Wikipedia talk:WikiProject Chemicals: Difference between revisions
→Chemical stub generator from e.g. PubChem?: chemboxformat |
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I wonder if there's a similar generator for chemicals, to fill out the chembox for me automatically? So I would just point it at https://pubchem.ncbi.nlm.nih.gov/compound/Allyl-phenylacetate for example, and it would generate wikicode containing the formula, synonyms, molecular weight, SMILES, and all that fun stuff. Does such a tool exist? (If not... would it make sense for me to create one??) —[[User:Keenan Pepper|Keenan Pepper]] 20:28, 19 April 2020 (UTC) |
I wonder if there's a similar generator for chemicals, to fill out the chembox for me automatically? So I would just point it at https://pubchem.ncbi.nlm.nih.gov/compound/Allyl-phenylacetate for example, and it would generate wikicode containing the formula, synonyms, molecular weight, SMILES, and all that fun stuff. Does such a tool exist? (If not... would it make sense for me to create one??) —[[User:Keenan Pepper|Keenan Pepper]] 20:28, 19 April 2020 (UTC) |
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:I have this partially on [[User:Graeme Bartlett/monobook.js]] in the part near the bottom labelled "chemboxformat". To use it I copy a selection of the identifiers to the edit box, highlight it and click the link that appears on my screen labelled chemboxformat, and it converts to wikitext. Only in alpha, it is not ready to be released as a tool for general use, but you are welcome to use it. I find that synonyms need a lot of manual curation and are not worth copying from PubChem as a whole. [[User:Graeme Bartlett|Graeme Bartlett]] ([[User talk:Graeme Bartlett|talk]]) 22:16, 19 April 2020 (UTC) |
:I have this partially on [[User:Graeme Bartlett/monobook.js]] in the part near the bottom labelled "chemboxformat". To use it I copy a selection of the identifiers to the edit box, highlight it and click the link that appears on my screen labelled chemboxformat, and it converts to wikitext. Only in alpha, it is not ready to be released as a tool for general use, but you are welcome to use it. I find that synonyms need a lot of manual curation and are not worth copying from PubChem as a whole. [[User:Graeme Bartlett|Graeme Bartlett]] ([[User talk:Graeme Bartlett|talk]]) 22:16, 19 April 2020 (UTC) |
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:: {{ping|Keenan Pepper}} Hi, can you provide a link towards the tool or the code of the tool ? Thanks. [[User:Snipre|Snipre]] ([[User talk:Snipre|talk]]) 08:20, 20 April 2020 (UTC) |
Revision as of 08:20, 20 April 2020
This is the talk page for discussing WikiProject Chemicals and anything related to its purposes and tasks. |
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This is the talk page for discussing WikiProject Chemicals and anything related to its purposes and tasks. |
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The worklist shows the actual work to be done to achieve the goals of the Chemicals wikiproject. The choice of important compounds articles to work on has been finalized in an earlier stage of the wikiproject (around mid 2005), and no further articles are added, although we remain open for strong suggestions on this talkpage. The work these days focuses on improving the articles, from Chem Stub all the way to Chem A-Class articles. The table below shows that progress.
Worklist historical status | ||||||||||
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2005 | 2006 | 2007 | 2008 | 2009 | ||||||
Grade |
Jun | Oct | May | Oct | Mar | Oct | Feb | Aug | Apr | Dec |
A-Class | 29 | 26 | 32 | 32 | 33 | 25 | 25 | 23 | 18 | 18 |
B-Class | 71 | 84 | 101 | 130 | 148 | 156 | 158 | 180 | 185 | 188 |
Start | 112 | 131 | 199 | 190 | 174 | 174 | 180 | 153 | 160 | 161 |
Stub | 97 | 130 | 46 | 29 | 27 | 27 | 19 | 26 | 19 | 18 |
unclassified | 76 | - | - | - | - | - | - | - | - | - |
Total | 385 | 371 | 378 | 381 | 382 | 382 | 382 | 382 | 382 | 382 |
percentage ≥Chem Start |
55.1 | 65.0 | 87.8 | 92.3 | 92.9 | 92.9 | 95.0 | 94.0 | 95.0 | 95.3 |
weighted progress, % |
42.2 | 50.4 | 57.8 | 60.8 | 62.2 | 61.7 | 62.4 | 63.1 | 63.2 | 63.9 |
The percentage ≥ Chem Start was indicative of the initial effort. Now that we are progressing to more advanced progress, the weighted progress indicator is used, calculated as (Unclass*0 + Stub*1 + Start*2 + B-Class*3 + A-Class*4) / (Articles*4).
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For the statistics for all chemicals, as registered by the bot, also see complete list
Sodium bisulfite is a nonexistent compound
News to me that sodium bisulfite is nonexistent. Several sources (J Chem Ed, Greenwood and Earnshaw, and Ullmann's) confirm this fact. Apparently, attempts to crystallize this salt yields sodium disulfite (Na2S2O5) , aka sodium metabisulfite. But the inconvenient fact is that something called sodium bisulfite is used extensively, and it is non-identical to sodium metabisulfite. So I am trying to figure out what to say it is. Organic Synthesis is usually careful about the provenance of their reagents but they dont help in this case. Aldrich gives a hint by indicating the %SO2 in their sodium bisulfite. I guess that sodium bisulfite is some ill-defined material that dissolves to give bisulfite, for use in wine-preservation, organic synthesis, and etc.--Smokefoot (talk) 01:17, 13 March 2020 (UTC)
- Well, that is a very unexpected development. Using Greenwood and Earnshaw (2nd ed., pg 717-720) as a ref: Sodium sulfite is real both in solution and solid state but sodium bisulfite is known only in solution, concentrating said solutions results in the following equilibria:
- 2 HSO3− ⇌ H2O + S2O52−
- Hence the aqeous chemistry of sodium metabisulfite and sodium bisulfite should be identical (if prepared from the normal lab chemicals). I note that we report very different solubilities for those 2 compounds. Some bisulfites with large counter ions are known in the solid state doi:10.1016/0022-1902(71)80558-4, I'm not sure how that applies to the K+ and Ca+ salts. --Project Osprey (talk) 10:20, 13 March 2020 (UTC)
- Interestingly, if you go the other way, the lithium salts are essentially unreported - even in solution. Lithium bisulfite only appears as a Marklush description in patents, lithium sulfite is mentioned as a boundary compound in lithium/sulfur dioxide batteries but dismissively and without real study. You should make some and call it Smokefoot's salt. --Project Osprey (talk) 13:14, 13 March 2020 (UTC)
Images of samples: remove them all vs Assume good faith
Since many of us have lots of time at home, here is an interesting policy issue: Check out [edit] with this edit summary "picture of white crystals cannot be verified a being of a particular chemical compound". Well, pehaps all images of samples should be blanked out since it is difficult or impossible to establish the identity of the sample shown. At the other extreme, we have AGF, i.e. we trust images. Somewhere between these extremes, some samples have distinctive morphologies, refractive indices, or colors that would give some clues. My vote is AGF and assume that readers dont trust Wikipedia too much? (confession: I have uploaded a lot of sample images). --Smokefoot (talk) 01:44, 2 April 2020 (UTC)
- I agree that the image (added here so readers don't need to check the EDTA page, where it has now been removed) can't be verified as any particular white solid, especially as in this case the vial isn't even labelled, which is terrible practice for a chemical! However, I don't think the issue is one of AGF, rather of "why does this article need any picture of the chemical?" The chembox for EDTA doesn't have a citation reference for any of the properties listed, including the "colourless crystals" property. I think I would prefer editors to focus on adding such references, rather than uploading unhelpful pictures. I think that most people know what "colourless crystals" mean without needing a picture. Michael D. Turnbull (talk) 13:35, 2 April 2020 (UTC)
- Excellent question and one to which most experimental chemists can rapidly respond! White solids often look distinctive to us: some are milky white (sodium thiosulfate), some are glistening plates (anthracene), some are chunky (NaCl), etc. Of course all or most can be pulverized to appear similar. Beyond white/colorless solids/liquids, we are also discussing colored materials. Who is to say that our image of sodium dichromate is legit?--Smokefoot (talk) 13:50, 2 April 2020 (UTC)
- I don't think that experimental chemists are our target audience for most articles. One file for NaCl as I've just added here from Commons would be very appropriate in an article commenting on mineral forms of rock salt but hopeless if discussing table salt. Sample images are too diverse in general to be useful without comment, and preferably verifiability. Thus I would deprecate the image of sodium dichromate not because it is incorrect (I recognise it as being close to what I have used in the past in the lab) but because it isn't properly referenced, has no label in the image and is "own work". In fact, none of the images of sodium dichromate on Commons meet my idea of ideal for an encyclopedia. Better perhaps to use pictures of compounds photographed alongside bottles and MSDS from legitimate lab suppliers, for example. Michael D. Turnbull (talk) 15:37, 2 April 2020 (UTC)
- Incidentally, your image of anthracene is better because the bottle is at least labelled but it's hard to find by search in Commons because you didn't put a space between "anthracene" and "in bottle", so typing the word "anthracene" into the search box there doesn't give it as a hit. Michael D. Turnbull (talk) 15:59, 2 April 2020 (UTC)
- Commons is often best-searched using categories (commons:Category:Anthracene has it), which avoids spelling (typos and different languages), spacing, punctuation, and shorthand variations. Links to them are often in the sidebar and/or in boxes towards the end of WP articles as well. We (speaking as a commons editor) would love help improving the specificity of some large-and-generic cats or adding cats to images that are not well-tagged at all...feel free to ask me for assistance. DMacks (talk) 02:38, 3 April 2020 (UTC)
- Pictures certainly have use in certain cases. Colour changing hydrates like copper(II) chloride for instance. --Project Osprey (talk) 17:21, 2 April 2020 (UTC)
- Yes, certainly, and the article on copper(II) chloride is a good use of images to clarify the text. Going back to the case of EDTA, which was the original example, another reason to dislike the suggested (now deleted) image is that it was of the sodium salt, which is not the topic of the article. If I were reading an article on acetic acid, I don't think I'd expect a picture of a sodium acetate sample in the Chembox. In fact, acetic acid uses a picture I approve of, with a clear label of "glacial acetic acid" and looking like an unopened bottle from a reputable supplier. Michael D. Turnbull (talk) 13:11, 3 April 2020 (UTC)
Let's not stray from the intended topic: are pictures of compounds useful even if their provenance cannot be established?
- I say that the images of white and colorless compounds should be retained ordinarily, because such images can be informative because they often reveal distinctive features (example of anthracene). On the flip-side, these images do no harm.
- I vote strongly for regaining images of colored species since the eye is so good at discerning colors.
--Smokefoot (talk) 15:55, 3 April 2020 (UTC)
- I agree with Smokefoot on this. That we should retain the images. They do indicate other information too, such as a likely size of a container for the substance. And it is better to have a picture than none at all. But we should use the best images, so certainly the ones that are of the substance in the article, and even better if we can be sure it really is the substance. I am also thinking that a much more magnified view of a few crystals will be useful as well. For a featured article we would want to be sure that the image was genuine and accurate. Own work does not prevent that. But photographing commercial pagages of the product amy be a copyright infringement of the label. Graeme Bartlett (talk) 04:13, 7 April 2020 (UTC)
Palladium on carbon vs Palladium black
Palladium on carbon and Palladium black have the same chembox (including CAS). Should they be merged? Or are they genuinely different things? --Project Osprey (talk) 09:04, 3 April 2020 (UTC)
- My strong impression is that they are quite distinct materials: Pd/C is a popular supported catalyst, Pd black, like Pt black is a material with the composition PdOx. --Smokefoot (talk) 12:45, 3 April 2020 (UTC)
- They bear the same relationship as Platinum on carbon and Platinum black (see DOI:10.1595/147106707X176210). That is, they are different samples forms of metallic palladium used in different ways in catalysis. I think they have all been given the same CAS (and e.g. Inchi / Smiles) as these are just the one for elemental Palladium. The synthesis of the Pd or Pt black is from the oxides, typically, but the substances themselves are the metal after reduction. Whether they get merged (possibly even with the article on Palladium) is a matter of debate: personally I'd leave them separate, with "see also" references. That's what the articles currently have. Michael D. Turnbull (talk) 17:28, 3 April 2020 (UTC)
- I guess they could be called different "sample forms" if "sample form" means one is 5% Pd by weight and the other is mainly Pd by weight. People use 5% Pd/C routinely for hydrogenations and hydrogenolysis. The prep in OS uses 95% by weight Norite, The diff is alluded to here: DOI:10.15227/orgsyn.026.0077. Pt black is ill-defined material popularized by Roger Adams. Mainly Pt with OH in it. DOI:10.15227/orgsyn.008.0092. Sample forms? What is a sample form? --Smokefoot (talk) 19:39, 3 April 2020 (UTC)
- Sorry, I use "sample form" as an expression from my past employment when I spent many hours trying to educate colleagues on the difference between a chemical substance and a chemical sample. We made new active ingredients (substances) and tested them for properties of interest. The sample made would initially be, say, a crystalline solid but by the time it was tested it might have been stored as a solution in DMSO (one sample form) or formulated with surfactants then added to water (another sample form) or, perhaps just dissolved in water (yet another sample form). All these forms contain the same substance at various concentrations: whether the difference is important or not depends on the context. For metallic Pd, it certainly matters which form of a sample you take when you want to use it as a catalyst. A lump of the metal won't work. Hence you acquire 5% Pd/C for hydrogenation reactions and perhaps use palladium black for some other purpose. I believe that it's reasonable for Wikipedia to have separate articles for Pd, Pd on C and Pd black because their properties and hence uses are so different depending on the form used, even though the "active ingredient" is just Pd. Michael D. Turnbull (talk) 15:05, 4 April 2020 (UTC)
Why are beta hydroxy acids a sub-category of aldols?
Aldols and the Category:Aldols are defined as "compounds with a hydroxyl group and a ketone (or aldehyde) oxygen separated by three carbon atoms that are single-bonded to each other". My question is why Beta hydroxy acids such as citric acid and mevalonic acid have been placed as a sub-category of Category:Aldols. None of the 29 compounds listed as being Category:Beta hydroxy acids have an aldehyde or ketone oxygen atom, only an acid carbonyl group. I don't know the correct way to fix this. Michael D. Turnbull (talk) 13:48, 9 April 2020 (UTC)
- Fixed. Activating HotCat (Preferences > Gadgets) might make it easier for you to make such edits yourself in future. Our Categories are quite hit and miss. Occasionally someone tires to sort them out but it's a massive job, I'm not even sure 1 person could do it all now. --Project Osprey (talk) 21:20, 9 April 2020 (UTC)
Chemical stub generator from e.g. PubChem?
I recently had occasion to create an article on a gene, and I found this nice tool where you just put in the Gene ID from NCBI and it automatically fills in this nice stub wikicode for you, which you can copy and paste into the new article.
I wonder if there's a similar generator for chemicals, to fill out the chembox for me automatically? So I would just point it at https://pubchem.ncbi.nlm.nih.gov/compound/Allyl-phenylacetate for example, and it would generate wikicode containing the formula, synonyms, molecular weight, SMILES, and all that fun stuff. Does such a tool exist? (If not... would it make sense for me to create one??) —Keenan Pepper 20:28, 19 April 2020 (UTC)
- I have this partially on User:Graeme Bartlett/monobook.js in the part near the bottom labelled "chemboxformat". To use it I copy a selection of the identifiers to the edit box, highlight it and click the link that appears on my screen labelled chemboxformat, and it converts to wikitext. Only in alpha, it is not ready to be released as a tool for general use, but you are welcome to use it. I find that synonyms need a lot of manual curation and are not worth copying from PubChem as a whole. Graeme Bartlett (talk) 22:16, 19 April 2020 (UTC)
- @Keenan Pepper: Hi, can you provide a link towards the tool or the code of the tool ? Thanks. Snipre (talk) 08:20, 20 April 2020 (UTC)