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List of aqua-ions and their hydroxo- and oxo- derivatives in aqueous solution

I've been working on this list for ca. three weeks, with valuable help from User:Petergans, and a few other WP:ELEM members. When I started I had little idea how it would turn out apart from supposing cations on the left and anions on the right. That is, of course, how it turned out but there were and still are many wrinkles between those two extremes.

Appreciate any observations folks here may have. I intend for it to be eventually listed at WP:FL.

thank you Sandbh (talk) 04:26, 8 August 2021 (UTC)

Is this a synthesis? As there seems to be nothing around outside of Wikipedia called "aqua-ions and their hydroxo- and oxo- derivatives in aqueous solution". Graeme Bartlett (talk) 13:08, 8 August 2021 (UTC)
For chemists, its not very useful. It presents an archaic view of chemistry (what is "HfO2+"?). As other editors indicate above and below this remark, its point is slightly unclear although the intent is admirable. One related topic that we could really use is a semi-comprehensive list of polyoxometalates, both homo and hetero.--Smokefoot (talk) 14:21, 8 August 2021 (UTC)
I think this list article has a lot of potential, but why not name it List of aqueous ions or List of aqueous ions by element? The detailed and somewhat convoluted title seems unnecessary and will be confusing to many. The list seems to include other common ions that are not aqua ions or contain oxygen, and in my opinion should do so (e.g., chloride). Since it seems like we don't have a broader, more comprehensive list, why not make this fill that gap? Also, I do not understand the "Combination of species" column. Probably some system I am unfamiliar with, but it is not described in the article that I can tell and many other readers will not understand it either. Mdewman6 (talk) 22:22, 8 August 2021 (UTC)
I agree that the article title is unhelpful, and I think either of your suggestions is superior to the current title and to the previous titles. FYI, the article started out as Periodic table (aqueous chemistry), then change to List of ions in aqueous chemistry, then to List of ions in pure water (aqueous chemistry), then List of stable ions in pure water (aqueous chemistry), and finally to the current title List of aqua-ions and their hydroxo- and oxo- derivatives in aqueous solution. I think your suggestion is so good that I am going to WP:BOLDly move the article.
Second, with regard to the "combination of species" column, it shows how many species (cation, oxycation, anion, oxyanion) a given element forms, and which of the four species it forms. I have added an extended footnote to this effect. Previously the only explanation was the (C), (xC), (A), (xA) located in the other columns, which was inadequate. Does the new addition make it clear? Would the meaning be clearer if the column title was "Number of species"? Or is there some way to improve the wording of the note? Or should the note be better presented using the {{abbr}} template that is normally used to explain an abbreviation like this: "Combinations". Or should a brief explanation be added to the paragraph before the table?
Thank you for your input! YBG (talk) 23:20, 8 August 2021 (UTC)
I now understand the column, but with the description buried as a footnote, I still don't think it is very accessible to most readers and will likely cause confusion. Since it seems simply an attempt to indicate which categories of ions are possible for a given element, isn't that information evident by whether the other columns have entries or not? I think this column should be removed as I feel it's likely just causing confusion rather than conveying useful information. Mdewman6 (talk) 16:19, 10 August 2021 (UTC)
@Mdewman6: You are absolutely correct that this column adds no additional information ... however it does add the capability of sorting by combination of species. As such, it is helpful for editors who wish to keep the periodic table up-to-date. YBG (talk) 00:50, 11 August 2021 (UTC)
@Mdewman6: By the way, it is no longer buried in a footnote, but visible in mouse-over text. Recognizing that the column less important than the other columns, I have moved it to the right of the table. YBG (talk) 06:00, 11 August 2021 (UTC)

I appreciate your help Graeme, Smokefoot, and Mdewman6.

Much information about which ions the elements form in water can be found in Schweitzer & Pesterfield 2010, The Aqueous Chemistry of the Elements. I say "much", as they sometimes abstract the species concerned. Sometimes they discuss what ions are involved in the abstraction, sometimes not. Consultation of the sources used by them, or sources such as Baes & Mesmer 1976, The Hydrolysis of Cations (which User:Petergans mentioned) or Brown 2016, Hydrolysis of Metal Ions, allows the unpacking of such abstractions.

On utility or being archaic, there is an evident periodic table pattern to the occurence of the ions concerned. Thus:

"Professional academic resources have begun to encourage an examination of periodicity with activities based on pattern recognition of element properties, the fundamental concept Mendeleev and Meyer used in the 19th century to create the first PTE"
— Bierenstiel M & Snow K 2019, "Periodic universe: A teaching model for understanding the periodic table of the elements", Journal of Chemical Education 96 (7), 1367–1376 (1367), doi:10.1021/acs.jchemed.8b00740

On HfO2+, S&P say about the Zr equivalent, "This formula is a simplification of the tetramic species that is believed to predominate, namely Zr
4
(OH)8+
4
." If that is the case for HfO2+, they do not say.

Petergans has been adding polyoxometalate species.

Aside from chlorine species there are no other species with chlorine in them, that I can see. Sandbh (talk) 03:38, 9 August 2021 (UTC)

There is a fundamental issue with this article: the establishment of which species exist in aqueous solution over a wide range of pH is based on computer modelling, see #model selection in Determination of equilibrium constants​. This is compounded by the fact that equilibrium with polymeric species is often reached rather slowly. A guide to model selection is provided by known structures of species that have been precipitated from solution, but it does not follow that those are the major species that are present in solution. Also, there may be ambiguity as in the empirical formulae of HfO2+ or Hf(OH)22+ which cannot be resolved for the presumably tetrameric species in solution. In my edits I have omitted those species whose existence in solution is most doubtful. Petergans (talk) 08:02, 9 August 2021 (UTC)

Many of the Cation species are not present as a bare metal ion in solution, but will be present as a hexaaqua complex. The colour depends on that octahedral arrangement of water molecules. eg Ni(H2O)62+ Graeme Bartlett (talk) 12:54, 9 August 2021 (UTC)

No stable oxyanion is given for hydrogen, is it not hydroxide? …and hydroperoxide, etc --Project Osprey (talk) 13:50, 9 August 2021 (UTC)

I think that the project is way too ambitious. And to do it right, one needs to be very familiar with metal ions in aqueous solution, rare knowledge. As Petergans points out, pH is a huge factor. Olation can be slow. 17O NMR studies show that even "simple stuff' like hydrated nickel halides and sulfates are partially associated. One approach would be to take on one important metal, say Zn2+, and nail it. I have been considering writing an article transition metal hydroxide complexes (vs just transition metal hydroxides) but most of the article would be on mixed ligand species like [Co(NH3)5OH]++ because few homoleptics exist. Also reviews on the topic are few.--Smokefoot (talk) 14:33, 9 August 2021 (UTC)
I agree that this page is ambitious, as the topic of aqueous speciation, ions, and complexes cover entire textbooks and is a function of pH, complex equilibria, and solution composition, and here we are trying to reduce it essentially to one table. But, I think it can be made clear that this article is not comprehensive nor complete, but instead is a compilation of the major ions for each element, with many links to WP articles. I don't think we need to get bogged down in pH-dependent equilibria and such here, that can be fleshed out in articles for specific ions as appropriate. Mdewman6 (talk) 16:19, 10 August 2021 (UTC)
Thank you@Mdewman6: that was my intent for the article. There are several monographs that give this information. But one has to have one's wits about oneself, as user:Petergans has intimated, and mention on what basis the authors of RS are making their claims. That was the purpose of the notes column, among other things, until it was removed for some reason. I supposed this could be done via footnotes instead.
I was interested to see what the periodic table distribution would be for these species. This is mapped in the accompanying periodic table but I haven't checked to see if it's still accurate since recent amendments to this list, some of which I intend to contest, in due course.
user:Petergans added the text accompanying the list (to whom, thank you!). This text needs some work as I feel parts of it are unintelligible to the general reader.
If things go as intended I'll post periodic updates to this talk page. Sandbh (talk) 06:16, 6 October 2021 (UTC)
Courtesy ping@Petergans: Sandbh (talk) 08:54, 6 October 2021 (UTC)

NaCl polyhedra

Hi, I hope someone here can help me out as I have nominated this image to become a Featured Picture and now there is some questions about this image.
I hope someone here have the knowledge to provide answers to the questions at this link. The questions are;
1) This representation is different to all the others I've Googled. Does it have Academic authentication?
2) But could you add to the description about which colors are which elements.
I'm a graphic worker and have no knowledge of this subject.
I really hope someone here can help me or tell me someone else who might be able, thanks. --always ping me-- Goran tek-en (talk) 17:18, 23 August 2021 (UTC)

I have got the needed information from another user so this is  Done, thanks. --always ping me-- Goran tek-en (talk) 19:55, 23 August 2021 (UTC)
Should the image could use PyMOL colors for the elements? Is this standard enough (to advise it)? -DePiep (talk) 05:37, 24 August 2021 (UTC)
I will make a new version with those colors so then anyone can use the version they want/need. --always ping me-- Goran tek-en (talk) 10:20, 24 August 2021 (UTC)

Class A assessment for Gold(III) chloride?

Back in July, I did a GA review of Gold(III) chloride, which failed. I just noticed that shortly after that, Keresluna changed the rating of the article to A Class. I'm not an expert as the assessment process, but my understanding is that A class requires a review, and I don't see that such a review was done. Could somebody please take a look at this? -- RoySmith (talk) 14:05, 23 September 2021 (UTC)

@RoySmith:I am sorry, I was not familiar with the process at that time, should I change it back? Keres🌑(talkctb) 15:57, 23 September 2021 (UTC)
The process is described at Wikipedia:Content assessment/A-Class criteria. -- RoySmith (talk) 17:34, 23 September 2021 (UTC)
@RoySmith:Should I change it back? Or should I initiate a review? Keres🌑(talkctb) 18:27, 23 September 2021 (UTC)
I would start by changing it back. Once you've done that, it's up to you whether you want to start a review. -- RoySmith (talk) 18:34, 23 September 2021 (UTC)
@RoySmith:Changed it back. Keres🌑(talkctb) 22:56, 23 September 2021 (UTC)

IUPAC Goldbook terms/definitions

I've been working with some of the IUPAC people in recent months, to try to find a way to get IUPAC definitions into our chemistry articles in a systematic way - something we've been trying to do since 2007. One problem we've had in recent years was that all IUPAC publications were tagged with copyright information showing licenses that are incompatible with Wikipedia policies. This even led to IUPAC definitions being deleted from articles.

We've worked with IUPAC for the last couple of years to find a solution, and we now have a set of terms/definitions released under a compatible CC-BY-SA license. This was because of concerns that official definitions might be corrupted if the "No-Derivatives" part of a CC-ND license were removed. The solution is that IUPAC has agreed to release all graphical versions of Gold Book terms & definitions under a CC-BY-SA license, and we had this agreement (including a signed letter from the IUPAC leadership) approved by the Wikipedia OTRS folks. If this works out well, it'll probably be extended to all terms & definitions.

So I'm hoping everyone here is supportive of the idea of adding IUPAC terms/definitions into articles where appropriate. This will only affect a limited number of articles, since there is a not a simple 1:1 relationship between articles and IUPAC terms - most articles don't have a corresponding Gold Book entry, and vice versa. But in cases where there is an obvious correspondence between a Gold Book term and an article or article section, I believe it would greatly enhance most articles. In many cases the IUPAC definitions have already been added as text or text boxes - in most cases this was done at a time before copyright limitations were added by IUPAC/DeGruyter.

Assuming people here are supportive of including IUPAC terms/definitions, the question becomes: What is the best format for using these images in articles? I've created a few example formats on my Sandbox page. I'm not sure if direct links from images are allowed in article space - does anyone know? We have thumbnails with linked captions, we have a simple linked image, and we have an image map that can provide links to both the PAC page and the Goldbook page as references. There are of course variations on these - feel free to add other versions to my sandbox page if you have a better one. Your ideas and feedback are most welcome, because we want to get this right, and maybe add it to the MOS if we find a nice consensus. Many thanks, Walkerma (talk) 09:14, 29 September 2021 (UTC)

A valid and useful goal - and it looks like it's taken a lot of back-and-forth to achieve. Well done. My only criticism would be that we only ever hear about these agreement with CAS or IUPAC after they've been finalised, it would be nice to know about what's being done on our behalf. From experience I think most goldbook links are handled by Template:GoldBookRef. If there are going to be hundred of images (and it sounds like there are) then something similar might be a good idea so we only need to enter the correct Goldbook code (e.g. 'M04002' for molecule) to bring up the image. Of course, that's easy for me to suggest, because I won't be the one writing the template. --Project Osprey (talk) 09:44, 29 September 2021 (UTC)
Thanks for your reply. I'm sorry if it seems like a lot of secrecy, but in the case of CAS we were specifically required by CAS to keep quiet during negotiations until their press release came out. In this case (IUPAC), most of the time was spent waiting for IUPAC to get legal advice and get the leadership on board with the idea of a CC-BY-SA license, and no Wikipedians were involved with that. Most recently, I've been the one who's been slow, but just because things got too busy at work for me to focus on it - I can certainly apologize for that. I wanted to get a range of options for this group to discuss. As for the template, yes - we should definitely do that! Thanks, Walkerma (talk) 12:58, 29 September 2021 (UTC)
I agree that it's important to have some authoritative referencing and definitions of key terms, such as from Gold Book. Make your own "gold-standard" joke here {{GoldBookRef|file=...|title=...}} displays the given title as a link to the given file-name on the Gold Book website. It would be easy to have a {{GoldBookDefImage|term=...}} that displays the image of the term's definition along with some standardized caption and/or linking. A standard on Commons is that that images that form a unified set and are used by a template should have a systematic naming pattern. Please consider however that you will likely get MOS pushback for including so much decoration and in-image text beyond the def itself. And that's even if there is MOS/ACCESSIBILITY acceptance of an image-of-text rather than the text itself: CC-BY-SA means replacing it with plain-text is potentially an allowable derivative (see also commons:Category:Images which should not be images, and whether commons might think these are more appropriate on Wikisource). DMacks (talk) 03:38, 4 October 2021 (UTC)

What about ethanoic acid?

IUPAC defs are useful when they are useful. But ...--Smokefoot (talk) 13:38, 29 September 2021 (UTC)

Let's not forget that the Preferred IUPAC name for AcOH is actually acetic acid!
I do know one use for IUPAC names that you might appreciate, though. I worked in the lab at a UK chemical plant for many years, and the guys from the plant were always stealing our acetone wash bottles and net returning them. One smart chemist renamed them with titles like "propanone" or "propan-2-one" or "dimethylketone" and it solved the problem immediately!
These Gold Book terms/definitions, though, are less to do with nomenclature and more to do with more general terms like carboxylic acids. Walkerma (talk) 19:26, 29 September 2021 (UTC)
To your question on linking, Walkerma, Help:Pictures#Links says this may be done and describes how to do it correctly. However I assume that the IUPAC boxes are to be held on Commons so the usual Wikipedia standard should be that clicking on the image takes you first to an enlarged version and then to "more details" which is the Commons page on which the image and its license are stored. I don't see any reason to alter that. So I support the simplest case in your sandbox where the doi for the Gold book is just a standard reference cited in the normal way (with a doi-access=free tag). On the wider question, I support using this IUPAC linking whenever possible, bearing in mind that WP:COMMON will override the IUPAC advice, particularly for article titles. Thanks for your efforts in getting this far. Mike Turnbull (talk) 10:15, 30 September 2021 (UTC)
Thank you for your feedback - that's very helpful! There's a lot of good advice there, which I appreciate, as I'm not as in tune with the nuances of protocol as I once was. I had suspected that we'd probably want to link to a reference, but I wasn't sure how the rules/guidelines have evolved in recent years. Thanks, Walkerma (talk) 17:09, 1 October 2021 (UTC)
I also don't see a reason to modify the standard linking of images to their commons page, on which there would be a link to the website itself. MOS:CREDITS advises not to use the caption to give credit specifically because it is on the file's own page. But a descriptive caption could state that it is the Gold Book def, with a wikilink for Gold Book and a footnote for the ref itself. DMacks (talk) 03:38, 4 October 2021 (UTC)

The Origin of Elements from Carbon to Uranium

Perhaps this extensive reference may be useful for some element and isotope articles?

Kobayashi, Chiaki; et al. (September 15, 2020). "The Origin of Elements from Carbon to Uranium". The Astrophysical Journal. The American Astronomical Society. 900 (2): 33. arXiv:2008.04660. Bibcode:2020ApJ...900..179K. doi:10.3847/1538-4357/abae65. 179.

Thanks. Praemonitus (talk) 04:59, 30 September 2021 (UTC)

MfD nomination of Portal:Biochemistry

Ambox warning orange.svg Portal:Biochemistry, a page that falls under the purview of this project, 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:Biochemistry (2nd nomination) and please be sure to sign your comments with four tildes (~~~~). You are free to edit the content of Portal:Biochemistry 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. North America1000 07:50, 4 October 2021 (UTC)

Nonmetal at FAC

I'd be grateful if anyone here has the interest and time to look at this one. Thank you, Sandbh (talk) 00:39, 11 October 2021 (UTC)

After two unsuccessful nominations, round 3 at FAC is here. Sandbh (talk) 00:49, 31 October 2021 (UTC)
The FAC has now rec'd its first Support. Is there anyone here who could assist? Sandbh (talk) 02:31, 14 November 2021 (UTC)

Requested move: Lists of IARC agents

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Wiki Science Competition 2021

Hi, I'd like to remind you all that Wiki Science Competition 2021 has started in many territories last week. It will last until November 30th or December 15th, depending on the areas.

WSC is organized every two years, and people from all countries can upload files (the goal are the international prizes) but specific national pages are also set up, for example for USA or Ireland. These national competitions (when they exist) act as an additional incentive to participate.

We expect a sitenotice to show up for all readers here on enWikipedia as well, but probably during the second half of the month when all countries with national competitions are open for submission. In the meantime, if you are planing to upload some nice image or video to Commons, please consider to submit them using the WSC interface, you might win a prize.--Alexmar983 (talk) 01:07, 9 November 2021 (UTC)

Structure diagram service?

Is there a service for producing high-quality structure diagrams, in the same spirit as Wikipedia:Graphics Lab/Map workshop? I'm doing a GA review of Riboflavin, which has some structure diagrams that are of such a low quality, they're nearly unusable. I imagine somebody who's a ChemDraw wiz could come up with high quality replacements pretty quickly. -- RoySmith (talk) 20:53, 18 November 2021 (UTC)

I can't currently help with new images, but the existing images look to have been made by badly editing File:Riboflavin Synthase Mechanism.png --Project Osprey (talk) 23:44, 18 November 2021 (UTC)
Maybe: https://www.cheminfo.org/wikipedia/ ? (no experience myself). -DePiep (talk) 11:53, 19 November 2021 (UTC)
I'd be happy to ChemDraw some images. We have Wikipedia:WikiProject Chemistry/Image Request, but nobody seems to use it lately. There are some tags on commons if you find a mistake or a low-quality image there, but those categories are large and again nobody is actively working through them. Probably best to just make a one-off request here or on a user-talkpage of a participany you know or that seems active if you have a specific need. DMacks (talk) 23:00, 19 November 2021 (UTC)
Cool, thanks. Foolish me thinks that you could just copy-paste the SMILES code from the article into some appropriate piece of software and out pops a perfect image, but I don't suppose it's quite that easy? -- RoySmith (talk) 23:13, 19 November 2021 (UTC)
Chemdraw can do that SMILES→PIC, but it does have limits, where it makes a mess. And my version does not make .svg files. Graeme Bartlett (talk) 03:16, 20 November 2021 (UTC)
Same with mine. I have no idea why...SVG on Mac has been widely supported for many years in general, but CD on that platform tends to lag in several ways. There are some online and some open-source programs that can do it. But in all cases, they make arbitrary choices about lots of layout/orientation details that might not match or make sense in the context of an existing article with multiple images (same as any machine translation). DMacks (talk) 05:08, 20 November 2021 (UTC)
I am very familiar with chemical drawing packages, which I've used since the 1980s, and can turn their output into .svg files of compact size. If RoySmith or anyone else makes a specific request on my Talk Page, I'd be happy to oblige. My recent efforts include those at molnupiravir and PF-07321332. There are some software packages that can give reasonable .png from molfiles (in turn available from Chemspider as downloads) but for fidelity the stereochemistry etc. really needs the attention of an organic chemist. Mike Turnbull (talk) 16:57, 20 November 2021 (UTC)

Template chembox - Lua and infoboxes

Hello! In the recent days I've been discussing about {{chembox}} in regard to changing its technical infrastructure to be rewritten in Lua so that we won't need tens of subtemplates to make use of its modular design. The discussion is currently happening here where the reasons for the proposed change are also discussed. It was suggested to me to also notify here so I'd appreciate any kind of feedback. Please make sure to comment there so we can have 1 single discussion for the topic. - Klein Muçi (talk) 12:27, 19 November 2021 (UTC)

To be clear: at Talk:Chembox § Convert Chembox into Lua module, Klein Muçi proposes to allow {{Chembox}} be changed into a Lua-based {{Infobox}}. -DePiep (talk) 20:53, 21 November 2021 (UTC)