki-authors" and "wiki-scholars" will invade Wikipedia and start citing this amateur stuff as if it is quality. We already have or at least had a problem with editors using Wikipedia as sort of a blog or a forum to cite themselves. Maybe I am too cynical. What next? Wiki-PhDs? Wiki Professors?--Smokefoot (talk) 12:10, 5 June 2019 (UTC)
Smokefoot, the example papers E&E has linked have gone through external public peer review by credentialed expert reviewers. I don't see how they're any less "adult" than conventional peer-reviewed papers. Adrian J. Hunter(talk•contribs) 12:57, 5 June 2019 (UTC)
Then what is the point of all this Wiki-journal exercise? Is this exercise a workaround for open access? No, Wikijournal looks like a workaround to give nonplayers the false impression (IMHO) that they are players.
Want to write a review? Fine, write one and send it to a real journal with an illustrious, established editor, anonymous and illustrious reviewers, all operating under an editorial board exerting expert scholarly control, copyeditors and layout experts, etc.
But like I said, this initiatives is one that will not be turned back because that is just how things seem to work. Those that edit Wikipedia catch a whiff of the scholarly universe in which they are not participating, and they want to participate more fully. And if they are not allowed to participate in that scholarly world because they are unqualified (or too lazy to try to submit to a real journal), then these editors/aspiring scholars will recreate the review-like system.
Those are harsh words from an old-school editor that loves and admires Wikipedia, and wishes Wikipedia would stay Wikipedia. --Smokefoot (talk) 16:35, 5 June 2019 (UTC)

Scientific references for s-p mixing and bond orders in diatomic molecules include Dekock and Gray's textbook [1] and Chen and Manz's recent journal article [2] . These two sources establish that s-p mixing makes the bond order in diboron greater than 1 and the bond order in dicarbon greater than 2. (1.) Diboron: The article Single bond states: "Usually, a single bond is a sigma bond. An exception is the bond in diboron, which is a pi bond." As the two sources listed above showed, the bond order in diboron is between 1-2 bonds and greater than 1 bond due to s-p mixing. Therefore, diboron is not an example of a single bond. (2.) Dicarbon: (a) The article Diatomic carbon states: "Molecular orbital theory shows that there are two sets of paired electrons in a degenerate pi bonding set of orbitals. This gives a bond order of 2, meaning that there should exist a double bond between the two carbons in a C2 molecule.[3] One analysis suggests instead that a quadruple bond exists,[4] an interpretation that was disputed.[5] CASSCF calculations indicate that the quadruple bond based on molecular orbital theory is also reasonable.[3] Bond dissociation energies of B2, C2, and N2 show increasing BDE, indicating single, double, and triple bonds, respectively." The statement about molecular orbital theory yielding 2 bonds for dicarbon is incorrect, because when s-p mixing is included molecular orbital theory gives a dicarbon bond order between 2-3 bonds. [1][2] (b) The article Molecular orbital diagram states for dicarbon "The molecule can be described as having two pi bonds but without a sigma bond.". This statement is known to be incorrect, because it neglects s-p mixing which is present in this molecule.[1][2] (3.) Information in the article Molecular orbital diagram is chemically inconsistent. The section s-p mixing correctly describes s-p mixing for Li2 to N2. The listed bond orders for diboron and dicarbon appearing on the same page are incorrect, because they do not include s-p mixing. Diboron is stated as having a bond order of 1; this should be ~1.75[2] (or 1-2)[1] because of s-p mixing. Dicarbon is stated as having a bond order of 2; this should be ~2.75[2] (or 2-3)[1] because of s-p mixing. (4.) Is there interest within WikiProject Chemistry to include an article or article section on diatomic bond orders? Would an article titled 'Diatomic bond orders' be appropriate? Would it be better to include a section on bond orders within the Diatomic molecule article? Would it be better to include a section on diatomic molecules within the Bond order article? The recently published heuristic model for all period 2 homodiatomics might make an interesting table of bond orders: Li2 = 1, Be2 = 0.75, B2 = 1.75, C2 = 2.75, N2 = 3, O2 = 2, F2 = 1, Ne2 = 0.[2] These bond orders are consistent with molecular orbital diagrams including s-p mixing for Li2, Be2, B2, and C2.[1] These bond orders also agree with bond orders derived from the bond lengths, as well as those computed using high level quantum mechanical calculations.[2]

Blue rover (talk) 21:01, 11 June 2019 (UTC)

  1. ^ a b c d e f Dekock, Roger; Gray, Harry (1980). Chemical Structure and Bonding (2nd ed.). University Science Books. pp. 183–271. ISBN 978-0935702613.
  2. ^ a b c d e f g T. Chen; T. A. Manz (2019). "Bond orders of the diatomic molecules". RSC Adv. 9: 17072–17092. doi:10.1039/c9ra00974d.
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