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Eyring Equation and Enthalpy of ActivationEdit

Dear WikiProject Chemistry,

I would like to kindly request that an article be written on Enthalpy of Activation in the Eyring Equation. I don't have experience in Chemistry so I didn't know which section of the article requests on Wikiproject Chemistry to place this under. I would also request that the symbol used for enthalpy of activation in the Eyring Equation article is changed from ΔH‡ to Δ‡H⚬. The first symbol is incorrect according to IUPAC: I am requesting an article on this because I am referencing a page called the List of Mathematical Uses of Latin Letters and enthalpy of activation came up. I do not have an appropriate article to link this chemical kinetics term to. I hope one of your fine chemists could help me out! If you have any questions please come to my talkpage! Kabiryani (talk) 11:57, 2 April 2022 (UTC)

Updating naming conventions for groupsEdit

The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section. A summary of the conclusions reached follows.
Consensus to implement the proposed revisions to the section of the chemistry naming conventions. Mdewman6 (talk) 23:34, 10 June 2022 (UTC)

I think it's due time to take a look at the content at Wikipedia:Naming_conventions_(chemistry)#Groups_of_compounds to see if the wording and examples need updating, and then work on bringing article titles in line with the conventions we've confirmed. Looking specifically at the first subsection:

  • Compound class and functional group are not clearly differentiated, using alkane as an example of a functional group, when in fact alkyl is the associated functional group that has a separate article. Also, an internal link to functional group would certainly be helpful to readers.
  • The first subsection goes on to confusingly state where the group is not considered to be functional, e.g. phenyl, trimethylsilyl, or is important for some other reason, e.g. trifluoromethylsulfonyl. The examples given are typically referred to as functional groups and can be the "functional" part of a molecule in chemical reactions, so this differentiation is at best confusing, if not completely unwarranted and incorrect.
  • It states that the normal IUPAC name (under general nomenclature) for the group is used. This likely runs into WP:COMMONNAME problems. I argue the article on one of the examples given, trifluoromethylsulfonyl, should be at its common name, triflyl, as the lede suggests as well. We should consider revising the guidance here to call for the use of names most commonly used in reliable sources, akin to the guidance for naming organic compounds.
  • Finally, it states...without adding the word "group". This is apparently an effort to conform to WP:CONCISE, but one of the most prominent examples, Phenyl, currently has its article at Phenyl group contrary to the current convention. The current format for article titles of functional groups vary even further, e.g. Tolyl groups. Personally, I do favor adding "group" to the titles of such articles, but recognize there are arguments both ways. Colloquially, chemists will refer to functional groups as nouns (e.g. "that compound has three phenyls" or something) but they are really adjectives that should modify a noun ("group") when used as an article title.

As for the second subsection:

  • I generally agree with the guidance here, except that the article titles for these articles are presently all over the place, as can be seen by following links from Template:ChemicalBondsToCarbon. Many have the format "Organo[element] compound" but are confused by WP:PLURAL as to whether or not the plural is warranted because the article is about a class, thus some are "Organo[element] compound" and some are at "Organo[element] compounds". Using the "chemistry" form of the name avoids this issue. Other articles are at related titles if the article for the related topic has been sufficiently developed, e.g. Organolithium reagent, with the other versions as redirects, which I think is okay. So, here I think we can just emphasize the current guidance and then bring all the affected articles into compliance and be consistent.

Please share comments and I will draft a proposed revision for us to consider and will link below. Mdewman6 (talk) 01:38, 12 April 2022 (UTC)

I have a rough draft of a proposed revision at User:Mdewman6/Chemical groups naming convention. The only major change is to specify that articles on functional groups include "group" in the title, e.g. phenyl group, not just phenyl. It also makes clear to defer to WP:COMMONNAME rather than going with whatever IUPAC may say. Please comment; if there are no objections I would like to institute these revisions in the near future and bring consistency to the titles of the affected articles. Mdewman6 (talk) 02:05, 19 April 2022 (UTC)

Any comments? I don't think we need an RfC for this, but I'd prefer not to go with WP:SILENCE for implementing a naming convention change either. But, given the page views the proposed version has received, I will take silence as consensus if there is no further discussion. Mdewman6 (talk) 02:58, 20 May 2022 (UTC)

Support. I think this proposal improves Wiki, because it standardises naming (-patterns) without enforcing nonintuitive routes. Maybe strengthen support by notifying/proposing at WT:MOS/Chemistry? After all, it is a MOS change. (I am not specialist in this chemistry; I do work with {{Chembox}} and {{Drugbox}} here). -DePiep (talk) 07:19, 20 May 2022 (UTC)
I will add a notification of this discussion at the MOS page. Mdewman6 (talk) 21:14, 20 May 2022 (UTC)
Support, but it has a major gap. What kind of disambiguation should be used for these articles, particularly for compound classes and functional groups that are named after their parent compound? Should we use plurals like Hydrazines or parentheticals like Diphosphene (functional group)? –LaundryPizza03 (d) 09:18, 20 May 2022 (UTC)
@LaundryPizza03: Excellent point. I was mostly trying to make sense of the naming convention as it stood, but we should definitely say something about these cases. I just noticed Wikipedia_talk:Manual_of_Style/Chemistry#Compound_class, where an example of yet another disambiguation strategy is given, Fulvalene (compound class). For groups based on inorganic parent compounds, another method is to add an organo- prefix, like Organophosphine vs. Phosphine, but I'm not sure I like this (certainly a good redirect at least). I lead toward thinking we should favor using plurals for this, which would fully comply with WP:PLURAL and WP:DIFFCAPS and also favor natural disambiguation over parenthetical disambiguation. I feel like a majority of such articles use the plural at present, like Silanes, Boranes, etc. but I'm not certain. Of course, if the article is setup to be more about the functional group than the class of compounds, then [singular] group could be considered per the above on a case by case basis. Hatnotes between the parent compound article and the compound class articles should also be standard. Anyway, I'll amend the draft soon to reflect this and we can see if like it or not. Mdewman6 (talk) 21:14, 20 May 2022 (UTC)
I support a change to the naming convention, in particular for adding "group" to the articles mainly about the functional group. For compound classes, I was raising this issue back in 2020. I like the idea of adding the "s". Yet another convention is shown in Alcohol (chemistry) (which has redirect alcohols) and Salt (chemistry) (with redirect Salts). Even though Fulvalene (compound class) is a current example in our convention, it is the only article using it. Also would anyone like to write the article on Compound class? We already do have "Functional group". Graeme Bartlett (talk) 22:28, 20 May 2022 (UTC)
Well, Alcohol (chemistry) is analogous to Alkane and other traditional compound classes and should be singular under the current and proposed naming convention, it's just that alcohol has parenthetical disambiguation because of all the other uses of alcohol, and a recent RM decided there was no primary topic. But I think we can keep those singular while using the plural for compound classes named after parent compounds; I don't think we want Alkanes, Ketones, Carboxylic acids, Esters, etc. as titles instead of the singular, which would be a widespread change from the status quo. Mdewman6 (talk) 00:06, 21 May 2022 (UTC)
Also, I think we can use the plural for salts/esters of acids, which you also mentioned in your last discussion. So Phthalate should be at Phthalates, then there is Benzoates, etc. In many cases, these will be redirects to the parent carboxylic acid, or in rarer cases the parent carboxylate, but notable cases will have their own articles, which should be at the plural to analogously differentiate them from the carboxylate.

I added a paragraph to the draft section (User:Mdewman6/Chemical groups naming convention) that is an attempt to capture the situations discussed above. If implemented, we'll need to revise Wikipedia:Manual_of_Style/Chemistry#Compound_classes which suggests parenthetical disambiguation. Mdewman6 (talk) 22:06, 21 May 2022 (UTC)

(late to the party) I support these functional-group, class, parent-vs-derivative and associated singular/plural approaches. Has Wikipedia talk:Article titles or similar sitewide been pinged about this discussion? DMacks (talk) 22:48, 21 May 2022 (UTC)
No, I didn't cast the net that widely, but certainly can and will leave a link there. Mdewman6 (talk) 23:48, 21 May 2022 (UTC)

If there is no further discussion in next 7 days or so, I will plan on implementing the proposal to replace the current section of the naming conventions with the proposed text. I'm sure it could be further refined and tweaked, which can certainly happen going forward, but there seems to be consensus this is at least an improvement over the status quo. Cheers, Mdewman6 (talk) 22:39, 3 June 2022 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Molecular graphicsEdit

Molecular graphics is a disaster zone. Huge amounts of the content are unreferenced and likely basedon OR, and much of the content seems to be disorganized and repetitive. I have attempted to remove some of the fluff, including textbook-like image labels that included an in-text description of an image that was deleted in 2019. –LaundryPizza03 (d) 07:38, 19 April 2022 (UTC)

What is the deal with User:Prototyperspective?Edit

Seems to be adding content from new issues of Science and similar journals. "Researchers have found ..." "A recent study shows...". Check out recent changes in Monoterpene. The contributions are not awful, but IMHO, misguided in the sense that Wikipedia is a forum for settled knowledge and, ordinarily at least, we dont do news. --Smokefoot (talk) 21:06, 24 April 2022 (UTC)

User script to detect unreliable sourcesEdit

I have (with the help of others) made a small user script to detect and highlight various links to unreliable sources and predatory journals. Some of you may already be familiar with it, given it is currently the 39th most imported script on Wikipedia. The idea is that it takes something like

  • John Smith "Article of things" Accessed 2020-02-14. (John Smith "[ Article of things]" ''''. Accessed 2020-02-14.)

and turns it into something like

It will work on a variety of links, including those from {{cite web}}, {{cite journal}} and {{doi}}.

The script is mostly based on WP:RSPSOURCES, WP:NPPSG and WP:CITEWATCH and a good dose of common sense. I'm always expanding coverage and tweaking the script's logic, so general feedback and suggestions to expand coverage to other unreliable sources are always welcomed.

Do note that this is not a script to be mindlessly used, and several caveats apply. Details and instructions are available at User:Headbomb/unreliable. Questions, comments and requests can be made at User talk:Headbomb/unreliable.

- Headbomb {t · c · p · b}

This is a one time notice and can't be unsubscribed from. Delivered by: MediaWiki message delivery (talk) 16:01, 29 April 2022 (UTC)

"Successfully de-orphaned! ..."Edit

User:Herravondure is removing orphan tags on articles with the edit note "Successfully de-orphaned" but no links are being created, so not so successful.--Smokefoot (talk) 14:16, 2 May 2022 (UTC)

What articles are you referring to? I do deorphan articles, and if I did that to one with nothing linking to it that was my bad, but I am not doing this intentionally. Herravondure (talk) 14:28, 2 May 2022 (UTC)

Related point: Regardless if they're manually tagged or not, orphan pages are detected and listed by bots, in this project there are [211 pages] at present. --Project Osprey (talk) 14:43, 2 May 2022 (UTC)
Do you happen to know how often that page updates? Herravondure (talk) 15:35, 2 May 2022 (UTC)
It would appear to auto-update weekly. --Project Osprey (talk) 15:44, 2 May 2022 (UTC)
Probably someone with tools should revert most of User:Herravondure's edits.--Smokefoot (talk) 17:01, 2 May 2022 (UTC)
I'm not really seeing the problem here. Many of the recent chemistry links seem to be coming from Glossary of chemical formulae. --Project Osprey (talk) 17:52, 2 May 2022 (UTC)
Well, many articles are listed as removed from orphanage, but the editor is not adding the links that would de-orphanize. The editor is simply removing tags. Nothing is being done.--Smokefoot (talk) 18:11, 2 May 2022 (UTC)
Yeah, but when you de-orphan, you're adding links to that page from other pages. The only edit you make to the de-orphaned page is to remove the tag. That's what I'm seeing, lots of link were made from Glossary of chemical formulae to a load of orphaned articles, which had then been de-tagged. --Project Osprey (talk) 18:31, 2 May 2022 (UTC)
Question for Herravondure: what article links back to Fructose-asparagine that was recently detagged? Graeme Bartlett (talk) 04:20, 3 May 2022 (UTC)
That's probably the article Smokefoot found. I have been adding chemical orphans that I have failed to deorphan thus far to the Glossary of chemical formulae article. I do them in small bunches, so I must have thought I added that one when I didn't. I have now added it to the glossary. Herravondure (talk) 15:56, 3 May 2022 (UTC)

Redox area merits attentionEdit

The following articles touch on big complicated themes:

  • redox (page views: 1,340/day)
  • reducing equivalent comment: it might be merged into reducing agent. (page views: 24/day)
  • electron equivalent comment: see previous entry (page views: 4/day)
  • reducing agent comment: would be useful to distinguish electron transfer kind of reduction vs hydride reduction and hydrogenation. (page views: 453/day)
  • oxidizer redirects to oxidizing agent. But akin to reducing agent, we might distinguish O-atom transfer from electron transfer. My guess is that many nontechnical readers are more interested in oxidizers from the safety perspective and not so keen on organic syn. (page views: 681/day)
  • redox potential (page views: 6/day)
  • hydride seems ok but covers a lot of territory. (page views: 196/day)
  • hydride reducing agents, readers would probably benefit from such an article listing the main borohydrides and various aluminum hydrides. Almost a disambiguation article. Maybe one exists and I missed it.
  • Organic redox reaction comment: scope is murky (page views 63/day)
  • one-electron reduction was recently merged into redox
  • partial oxidation comment: seems to be mainly oxygenation reactions, stopping short of full combustion. (page views: 23/day)

Probably more articles on this theme exist.--Smokefoot (talk) 15:05, 3 May 2022 (UTC)

ECHA InfoCardEdit

This isn't my area but I thought this might be something worth flagging. ECHA InfoCard used to be a redirect to a section of European Chemicals Agency but that section no longer exists. However that redirect has incoming links from >10k articles - I assume it's in a template somewhere. I'd suggest this needs a bit of attention - either the template needs tweaking or some information needs to be added about the InfoCard. Le Deluge (talk) 14:55, 8 May 2022 (UTC)

The link is made in {{Chembox}} and {{Infobox drug}}. Heavily tied to wikidata ECHA Substance Infocard database (Q59911453) and its ID property. If the European Chemicals Agency article does not contain a good target, nor any other article, one wonders whether it is important. -DePiep (talk) 16:17, 8 May 2022 (UTC)
The ECHA article is not very good (e.g. it has external links in the body of the text and few/no secondary sources). I'm happy to add it to my "to-do" list and at the same time create a subsection on the Infocard, which is a fairly useful part of the European regulatory system and gives Wikipedia a less US-centric view. Thanks, Le Deluge for highlighting this. Mike Turnbull (talk) 16:52, 8 May 2022 (UTC)
  Done The redirect now goes to a newly-created section of the article, which I'm continuing to improve. Mike Turnbull (talk) 09:22, 10 May 2022 (UTC)
By Wikidata: the ECHA Infocard has no lang-wiki articles anywhere. The good news is: both chem templates here pull the ECHA ID from Wikidata, and so some 10k articles have this external Infocard ID+link. Data is well (mass-)maintained at WD, IIRC. -DePiep (talk) 19:43, 8 May 2022 (UTC)

Wikidata datamodelEdit

Creating a template?Edit

Useful links:

I originally posted this at the Teahouse, but upon advice of the venerable Mr Turnbull I have posted it here too.

Hi, I just noticed whilst browsing through List of named alloys that none of the alloys have infoboxes, and I'm sure it would be a useful idea. I just came here to ask two things, would it be useful (to create an infobox) and should I also make a navbox for alloys? Thanks. My username is actually based off an alloy too! X-750 Rust In Peace... Polaris 22:32, 11 May 2022 (UTC)

Hi @X750, I saw your question at the Teahouse. Many alloy articles here and on other language Wikipedias use {{Infobox material}}. See 7075 aluminium alloy and Constantan. That infobox isn't able to include the components of the alloy, but that might be a place to start. StarryGrandma (talk) 23:04, 11 May 2022 (UTC)
Thanks, StarryGrandma. I saw that infobox and I was actually going to use that as my substrate. What do you personally think should be included on the new template? Most of the fields are covered, but things such as composition are probably going to be one of them, similar to the chemical formula present on {{Infobox drug}}, but instead of a formula having the % ranges for each element present in said alloy. I was thinking a market names/alternate names section too for alloys such as inconel that have variations, a distinction between different types of alloy (e.g superalloy, nickel-chromium, etc), the UNS number, and that's all I can really think of. Cheers X-750 Rust In Peace... Polaris 23:25, 11 May 2022 (UTC)
Actually nine of our articles about specific alloys do have chemboxes, but that is obviously a small minority. But I don't think that box (as it currently exists) is well-tailored to alloys because so much assumes a molecular or ionic substance. We would need a sentinal value for SMILES to avoid a diagnostic for having no SMILES. And we'd need to inhibit mol-wt even though there would be a stoichiometric-composition formula. We have a similar problem for polymers, where mol-wt is either for the repeating unit (that's especially mis-leading for non-alternating co-polymers) or the molecular formula and weight need some typical lengths or "n" coefficients (chembox doesn't have a standard for that). {{Infobox material}} looks like a better start, just needs composition and some database tokens (even already our materials should be including that in the infobox, not just in the lede). Drugbox and chembox have equivalent internal handling of molecular formulas. But for material (including alloy) should it should render as a {{ubl}} of the components rather than a "molecular formula" type of output? DMacks (talk) 23:33, 11 May 2022 (UTC)
Correct DMacks, we would have something pretty much akin to a parameter such as composition, and then a {{ubl}}, as that's the easiest way I believe we can implement them. I haven't examined polymers so much, and I did not intend to use molecular formulas, weights, SMILES or anything of the sorts, just something akin to what's present at {{Infobox drug}}. For the database tokens, which is the UNS number, is there another internal system within Wikipedia that can categorise these things? I'm not too well-versed in the technical things (I do have experience with modules at Wiktionary if that's helpful at all), so I'd like some pointers as to what I should go about doing there. X-750 Rust In Peace... Polaris 23:45, 11 May 2022 (UTC)
Check out my hacking on ferrotungsten. Only reader-visible bug is that it should display a label of "Chemical composition" instead of "Chemical formula". It would be easy to implement a switch field that controls that output and also inhibits things that don't apply. Careful talking about drugbox, it includes essentially everything chembox does, and more. DMacks (talk) 23:51, 11 May 2022 (UTC)
Interesting, but I don't have the expertise nor the motivation to implement such a switch, perhaps once I publish the template you could do a bit of fiddling in the sandbox of the respective template? As for drugbox, I just personally have more experience with it, as I've used it often to write articles about, well, drugs & antibiotics.X-750 Rust In Peace... Polaris 23:58, 11 May 2022 (UTC)
Allow me to join in. I've worked on developing {{Chembox}} and {{Drugbox}} templates, but I am no chemist.
Having read this, I suggest to expand {{Infobox material}} with a extra section (subheader) "Alloy", to appear in top ;-). It can contain alloy-specifics, such as composition. If I understand correctly, some parameters (properties) from eg {{Chembox}} could be added (please start hinting). As said, for the chemical details (parameter subtleties) I'll have to be educated. -DePiep (talk) 02:20, 12 May 2022 (UTC)
Started sandboxing {{Infobox material}} (/testcases). @DMacks: I saw ferrotungsten. I think a dedicated parameter(s) for alloys is preferable. Do you think we should pursue alloys-in-{{Chembox}}? Or IB materials? -DePiep (talk) 04:43, 12 May 2022 (UTC)
Oh dear I should've read this sooner, DePiep check out User:X750/Infobox alloy for what I have so far.
If you have the time, a double-pronged approach can be done (i.e. you do you, me do me), and we can decide via consensus/vote of some sort which one we can roll with. Cheers X-750 Rust In Peace... Polaris 04:52, 12 May 2022 (UTC)
Things happen. Preferably I don't work parallell=double. Apart from parameters you added to the IB-material (which?), what is the alloy feature you aimed at? (IMO, a dedicated section, in top, could handle the alloy specs nicely). -DePiep (talk) 04:58, 12 May 2022 (UTC)
I am still working on it! I'll ping you when I think it's almost ready for publishing. Understood point on working in parallel. X-750 Rust In Peace... Polaris 05:00, 12 May 2022 (UTC)
Hey DePiep, I've drafted up a testcase at User:X750/Infobox alloy/testcases, see what you think. I was also wondering, is there something we can change in the documentation so that units are automatically added? Although that would pose problems if people have a specific unit and need to convert them... can we put the convert template in there somehow too? Thanks X-750 Rust In Peace... Polaris 01:27, 13 May 2022 (UTC)
OK, good to see. Question on content: what does the chem formula mean, for alloys? AFAIK, an alloy is not a compound, but more like a mixture. Does the formula need a clarification then?
About the presentation: I still think the alloy properties should be grouped under one subheader. For me, a layman reader, it makes things much more clear right away (for example, that UNS and SAE are alloy codes). The existing parameter |type= can stay (and get label "Material type"). Be as specific as possible, especially if its free!
Also, I think it can easily be an extension of current {{Infobox material}} (as I did in the sandbox). Makes maintenance of those parameters easier, and no conflicts foreseen. I'll add the parameters you added to that sandbox. See /testcases. -DePiep (talk) 06:37, 14 May 2022 (UTC)
Yes, I'm leaning more and more towards simply expanding {{Infobox material}}. Also, as to your question as to chem formula, it's description in the doc simply says Chemical formula of the alloy (if listed), please hard-code with subscripts. Which means if the formula is listed, it can be added as it's a suggested parameter. And yes, I shall amend that label you have mentioned. I just have a singular question, at the {{Infobox material/testcases}}, you have put "T2 tool steel" under type, I presume that is a filler as is SAE999. I think we should also rename the subheader to "Alloy properties". Looks like it's coming together. I'll sort the navbox out, I've got experience with music group navboxes, and I'll simply follow the layout of something like {{Hydrides by group}}, with the groups probably shaping to be "non-ferrous", "ferrous", and under non-ferrous, probably division into nickel-based, aluminium-based, etc, and others. I'll be using Category:Alloys for the navbox too, so if you know any pages that might be missing just mosey on over & add it to the page. Sound good? X-750 Rust In Peace... Polaris 10:01, 14 May 2022 (UTC)
Afterthought: We have footnotes for a reason, we could simply explain it in the footnotes, or add something like chemical_formula_note. Quite obvious innit? X-750 Rust In Peace... Polaris 10:03, 14 May 2022 (UTC)
If you think the chem formula is a correct presentation, it's fine with me. (but, if it is a ratio like the percentages — not a compound, it is wrong). Anyway, we can proceed and improve later.
Yes I took some random data, eg 'T2 tool steel'. Just testing the parameters.
I've adjusted the /sandbox, see testcases.
The navbox is a different topic. I ignore that one for now here.
I strongly propose to make {{Infobox material/sandbox}} the proposed version, not your subpage (I've made some other needed changes in there already). I understand current version reflects all your proposals. So, publish? -DePiep (talk) 09:23, 15 May 2022 (UTC)
Ah that chemical formula thing, it's optional, we'll let the other editors include if they want to. I'll leave it blank when editing articles for the sake of not confusing readers. Yes, I will handle the navbox. You can brush that away.
Yes, to your proposal too, very pleased with how the testcases has turned out. Full steam ahead. X-750 Rust In Peace... Polaris 10:41, 15 May 2022 (UTC)
  Done. -DePiep (talk) 11:06, 15 May 2022 (UTC)

Infobox material: changesEdit

  • Boldly added {{para|synonym, synonyms]]; changed label for |type= (live now)
  • Alloy (in sandbox):
    |alloy type=
    |alloy composition=
See testcases. -DePiep (talk) 04:39, 12 May 2022 (UTC)
from OP. -DePiep (talk) 08:00, 12 May 2022 (UTC)
also applying comments by X750, above. -DePiep (talk) 09:23, 15 May 2022 (UTC)

  Done Updated {{Infobox material}} as discussed. Created {{Infobox alloy}} synonym. -DePiep (talk) 11:06, 15 May 2022 (UTC)

JSmol model for zwitterionic lysine is wrongEdit

A comment on Talk:Lysine#Wrong_3D_model just noted that he JSmol model for zwitterionic lysine is wrong! The molecule should be protonated on the epsilon amino group!. Could I get this double-checked by a chemist? T.Shafee(Evo&Evo)talk 00:24, 18 May 2022 (UTC)

Evolution and evolvability I think this is debatable and I'm not sure how the issue should be resolved. The change needed to show the epsilon-protonated version instead of the alpha-protonated version is to alter the relevant Smiles to [NH3+]CCCCC(N)C(=O)[O-] instead of its current NCCCCC([NH3+])C(=O)[O-] in the Chembox. However, in most other amino acids the relevant Zwitterion is the alpha one (i.e. they don't have a second protonatable centre) and even in lysine the balance of protonation between the alpha and epsilon nitrogens will depend on factors such as their respective pKa, the solvent and the temperature. On balance, I think my preference would be to remove the Zwitterion and the protonated Zwitterion from the Chembox altogether and add some comment about pKa etc. (with reliable sources) to the body of the article or on Lysine (data page), if it is important to readers that this be discussed. Mike Turnbull (talk) 11:20, 18 May 2022 (UTC)
Hi. If we consider Lys only as a molecule isolated from biological systems (as the model does), then we can fairly reliably assume which amino group will be protonaned most of the time. The main factor that will change pKas under this condition is the proximity of -COO- group on the alpha carbon atom. This group has a -M effect. This means that electron density of alpha -NH2 group will be slightly pulled towards it compared to epsilon -NH2 group. As such, the lone pair on the epsilon -NH2 group will be more able to bind to a proton. Epsilon group pKa will be considerably higher than alpha group pKa. And naturally, empiric evidence supports this claim -- please see a table of amino acid pKa values, such as this. (talk) 12:10, 18 May 2022 (UTC)
OK, that's a convincing argument even though the precise values in the linked URL don't quite match what our data page says. More significantly, all the interactive images in the article gave the wrong absolute stereochemistry for (S)-lysine, so I've changed them all. Please check and make sure everyone can be happy with the outcome. Mike Turnbull (talk) 15:15, 18 May 2022 (UTC)
Good catch about the stereochemistry! It would be great if we could somehow document when SMILES is omitting that info (or better, as you did, actually include it). But your two "zwitterionic" forms have the carboxyl still protonoated. DMacks (talk) 15:27, 18 May 2022 (UTC)
Oops! Now corrected. That's why we need the wisdom of crowds. Thanks DMacks. Mike Turnbull (talk) 15:57, 18 May 2022 (UTC)
I wonder what the shortest wikilink-following path is between swiss cheese model and mean free path :) DMacks (talk) 16:15, 18 May 2022 (UTC)
Worth noting that in the crystal structure of pure lysine, it's primarily the alpha amino group that's protonated, although there is a bit of H-atom disorder near one of the two epsilon amino groups: Angew. Chem. Int. Ed. (2015), 54, 3973-3977, CSD entry CUFFUG. The Chembox PNG images (File:Lysine-from-xtal-3D-bs-17.png and File:Lysine-from-xtal-3D-sf.png) reflect this. --Ben (talk) 19:05, 18 May 2022 (UTC)

Thanks, Ben, I'll let you fight this out with the IP editor. This is well beyond my pay grade. At least you both now know how to alter the SMILES in the article to reflect whatever you decide is "the truth" (or "the most useful")! Mike Turnbull (talk) 19:16, 18 May 2022 (UTC)

So glad that I referred this over to this group. Very interesting discussion! T.Shafee(Evo&Evo)talk 22:52, 18 May 2022 (UTC)
I've also updated the zwitterionic model for Arg, even though it took me three tries now it should be (more) correct. The main driving force here is of course the delocalization of the positive charge (even shown in a picture in the article); the discussed pKa difference is even greater. Hopefuly I didn't mess it up instead. (talk) 05:51, 19 May 2022 (UTC)
The catch with many articles on amino acids is that the free amino acids are rare (I think, I have been looking for a source of occurrence of free amino acids). Some Wiki articles on amino acids actually discuss amino acid residues, but dont make that distinction clear. --Smokefoot (talk) 13:42, 22 May 2022 (UTC)
Agreed that samples of the free amino acids may be rare but here we are discussing the substances/IDs and representations in the Chemboxes. I've now checked these for all proteinogenic amino acids to ensure, inter alia, that the Jmol depictions are accurate/useful and that we have more comprehensive IDs: L, D/L and D (in that order) in many cases. Arginine and aspartic acid) needed overhaul and careful updating — which I now believe to be correct. Mike Turnbull (talk) 15:39, 22 May 2022 (UTC)

JSmol in infobox ChemboxEdit

Here the template background for {{Chembox}} having Jmol (or JSmol). In short: Jmol uses |SMILES=, but can be overwritten.

Jmol demos
3D model (JSmol)
  • A: O=P(O)(O)OP(=O)(O)OP(=O)(O)OC[C@H]3O[C@@H](n2cnc1c(ncnc12)N)[C@H](O)[C@@H]3O
  • F: [CH-]1C=CC=C1.[CH-]1C=CC=C1.[Fe+2]
  • L, zwi.: [NH3+]CCCCC([NH3+])C(=O)[O-]
  • L(none): [NH3+]CCCCC([NH3+])C(=O)[O-]
  • FYI: This is what {{Chembox}} can do with SMILES and Jmol. (The demo uses indexes 1-4, see code).
A Regular, default: Jmol reads SMILES and creates the interactive image at the external link  Y
F Ferrocene: its SMILES is incorrect for 3D, |Jmol=(another SMILES) is fed an adjusted SMILES string → shows OK in 3D  Y
L Lysine (Zwitterion): SMILES read by Jmol (default route), 3D image under discussion  ?
L(none) Lysine Zwitterion: same SMILES but |Jmol=none → Jmol does not show for this one  Y (no error)

Not done: possibly an adjusted SMILES string would show 3D correct in Jmol.

-DePiep (talk) 13:06, 18 May 2022 (UTC)

Merger discussion for Chemical oceanographyEdit

  An article that you have been involved in editing—Chemical oceanography—has been proposed for merging with another article. If you are interested, please participate in the merger discussion. Thank you. Chidgk1 (talk) 06:52, 18 May 2022 (UTC)

Tammann and Hüttig TemperatureEdit

Hi. I've created a Tammann and Hüttig Temperature article recently. Would love to see some feedback on it. It's pretty short and mostly serves purpose of a data page. Please checkout. Thanks. --AXONOV (talk) 23:46, 28 May 2022 (UTC)

I have renamed it (and reviewed for copyright infringement). Graeme Bartlett (talk) 12:04, 30 May 2022 (UTC)
It's very specialised stuff. It presumable needs links to and from premelting? Who was Hüttig? --Project Osprey (talk) 12:14, 30 May 2022 (UTC)

Borax as a mineral speciesEdit

Discussion at Talk:Borax#Borax as mineral species --Kent G. Budge (talk) 16:05, 3 June 2022 (UTC)

Graphite as a mineral speciesEdit

I will set up a discussion akin the borax one above at Talk:Graphite#Graphite as mineral species. Quick reading of Greenwood and Earnshaw indicates that both mineral and synthetic graphite are widely used commercially. --Smokefoot (talk) 02:02, 10 June 2022 (UTC)

Discussion at WP:Fringe over some COI edits.Edit

Editors with good working chemistry knowledge might be useful in this discussion at WP:Fringe. It's a question of surprising chemistry claims being sourced to the editor's own papers.

ApLundell (talk) 04:40, 10 June 2022 (UTC)

Thank you for posting that here. I am the editor who started that discussion, and I don't know how to proceed at this point.
About 80 science/chemistry articles on Wikipedia currently include claims about the chemistry of oxygen that are nonsensical in the standard framework of chemistry, confusing, and potentially harmful.
These have been added by a single editor, backed up with references to a few papers by that same editor.
I've made a list of the problematic articles and edited a few; the editor who added the claims restored them.
The statements in question are, frankly, embarrassing to have on Wikipedia. I'd appreciate any advice on how we can go about removing them. (If you think I'm the one who has a problem with perfectly good science here, I'd also appreciate a short note telling me that!)
IpseCustos (talk) 14:58, 11 June 2022 (UTC)

Request for advice from new page patrollerEdit

The new article Xerosydryle has a sundry of scientific material in it but from what I see only one source even mentions the term and a quick google search came up with nothing on the term. Am I right in deducing that the article represents trying to establish a new term? If so, Wikipedia would not be the place for such an effort. So if an article by that name were not to survive, is there a recognized topic for the material in the article? Thanks. North8000 (talk) 20:17, 10 June 2022 (UTC)

I labelled this as a hoax earlier, but that was contested by @Cranloa12n:. I think Wikipedia would be better off without this page. The topic is an invention by one person. Perhaps AFD is the way to go as there s some controversy. Graeme Bartlett (talk) 02:25, 11 June 2022 (UTC)
It is a hoax, as the lead text accumulated clumps of xerosydryle appear as a white-ish fluffy, dry substance, alone makes clear. Water is probably the most studied substance of all and "dry" water is a contradiction in terms. Let's not waste time on WP:AFD. Mike Turnbull (talk) 11:30, 11 June 2022 (UTC)
On reflection, I think it is a bit unfair to call the Wikipedia article a hoax. Oakwood actually did a pretty good job of summarising a load of WP:FRINGE publications, of which DOI:10.14294/WATER.2021.2 is the latest and most egregious (and introduces the neologism xerosydryle). That journal article is so way-out that it actually makes an interesting read as an object-lesson in bad chemistry! PROD is still the way to go for the moment, I think. Mike Turnbull (talk) 12:55, 12 June 2022 (UTC)
Then should I use PROD or {{db-hoax}}? –LaundryPizza03 (d) 13:48, 11 June 2022 (UTC)
I'll leave my "in progress" tag just to make sure that somebody doesn't accidentally pass it if the prod disappears. North8000 (talk) 14:22, 11 June 2022 (UTC)
I don't know about Xerosydryle but I'm pretty sure that 'dry water' is a real thing. It's essentially large vesicles of water wrapped in a shell of hydrophobic fumed silica. The end result is a fine powder, dry to the naked eye but which is >95% water. Cohesion between the silica particles is strong enough to avoid coalescence of the water. It gets fancy names, as you would expect: liquid marbles, dry water etc. --Project Osprey (talk) 20:41, 12 June 2022 (UTC)
If it is a WP:HOAX we don't want to PROD it because we don't want there to be a WP:REFUND option for the perpetrator. WP:PROD is for uncontroversial deletions. Based on the discussion I see here, it does not appear there is consensus on why this should be deleted. It is not clear Project Osprey is onboard with deletion. The right thing to do I think would have been to send this immediately to WP:AFD and have this discussion there. That didn't happen and I'm reluctant to WP:DEPROD because WP:POINTY. ~Kvng (talk) 14:09, 16 June 2022 (UTC)
I would support deletion, the article is little more than technobabble.--Project Osprey (talk) 14:19, 16 June 2022 (UTC)

The creator posted the following at the talk page, but did not remove the PROD tag:

Let me address [ North8000's ] concerns. The name has been already used by other authors, apart from the first proponent, I have added references in the article.

About the recognized topic for the material in the article, it can be "Supramulecular Chemistry", or "Scence of Nanomaterials".
Moreover, about the article being "based on mirrors of a single source by Roberto Geremano et al. (2013)". The origin of the research on this new material can be dated at least back to the article by Pollak's group, published in 2006 on "Advances in Colloid and Interface Science", because the Exclusion Zone mentioned by Pollak is the same material (supramulecular structure) as the Xerosydryle mentioned by Germano. Even earlier research dates back to 1960, although less explicitly linked to the material.
Finally, the scientific papers referenced in the article are published not only on (bogus?) Water journal, but also on "Advances in Colloid and Interface Science", which has h-index 194 and is solidly in the first quartile for its field (, "Journal of Molecular Liquids", which has h-index 132 and is also in the first quartile, "Journal of Thermal Analysis and Calorimetry", h-index 101, second quartile, "Journal of Porous Media" (h-39, Q3).
So, I believe that it is really inappropriate to describe the content of the article as highly dubious, as said by @LaundryPizza03, the proponent of the deletion.
— User:Oakwood 19:07, 16 June 2022

LaundryPizza03 (d) 19:17, 16 June 2022 (UTC)

The research by Germano and colleagues is in continuity with the research by Pollak, which has been published on a Q1 journal. The statement that the material in the article (e.g. the Exclusion Zone reported by Pollak) is an hoax, is in disagreements with the reviewers and the editors of several prestigious journals. I have removed the PROD tag, based on the arguments written here and in the Talk page of the article, and on the extra references added. Oakwood (talk) 19:42, 16 June 2022 (UTC)

Regardless, I think that right here is the best place to pick a general direction on this. Flow wise, here are possibilities:

  1. Send to AFD. Some of you experts would need to weigh in there.
  2. Me mark it as reviewed.

Sincerely,North8000 (talk) 19:48, 16 June 2022 (UTC)

I am a bit confused about the right place where to discuss the deletion: here? in the page 'talk' section? in the deletion talk page? could you please clarify? thanks! Oakwood (talk) 05:52, 18 June 2022 (UTC)

@Oakwood: Graeme has made the deletion discussion a formal process per WP:AFD. The correct place for further discussion is now at the link in his latest message above (also notified on your Talk Page). As part of any comment you add, it would be interesting to say how you know articles are in the review process, and should be published in the near future from your earlier comment. Mike Turnbull (talk) 10:05, 18 June 2022 (UTC)
This is probably not so much a hoax in the sense of a deliberate fraud by the investigator, but anomalous science in which the investigator has deluded or deceived himself. This is claimed to be water behaving in a very non-standard way under ordinary conditions due to supposed unusual supramolecular structure, that is, hydrogen bonding behaving in an unknown fashion. This seems to be just a different form of polywater. Robert McClenon (talk) 23:38, 22 June 2022 (UTC)
You mean pathological science? –LaundryPizza03 (d) 00:54, 23 June 2022 (UTC)
User:LaundryPizza03 - Yes. My error. This is pathological science rather than a hoax. Although the reported physical properties are different than those reported for polywater, it is still polywater. The differences in reported properties don't matter, because it isn't a real material and so doesn't have physical properties. It is polywater and so is pathological science, again. Robert McClenon (talk) 14:55, 23 June 2022 (UTC)

Feedback on Draft:Energy-rich species: keep or delete?Edit

In relation to the ongoing discussion about whether oxygen is a "high-energy molecule", I've started drafting an article on "energy-rich species" or "high-energy species". The term appears to be in fairly wide use in introductory material, but I haven't been able to find a decent well-sourced definition of it. It's not quite a dicdef as usage varies and there are several similar terms; it's not quite equivalent to "unstable"; it doesn't really fit into "chemical energy".

I'm honestly undecided whether this article is a good idea. I thought the definition so obvious that spelling it out would be dictionary work, but of course the whole "high-energy oxygen" idea kind of demonstrates that it isn't.

Anyway, in order of preference, I'm asking for offers to take over the draft (yeah, right); opinions that the draft should be deleted (with or without reasons); or opinions that it should be kept and how to improve it. In particular, if anyone can remember a textbook or article that defines the term rigorously, I'd know where to continue looking.

IpseCustos (talk) 18:09, 12 June 2022 (UTC)

Feels like WP:NOR. Terms like 'high energy' or 'energy rich' are often used to describe materials, but there is no formal definition, which makes trying to write an encyclopaedia article on those terms fairly pointless. --Project Osprey (talk) 14:41, 16 June 2022 (UTC)
Agree with Project Osprey. On the other hand, we (Wiki-chem project) aim to have articles or redirects on commonly used terms. One possibility is to redirect "Energy-rich species" to Energetic materials, things like ammonium nitrate that blow up spontaneously. We could expand the article to include exergonic hydrolysis reactions. One problem with many energy-rich species is that their tendency to release energy depends on another reactant. Folks call ATP energy-rich, but only if it is contacted with water (or O2 and a spark).
BTW, an even more common chem-slang is electron-rich, which redirects to polar effect, I have no idea what polar effect means, so I am considering redirecting to redox potential.--Smokefoot (talk) 15:29, 16 June 2022 (UTC)
I think that although there is no formal IUPAC definition for any of these terms, they are sufficiently often used that they form part of the jargon of (bio)chemistry. Thus Wikipedia would be improved by having an article along the lines that IpseCustos proposes and the current draft should be moved into Mainspace. I would be happy to add to it. It needs to have an explanation along the lines of the lead at thermodynamic free energy that in practice only changes in free energy are physically meaningful, so all reactants and products are relevant, with no single one really being the "energy rich" species. Those of us who have made nitrogen triiodide would nevertheless happily call it that! Mike Turnbull (talk) 14:18, 21 June 2022 (UTC)
By all means, feel free to edit mercilessly. I disagree that all reactants are relevant, but in the case of nitrogen triiodide it makes no difference as there is only one of them. IpseCustos (talk) 19:53, 22 June 2022 (UTC)

User:Ll0103, ref spammer, admin help neededEdit

User:Ll0103 has made several edits over the recent past, always and only citing his primary journal articles. I tried to revert these things, but it would be helpful if some administrator would intercede. I am sure that this person is convinced of the brilliance and notability of their publications, but he's abusing our system. --Smokefoot (talk) 13:08, 21 June 2022 (UTC)

Good Article assessment: Bisphenol AEdit

Bisphenol A is currently being assessed for Good Article status. I'm aware that we don't usually go in for such baubles, but it seemed a fairly rare example of a non-drug small-molecule which is of public interest. I would welcome input at Talk:Bisphenol A/GA1. --Project Osprey (talk) 12:04, 28 June 2022 (UTC)

Well there's baubles, and there is service to society, and this article falls into the latter category. For baubles, you might consider shifting your editing toward Elvis or such. More seriously, BPA is highly topical for many reasons and I worry that some views on the topic are uninformed, so its important that the world see a balanced technical summary. --Smokefoot (talk) 13:23, 28 June 2022 (UTC)