Wikipedia talk:WikiProject Chemistry/Archive 37

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Archive 35

Chemical element : french and english definition

Hi folks, an important question on the interwiki front : It seems that the french and english definitions for chemical elements are different:

type of atoms characterized by a constant atomic number in France
pure chemical substance with only atoms with the same atomic number in English

Anyone can confirm ?

It's a problem for the interwikis, in Wikidata such definitions needs two different item, and the french article will be linked to another items. This can be solved by adding some redirects though ... any comments ? (also @Emw:). sign: TomT0m 13:18, 7 June 2015 [1]

I think this quite simple to solve if we take the definition of chemical substance: "A chemical substance is a form of matter that has constant chemical composition and characteristic properties. It cannot be separated into components by physical separation methods, i.e., without breaking chemical bonds." How an element can have some chemical bonds ? An element article should focus on the atom structure of element and not on the chemcial subtances based on elements.

If we take the definition of IUPAC for chemical substance: "Matter of constant composition best characterized by the entities (molecules, formula units, atoms) it is composed of. Physical properties such as density, refractive index, electric conductivity, melting point etc. characterize the chemical substance.", we see that element is not included in the chemical substance.

We need better definitions for element, chemical substance and chemical compound because right now this is difficult to manage items in WD due to these different definition from WPs. I think we need to find one ontology or at least one chemical terms classification and based our articles or the WD items according to one unique definitions system. IUPAC seems a good start but IUPAC never provides a complete system. Snipre (talk) 15:04, 7 June 2015 (UTC)

What's about chemical ontology ? Snipre (talk) 15:06, 7 June 2015 (UTC)

@Snipre: ChEBI (online browsable) is also a candidate, but for the record, they don't use metaclasses, because I think they did their model with OWL 1 DL (in its DL version 1 flavor) in mind, which does not have it. With metaclasses, we can have Hydrogen (french) instance of chemical element (french) and the atom(s) in my glass of water instance(s) of Hydrogen. Without it it's impossible. ChEBI has a hydrogen atom class which could be the (english) equivalent of the hydrogen (french) concept ... then we could split the items properly, but this means we would have to split for all chemical elements ... This is doable though. TomT0m (talk) 15:12, 7 June 2015 (UTC)

Good luck to find the definition of chemical element in ChEBI. I am not a fan of ChEBI because they have not a common sense of classification. I totally agree with their system but I think this is something which don't integrate the usual concept of chemistry. Snipre (talk) 16:03, 7 June 2015 (UTC)

@Snipre: I looked at http://www.ontology4.us/Ontologies/Chemical%20Ontology/index.html and this does not work. Nuclide can't be a synonym of atom. And if a chemical element has atom as component, plus they have a warning at the beginning, the information is derived from Wikipedia articles ... which put us in a loop. I think it's inconsistent and sometimes an element is a type of atoms and some other an element is a chemical substance. And that this inconsistency come from the english Wikipedia ... TomT0m (talk) 16:06, 7 June 2015 (UTC)

@TomT0m: What is your definition of nucleide and of atom ? Instead of saying things like that start once by giving DEFINITION for each term you use. I can't discuss with you because I don't know which definition you use. So just once do a list of definitions for all main terms like chemical element, chemical substance, chemical compound, molecule, atom, ... and after we can can create the relation between the terms. Nucleide can be atom if we define the term to allow it. So definition first. Snipre (talk) 16:15, 7 June 2015 (UTC)

@Snipre: Looking at the periodic table by element: http://www.ebi.ac.uk/chebi/periodicTableElementsForward.do in Chebi, when you click on an element you get to the <element atom> entity. So overall it's quite in line with the french definition ... But overall, I think the scheme I proposed in Wikidata with chemical element as a class of class of atoms works pretty well and is exactly the definition given in french definition. TomT0m (talk) 16:30, 7 June 2015 (UTC)

My definitions : an atom is the fudamental structure in chemistry. My arm is made of a lot of atoms. Atoms are made of electrons, protons and neutrons. Hydrogen is a class of atom : the atoms in my glass of water who are not oxygen atoms or else are instances of hydrogen. The class of all classes of atoms, characterized by the same atomic number for all instances of atoms in each, is the element metaclass. There is other ways to class atoms than by element, by isotope for example. the nuclide definition is the one of Wikipedia, if I remmeber well, and provides yet another way to class atoms. Let's call nuclide the set of all classes given by the different ways to classify atoms. Then the set of all isotope classes is a subset of it. This establishes isotope subclass of nuclide. TomT0m (talk) 16:30, 7 June 2015 (UTC)

Sorry but this is not definition. A definition should give parameters or characterists which allows to include or exclude different entities. Typically an atom is a group of electron, proton and neutrons, element is the group of all atoms with the same number of protons, ... We don't need class or class of class for that. Snipre (talk) 16:42, 7 June 2015 (UTC)

@Snipre: I think we're on the same page, except what I call class you call group. Each class in math and in ontology as a definition, which is the definition you give : Let's say atom is a class defined, and say group of electron, proton and neutrons is it's characteristic property. Let's call instances of a class the set of all real world entities that satisfies the property. In Wikidata and in other ontologies, the fact than an object satistifies the characteristic property of a class is expressed by P31. To go a little further, the group in group of electron, proton and neutrons is given by the has part property, which is not instance of. Now we can also give classes of classes with metaclass (Semantic Web) Metaclasses also have characteristic properties, that refers to similarities of the characteristic properties. In the Hydrogen instance of Element and Oxygen instance of Element, for example, the characteristic property of Hydrogen would be "an atom with 1 as an atomic number" and for Oxygen "an atom with 8 as an atomic number". The similarities become obvious, element is "[the metaclass of all classes with a characteristic property an atom with X as an atomic number with X a number]". So your group word become two in my model :) TomT0m (talk) 17:15, 7 June 2015 (UTC)

(also started a thread in the french chemistry project) TomT0m (talk) Forgot to mention that I took on myself to create an element for the type of atoms with same atomic number concept. TomT0m (talk) 15:35, 7 June 2015 (UTC)

Stupid reaction: why do you create items by your own if you come here to ask how we should consider the topic ? You just add confusion by creating items without having a general overview of the classification. Snipre (talk) 16:09, 7 June 2015 (UTC)

Thank for the stupid :) I created the item before I started the discussion. Anyway, I knew the elementically pure substance still could have an item. If it turns out we'll have to swap the definitions, I just will merge it and create another one. No big deal. TomT0m (talk) 20:09, 7 June 2015 (UTC)

Just my perspective as an English person: the French definition makes more sense. We were always told, in school and in books, that an 'element' is a pure substance composed of only one type of atom. However the term, in its common usage, is almost synonymous with 'type of atom'. For example, when a new element is discovered, the discovery is notable because it is a new type of atom, not because the uncombined forms of Flerovium or Livermorium have any interesting or useful properties. Some elements also exhibit allotropism, meaning two very different substances can still be the same element. I believe the English definition persists largely due to historical inertia. Isolation of elements preceded atomic theory by a long way. - Jynto (talk) 18:30, 7 June 2015 (UTC)

IUPAC definitions

In the Goldbook, two definitions to "chemical element" :

A species of atoms; all atoms with the same number of protons in the atomic nucleus.
A pure chemical substance composed of atoms with the same number of protons in the atomic nucleus. Also calles « elementary substance ». [2]

Puce Survitaminée (discuter) 7 juin 2015 à 22:08 (CEST)

So we would need a disambig page (optionally) and two items, maybe two short articles. What do you think ? TomT0m (talk) 17:30, 8 June 2015 (UTC)

No chemical substance can't be used. If I take the IUPAC definition of chemical substance, this specifies that [a chemical substance] cannot be separated into components by physical separation methods, i.e., without breaking chemical bonds. Or we can separate Uranium 235 and uranium 238 using only physical means like centrifugation. So I prefer to have only the first definition and find a good description of what is a species. Snipre (talk) 19:57, 8 June 2015 (UTC)

There is clarification about this in a cite note : [3] which seems to make sense. But obviously it refers to this definition, so only one of the two WD items. I guess the question left is if we link the english Wikipedia article to the new item or to the old one ... the french article is clear, that one is ambiguous. TomT0m (talk) 20:25, 8 June 2015 (UTC)

@Snipre: species here is just one of the many ways to say types, or class, or kind ... If there was only me and if the article was better, I would just redirect to class (knowledge representation).

My change was reverted. Do I have any support here ? :) TomT0m (talk) 10:28, 12 July 2015 (UTC)

Proposition

A proposition of introduction, to advance a little bit : A chemical element (often just element when the chemical context is implicit) is a species of chemical objects, chararacterized by a number of protons in atoms nucleus. Two alternative definition are encoutered: either it is a type of atom with a constant number of proton, 1 in the case of hydrogen, or in a second definition a pure chemical substance consisting of a single type of atom distinguished by its atomic number<ref name="goldbookdef">IUPAC (ed.). "chemical element". http://iupac.org. doi:10.1351/goldbook.C01022. {{cite web}}: External link in |website= (help)</ref>. Those two definitions are closely related, as the second one has the first one is a part of it. In the first one, we will say that an atom with one proton is hydrogen, or with 2 protons helium, and in the second one we will say that the content of an Hydrogen gaz bottle is hydrogen.

OK, if nobody objects I guess I'll put it on the article in a few days. TomT0m (talk) 21:20, 10 June 2015 (UTC)

For me we can simplify with one definition saying "a group of atoms (undetermined number of atoms in the group from 1 to all atoms in the universe). Snipre (talk) 12:49, 15 June 2015 (UTC)

@Snipre: that would not really be precise and even be confusing : that's like saying humanity is a group of human. That way a music band could be humanity by himself, or human ... It's clear in that case that there is a big difference beetween a kind and a group of objects of that kind. And this left us into the dilemna that lead me here, so it's not much of an improvement.

PS: forgot to mention it but I made the change already. TomT0m (talk) 14:30, 15 June 2015 (UTC)

I cannot articulate it that much, but something smells wrong. I read "a species of chemical objects, chararacterized by a number of protons in atoms nucleus". A species? Not a definition? A character? And what is left of the "undividable" and "chemical properties" I learned at school? I'll have to spend a time into this. -DePiep (talk) 20:32, 12 July 2015 (UTC)

@DePiep: I don't know, do you have an idea of the sources your professors used ? Species is a synonym of kind, or type, see wiktionary for example : https://en.wiktionary.org/wiki/species TomT0m (talk) 17:36, 13 July 2015 (UTC)

Species is a normal word in chemistry, see chemical species. Christian75 (talk) 17:46, 13 July 2015 (UTC)

@DePiep: I want to keep this hot :) did you find a minute to think about it ? TomT0m (talk) 11:01, 18 July 2015 (UTC)

If "specimen" is the word to use, then go ahead. To me it reads like WP:JARGON and I only want to suggest to resolve that. Next, I note that the proposal says "characterized", i.e. not as strong as "defined" or "identified" then. (And, ...by a number of... shouldn't that be "..by the number of.."?). -DePiep (talk) 13:09, 18 July 2015 (UTC)

@DePiep: You're right, it would be great if we could make this a little less technical. For example the relationship element/compound should appear in the introduction.

What about something like

In chemistry, chemicals elements are the basic types of components matter made of atoms, ordinary matter like molecules and other chemical compounds are made of. Elements can be defined of two different ways, but in either way the number of protons in atoms nuclei is used to define elements, called the atomic number, because two atoms with the same atomic number have the same chemical properties. Either it is
* a type of atom with a constant number of proton, 1 in the case of hydrogen,
* a pure chemical substance consisting of a single type of atom distinguished by its atomic number<ref>IUPAC (ed.). "chemical element". http://iupac.org. doi:10.1351/goldbook.C01022. {{cite web}}: External link in |website= (help)</ref>
In the first one, we will say that an atom with one proton is hydrogen, or with 2 protons helium, and in the second one we will say that the content of an Hydrogen gaz bottle is hydrogen.

It's less jargonish and explains a little bit how elements are important and how they are classified, and why. @DePiep and Sniper: What do you think ? (sign:) TomTom

minor: ping @Snipre: fix. -DePiep (talk) 15:29, 19 July 2015 (UTC)

Sounds better indeed. I must leave it to you, because I can not contribute here to improvements in a lede (command of English, command of chemistry :-) ). OK for picking up the jargon thing. -DePiep (talk) 15:46, 18 July 2015 (UTC)

@DePiep: https://en.wikipedia.org/w/index.php?title=Chemical_element&oldid=281088028 sounds like the definition has a history here ... I'm beginning to understand I might have fallen into an obscurancy nest ... TomT0m (talk) 10:27, 19 July 2015 (UTC)

I think I should stop writing here, because the Snipre discussion above (ontology, definitions, classification, connecting that to WD) is much more important. -DePiep (talk) 15:29, 19 July 2015 (UTC)

Unfortunately it's related : I'd like to keep enwiki and frwiki (and many others) directly connected the same article, this seems important for a topic like this. This is impossible if the definition of the article is the substance one. TomT0m (talk) 17:18, 19 July 2015 (UTC)

Unfortunate indeed. But doesn't this say the the RL situation is unclear too? Even with the institutions & scientists involved? It would be very ambiitous of wiki to have same-definitions between sisters (WD, fr, en wikis). I've seen this in the topics of "periodic table category" (a word used in enwiki, not by IUPAC: used locally for an existing concept) and "Elements in group 3 (of the periodic table)" (depends on criteria chosen). In these, we at enwiki have reached a sort of stable situation by converging to a mainstream 'definition' (or agreement; both in science and enwiki), and noting the side options separately in the relevant articles. IMO it makes readible articles, diving from general lede into sections as detailed as possible (see metalloid). And also gave me a rest of mind. Have a nice edit. -DePiep (talk) 22:39, 19 July 2015 (UTC)

@SePiep: And also gave me a rest of mind Sorry I'm not good enough to understand that ;) , what does that mean ? It would be a lie to the reader to present only one facet of the coin and a clear situation when actually the definition is vastly disputed ... and it seem to bury really important property : it seems that the introduction right now does not really mentions that the elements a compound is made of gives him his properties ... And I think it just can't because of the - chosen - definition. It's indeed clear, but to me somewhat empty. And it is burying a controversy so it's POV, which on wikipedia does mean something and is the real problem. TomT0m (talk) 10:04, 20 July 2015 (UTC)

a rest of mind I meant: I think we solved (we are presenting) these two examples nicely and correctly at enwiki.

The opening post here ("Hi folks") two definitions are mentioned (fr, en). I assume both are valid (well-sourced). After that, you aim to somehow turn the two definitions into one major, also to serve a single wikidata definition. To me this looks a bit strange: wd requires such a solution, while in RL (in science that is), two definitions exist. It is not for wikipedia to prefer one, especially not for that iw reason. I mentioned the examples to illustrate: well, these are situations with multiple claims in RL (science), so we can not leave one out. However, we do present them with gradual importance (for example, writing the fringe scientific opinions in a section only). I note that different opinions in sources do not count as a WP:POV, only wiki-editors choices may. Right?

For example. In metalloid, there is a list of 194 sources that each build an argument for a list of elements. The article adds a occurrance (% of the sources) per element: "rarely considered a metalloid" etc.

For example. About group 3 in the periodic table. The list of elements is not fixed in literature. Using different criteria, sources end up with a different set. That is reflected in the article. Wiki does not take a preferred opinion (though sources with a more fringe statement me be moved to a section not in the lede).

So, an article reflecting the RL diverse opinions (in sources) is OK with me. If the article describes bot french and english definition, that's fine. And wikidata should be able to handle that. -DePiep (talk) 11:03, 20 July 2015 (UTC)

Oh, OK, of course, we're working on considering different definitions in Wikidata (you might be interested into joining d:Talk:Q18225 for example which is a good and hot example. It's not easy, as collaborative work can be, but I'm confident we'll end up with something solid. My problem here is that the current version does only account for one definition of element, that my attempt to add the second one, who is not fringed at all as it is present in the UIPAC goldbook, has been reverted and that I fear this will happen again without a clear concensus on talk page because at least one user is opposed to this there :) TomT0m (talk) 11:33, 20 July 2015 (UTC)

Template:Recent changes in Chemistry

{{Recent changes in Chemistry}}'s talk page redirect here... I suggest we add WP:Chemicals to the title too, so it looks like: [4] because it covers both projects. DePiep reverted the idea (without any Edit summary) Christian75 (talk) 00:41, 22 July 2015 (UTC)

As it is now: looks good to me. Very good. -DePiep (talk) 01:55, 22 July 2015 (UTC)

Recent changes in Wikiproject Chemistry

I made the template {{Recent changes in WikiProject Chemistry}} - which covers all article tagged with WikiProject Chemistry. Originally I moved {{Recent changes in Chemistry}} to ... in Chemicals; because its covers articles with the chembox (which belongs to the chemical project), but somebody didnt like that. Thats the reason for the name. Christian75 (talk) 01:58, 17 July 2015 (UTC)

The template is named {{Recent changes in Chemistry}}. This one is a fork and is misleading. -DePiep (talk) 06:59, 18 July 2015 (UTC)

Please explain. {{Recent changes in WikiProject Chemistry}} has all articles included in WikiProject Chemistry. {{Recent changes in Chemistry}} has close to zero of the articles in WikiProject Chrmistry. I suggest we rename {{Recent changes in Chemistry}} to {{Recent changes in Chemicals}}. Any comments? (it should be discussed on this page because the talk page of the matter is a redirect to this page). Christian75 (talk) 09:35, 18 July 2015 (UTC)

All by a shortcut: I prefer good old {{Recent changes in Chemistry}}:

Recent changes in WP:Chemistry and WP:Chemicals
Most popular pages in Chemistry (source) Most popular pages in Chemicals (source) In Chemistry articles In all Chemistry pages In chembox articles In drugbox articles
List overview · Updated: 2017-05-20 (infobox articles) · This box: v t

-DePiep (talk) 01:58, 22 July 2015 (UTC)

Modify identifiers section of drugbox

A proposal to move the identifiers section of {{infobox drug}} (that contains CAS numbers and links to chemical/drug databases, etc.) from the infobox to the bottom of the article has been made at the above link. Your input is welcome. Boghog (talk) 15:47, 2 August 2015 (UTC)

[4+3] or (4+3) - which one

A lot of articles (text and titles) has been changed from eg. [4+3] cycloaddition to (4+3) cycloaddition (see 4+3 cycloaddition) (btw. MediaWiki has no problems with titles staring with "("), and Pauson–Khand reaction. Personally I think it look strange. And I cant remember I have seen it in either Clayden's, March's or Carey & Sundberg's books. Any comments? — Preceding unsigned comment added by Christian75 (talk • contribs)

I've never seen it with parentheses. I've gone ahead and reverted the edits and directed the editor to come here to discuss. shoy (reactions) 17:42, 3 August 2015 (UTC)

"Radical"

The naming of Radical (chemistry) is under discussion, see Talk:Radical (chemistry) -- 67.70.32.190 (talk) 04:58, 6 August 2015 (UTC)

Help for identification

Is the Ormeloxifene a mixture of stereoisomers or the stereoisomer of the Levormeloxifene i.e. the dextrormeloxifene ? Snipre (talk) 13:32, 6 August 2015 (UTC)

I dont know. The images and/or IUPAC names are not correct. From the images it looks like it enantiomers but the names suggest they are are not (3R,4R and 3S,4R) Christian75 (talk) 15:40, 6 August 2015 (UTC)

PubChem link in Ormeloxifene's chembox agrees with the diagram we have and identifies its stereochemistry as 3S,4S. The PubChem link in Levormeloxifene agrees with the structure and 3R,4R we have there. DMacks (talk) 19:56, 6 August 2015 (UTC)

And right there is a reason to keep external-database links easily available:) DMacks (talk) 19:57, 6 August 2015 (UTC)

@DMacks: External DB like Pubchem are not really the best reference when considering isomerism. We miss a good database to distinguish stereoisomers from their racemate. Snipre (talk) 08:19, 7 August 2015 (UTC)

@Snipre: I would modify what you say here - databases can distinguish racemates from enantiomers. However, once you start to look at relative stereochemistry for compounds that have more than one stereocentre there are often problems that arise from limitations in chemical structure file formats in combination with the standard conventions used by most of the chemistry community when drawing such species. The key thing is to be aware of the potential problems and be critical in the use of data from databases understanding their datamodels, dataquality and limitations. --The chemistds (talk) 09:30, 7 August 2015 (UTC)

Yes I agree about the fact that DB can handle and often distinguish between isomers and racemate. But we don't have some systematic process with creation of elements in the DB for all cases (ex. for a simple stereisomer wit two elements for the single isomers and one element for the racemate). The problem is not the representation, but the complete representation of the possible cases. We miss a tag or label which allows us to identify clearly the component pictured in the DB and in the case of PubChem I found several examples where the names were not coherent with the representation. Snipre (talk) 10:12, 7 August 2015 (UTC)

Almost always where you have a compound name like Ormeloxifene and then a variant that has the dextro- or Levo- prefix the name without such prefixes is for the racemate. In this case this appears to be true see the INN documentation for the two names Ormeloxifene: [5] and Levormeloxifene: [6]. --The chemistds (talk) 09:30, 7 August 2015 (UTC)

I know that but in the case of PubChem we can't use that rule so that was the ground of my question and if someone can find a DB which uses dextrormeloxifene or a similar name, this will solve the problem. Snipre (talk) 10:12, 7 August 2015 (UTC)

Scifinder also appears to be having a problem with this: Ormeloxifene resolves to 31477-60-8 which is described in the text as being R,R but has an accompanying image labeled S,S by relative stereochemistry. Levormeloxifene resolves to 78994-23-7, which is also described in the text as being R,R but has a matching image labeled R,R by absolute stereochemistry. A lesser used CAS exists which is described as being S,S in the text and displayed as S,S by absolute stereochemistry, it's listed as being named Centchroman (CAS: 78994-25-9). Made of that what you will. --Project Osprey (talk) 10:47, 7 August 2015 (UTC)

Hydrolysate

This article is very sad. Anyone want to take a stab at cleaning it up, or should we just soft redirect to wiktionary? shoy (reactions) 15:05, 11 August 2015 (UTC)

Allotrope of oxygene

Can singlet oxygen and triplet oxygen be considered as allotrope of oxygen ? According to allotropes of oxygen yes but according allotropy no. Snipre (talk) 08:17, 7 August 2015 (UTC)

The physical and inorganic experts can correct this, but my general understanding is that O2 (dioxygen), O3 (ozone), etc. are the allotropes of oxygen, and triplet and singlet are the ground and excited electronic states of the dioxygen allotrope. See this source [7]]. But again, my field is not phys or inorg, and so there may be nuances of current usage, or new trends in meaning, of which I am unaware. Le Prof Leprof 7272 (talk) 21:12, 11 August 2015 (UTC)

swastika formulas

Hello.

Please let me kindly point you to Wikipedia:Administrators'_noticeboard#Swastika_formula. Regards. --Itu (talk) 03:20, 11 November 2015 (UTC)

SpecBox idea

Here's an idea where editors who are semi-clever on formatting could join forces with editors who are semi-clever at spectroscopy: One might create a "spectroscopy box" that would list core information related to various forms of spectroscopy. These contents would be useful to many technically oriented readers. Some table entries might be

wavelength range
frequency range (a formula could convert wavelength to the frequency, minimizing errors)
lifetimes (1/frequency), which says something about the dynamics being studied, again linked to the preceding data by a formula
selection rules (related to intensity of absorptions) or sensitivity

Other parameters might be suggested by others. Light source is probably too variable. Populations (big deal in NMR where the excited state is virtually as populated as the ground state) could be calculated, again by formulas (that depend on field).

Such a table could be applied to magnetic resonance techniques: EPR at various bands, NMR for various nuclei (we have individual articles on many nuclei), NQR also I guess. Moessbauer. IR. UV-vis. Raman and resonance Raman. Rotational spectroscopy. The unifying feature is the use of electromagnetic radiation. --Smokefoot (talk) 00:23, 15 August 2015 (UTC)

I would be interested, but perhaps the input is too diverse to be useful. One issue I have is the line might be a frequency in Hz, MHz, GHz or THz, a wave m=number in cm^-1, a wavelength in cm, Å or nm, or an energy in eV. Substances can have a great many spectral lines depending on conditions. Eg helium has several series, then there is He^II, and also He₂ occurs enough to appear in the spectrum in a discharge. Things get very complicated very quickly even for the simplest things. Molecules can have bands, and there are also "continuum" when you head into the UV. For many substances it may be worthwhile to have a spectrum of X article, eg spectrum of calcium and I plan to write such: User:Graeme Bartlett/spectrum of calcium, User:Graeme Bartlett/spectrum of magnesium. Also I would like to see support for Grotrian diagrams. Graeme Bartlett (talk) 01:41, 15 August 2015 (UTC)

For the record, Wikidata will soon create a datatype "number with units", so retrieving and storing the informations from Wikidata will allow to render the value correctly in the Infobox. TomT0m (talk) 11:20, 15 August 2015 (UTC)

I like the idea, Smoke, but also appreciate Graeme's reservations; let me know where the drafts are being developed. Le Prof Leprof 7272 (talk) 21:19, 18 August 2015 (UTC)

Maybe one way of organizing would be by frequency value, so there would be a clear principle of ordering (the regime, like UV or IR, and then within each, in order of the frequency variable). Then each value would associate with a Note on the conditions under which it was observed. Shortcomings I see are (1) the tendency this would have to drive us to primary sources, a no-no, and (2) the rigour required to decide which transitions should be listed (i.e., the subjectivity associated with having to decide which from among a list of lines to list, having been there). But I will look to what you start trying to come up with. Cheers. Le Prof Leprof 7272 (talk) 21:27, 18 August 2015 (UTC)

Thank everyone for suggestions and comments. Maybe the way to go is start small, and focus on an "NMR box." Include natural abundance, mag moment, frequency vs H NMR, chem shift range.... Nothing imminent.--Smokefoot (talk) 22:06, 18 August 2015 (UTC)

Agreed, let us know where we might look in to help. Even with NMR, as you well know, lines will be solvent dependent, and in some cases concentration dependent. Do this based on a standard spectra like from Aldrich (or the Japanese set)? Exclude computed data sets? Cheers, Le Prof 71.201.62.200 (talk) 23:39, 21 August 2015 (UTC)

Discussion opened regarding lack of datum-source correspondence in infobox citation "system"

The current "system" of directing readers to infobox sources—occasional inline citations following the datum/fact, but most often, just a general "Infobox references" link that takes the reader to a disorganized, poorly formatted, general (possible) list of sources—has been raised for discussion. Please, chemistry experts, join in, here [8]. Without an upswell in interest from chemistry experts, this process and so situation will remain poor, and the connections between data and source will remain untraceable (on any practical time scale). This "just trust us" aspect of many, many chemical articles leaves this aspect of them unhelpful to readers and unaddressable by time-limited editors (and formally in WP:VERIFY violation). Le Prof Leprof 7272 (talk) 21:02, 11 August 2015 (UTC)

This discussion si still going pretty strong, stop by if you care about how chem data and information are being sourced, and state your perspective. Le Prof 71.201.62.200 (talk) 23:44, 21 August 2015 (UTC)

Freeware

Does someone know a freeware to draw molecules able to generate the SMILES, the InChI and InChIKey from the structure ? A soft with a very low cost (max 200$) is ok too. Thank you. Snipre (talk) 12:47, 25 August 2015 (UTC)

You might need an academic E-mail address for this but tis a fairly good package http://www.acdlabs.com/resources/freeware/chemsketch/. --Project Osprey (talk) 13:38, 25 August 2015 (UTC)

Article on Römpp

Hi folks. I noticed today that the english wikipedia doesn't have an article on Römpp, a chemical encyclopedia published in germany. We've got articles on it in a few other languages and I suspect it's notable enough for the english wikipedia. However, I'm neither a chemist nor a german speaker, so my ability to sift mentions of Römpp in the press from citations or other confounded search results is somewhat limited. If anyone has english language sources on the subject I'd be happy to write a short stub on the subject. Thanks. Adam (Wiki Ed) (talk) 17:29, 19 August 2015 (UTC)

I created Römpp Encyclopedia Natural Products, including a link to the Google-translation of the DEWP article (has lots of technical and historical info, but no independent refs to support WP:GNG). May as well get at least a minimal item here as another for the ACS editathon. DMacks (talk) 20:54, 19 August 2015 (UTC)

Thanks, DMacks. I found one article comparing Rompp to WP, and there are a few others out there (most of which I can't read, so I didn't add them). Adam (Wiki Ed) (talk) 23:01, 19 August 2015 (UTC)

Thanks for finding that, a great ref for this subject, and for WP research. DMacks (talk) 02:31, 20 August 2015 (UTC)

Römpp Encyclopedia Natural Products is just a spin-off. I've created an article to the main Römpp's Chemistry Lexicon.--Kopiersperre (talk) 14:11, 25 August 2015 (UTC)

Clarification needed on substituted chemical classes

I'm posting here with regard to a discussion over at Talk:Substituted amphetamine. Are the parent molecules of a class of substituted molecules considered to be in that class. For example, is Amphetamine considered to be a Substituted amphetamine; is Tryptamine considered to be a Substituted tryptamine? Sizeofint (talk) 21:57, 25 August 2015 (UTC)

'tele' and 'pros' tautomers

Has anyone here ever heard of 'tele' and 'pros' tautomers as described in Histamine? I've never encounters the terms before. Google does give hits but these are also largely discussing histamine, which makes it feel slightly cyclical. --Project Osprey (talk) 12:55, 28 August 2015 (UTC)

Never heard that term, but I know that in bioinorganic there is much interest in which of the two N's are coordinating in histidine. --Smokefoot (talk) 13:17, 28 August 2015 (UTC)

Misidentified chemical elements

Category:Misidentified chemical elements currently contains 17 articles, all of which are small, many very small and borderline notable. They all would fit neatly into one article named Misidentified chemical elements or some such. Would it make sense to merge them? — Sebastian 22:04, 30 August 2015 (UTC)

It seems that, understandably, there's not much interest for these articles. I'm thinking of proposing them for deletion. — Sebastian 00:41, 3 September 2015 (UTC)

Why? If you think they'd serve their purpose better merged (I think that's reasonable), and are bothered enough by their unmerged presence to delete them, WP:SOFIXIT and merge them :) Opabinia regalis (talk) 01:09, 3 September 2015 (UTC)

The heart of WP:SOFIXIT is "Don't be upset if your bold edits get reverted". Merging is a lot of work, and it would be foolish to invest time just to get reverted by those who are better acquainted with chemistry. That's why I'm asking here. Moreover, even if I didn't get reverted, I'm contributing to this community endeavor because I want to help as best I can, and I don't want to waste time on something nobody else finds worthwhile. — Sebastian 03:42, 3 September 2015 (UTC)

Sure, it makes sense to ask if anyone objects. But silence is assent. Maybe I'm just grouchy today but I'm having a hard time squaring 'I don't want to have my hard work reverted if I merge them' with 'nobody cares very much so let's delete them instead'. Isn't that almost as much work as a simple merge into a list? Opabinia regalis (talk) 05:23, 3 September 2015 (UTC)

Thank you for asking. In my impression, Wikipedia has a problems with articles that have been created once, but are not cared about later. These drag the overall quality of Wikipedia down, which is recognized that the fact that such articles typically are declared as stubs with the request to readers to improve them, which in turn is a distraction for both readers and editors. — Sebastian 11:01, 3 September 2015 (UTC)

No objection to merging. But I don't think they all are best lumped into a single article. It seems like most of them are discoveries or declarations of "elements" that later turned out to be mixtures. But bohemium and helvetium were instead incorrect discoveries of what did turn out to be actual elements. Those latter cases would be better covered in the articles on the actual elements of those atomic numbers (neptunium and astatine, respectively) as part of their historical discussion. Maybe the ones that are mixtures could be mentioned in the articles about the actual components? That's encyclopediac info about those chemicals, whereas putting together an article about mis-identified entities feels like we (WP) are creating a topic that might not be notable. Lots of scientific discoveries are discredited, lots of things are reported that were later found to be incorrect, etc. DMacks (talk) 05:38, 3 September 2015 (UTC)

Very good point about the distinction. For a mixture, another possible location might be the article of the chemist who proposed the element. — Sebastian 11:01, 3 September 2015 (UTC)

I'd oppose the merge, although a list article could be created in parallel. A sortable table would be a good start.

I don't care if these are a set of very short articles. Provided that they each say enough, and that what they say is credibly sourced, then that's enough to be going on with. Just being short isn't a problem of itself. Andy Dingley (talk) 11:15, 3 September 2015 (UTC)

Interesting topic. I've put a list together at List of misidentified chemical elements, which wants polishing by those better able to do so.

The more I look at this, the less inclined I am to a merge. Except for Dianium, Ilmenium & Pelopium, which might be better explained as a group and certainly deserve footnotes in niobium and tantalum. Andy Dingley (talk) 11:55, 3 September 2015 (UTC)

I too would oppose a merge. Most of the articles look perfectly fine, even if some are small. Graeme Bartlett (talk) 22:03, 3 September 2015 (UTC)

That's what I meant in my reply to Opabinia regalis; it's just to be expected that there will be opposition in such cases, and I respect that. I am, however, disappointed with the fact that an administrator like Graeme Bartlett would just negate other peoples' arguments without addressing or even acknowledging their reasons; that is just a contradiction - a step down in Graham's hierarchy of disagreement. — Sebastian 21:01, 4 September 2015 (UTC)

Striking my last sentence, since I agree that these articles by themselves are not worth fighting over; only one was marked as stub when I checked. Some time ago, I gained the impression that we have too many stubs in general, but maybe that has changed, and at any rate it's not a topic for this page. — Sebastian 21:26, 4 September 2015 (UTC)

I think the list page is a good idea. Many of these are not stubs, even though they are small, because there is not much more to say about them. One reason to keep, is that if a reader comes across one of these and wants to read about it, all the information is in one spot. They do not need to find the name in a bigger article. Small well written articles are perfectly fine. These articles don't "degrade" Wikipedia, compared to the large number of sub-stubs about moths and beetles generated by bots. I am sure there exist many stubs in this project, particularly among the chemical pages. Too many stubs could be a topic for this page though! Usually when I write something I prefer to start something new rather than add to what is there before. Graeme Bartlett (talk) 21:34, 4 September 2015 (UTC)

I like the list idea also, which satisfies my reasons for saying a merge seemed reasonable in the beginning - that these are collectively an interesting historical topic. Opabinia regalis (talk) 22:01, 4 September 2015 (UTC)

Discussion about whether to deprecate Template:Cite doi

Template:Cite doi allows editors to generate a citation from a digital object identifier. There is a discussion about whether to deprecate this template. Since doi's are used the sciences and this is a science WikiProject, I am inviting anyone here to comment. Blue Rasberry (talk) 14:26, 9 September 2015 (UTC)

Woulfe bottle

May I ask for the help of some native speakers: The adjacent picture is denoted as "Woulfe bottle" (named after Peter Woulfe and shown in his article). From my personal experience I would say it just shows a washing flask. This picture shows some flasks that I would call Woulfe bottles, but I can not judge, if the file name of this picture shown here is correct (if "Woulfe bottle" is also used for the shown flask) or if it should be corrected.--Mabschaaf (talk) 09:45, 2 August 2015 (UTC)

I've seen different glassware companies list it under either name. I'd never heard of "Woulfe bottle", but I have used 2- and 3-neck wash bottles, so maybe use of this specific name is limited to certain fields? DMacks (talk) 18:00, 3 August 2015 (UTC)

When I looked at it I just thought it was a variant of a Drechsel bottlem where a screw cap replaced the ground glass joint, the following Chemistry World article ([9]) contains a reference to the Woulfe bottle with a written description. In some respects the image to me seems to be a modern hybrid of the 2. --The chemistds (talk) 09:16, 4 August 2015 (UTC)

As an addition comment - I wouldn't associate the term Wash Bottle with this glassware. I think that the common usage of wash bottle would be a plastic squeezable bottle that dispenses a solvent/solution. Depending on the situation that it is used I would generally expect this glassware to be considered as a bubbler or scrubber (when gas is passed through a liquid), or as a trap when used to remove solid/liquid material from a flow of gas. --The chemistds (talk) 09:24, 4 August 2015 (UTC)

That squeeze bottle is also called a wash bottle, but so the bubbler/scrubber type. Often specifically a "gas-washing bottle" (it washes the gas) in many supply catalogs. Our wash bottle article needs some work. DMacks (talk) 14:54, 4 August 2015 (UTC)

The Woulfe bottle as i know it is a safety flask to prevent an evacuated experiment from sucking in water from an aspirator in case of water failure. It has three plugs, one of which has a valve that can be opened to the surrounding air, and the other two connect to the apparatus and the aspirator. The valve is opened before turning off the water, to prevent backwash into the bottle. The thing in the picture is totally unsuitable. The article Peter Woulfe is also not clear as to what Woulfes bottle actually is.--Maxus96 (talk) 00:06, 6 August 2015 (UTC)

I moved the image to File:Waschflasche 2.jpg, corrected the term but still in German. --Leyo 16:02, 10 September 2015 (UTC)

Request for help

I'm currently working on improving the article Paper chemicals and am looking for assistance. Initially I need help converting chemical formulas in the table in the first section of the article. I formatted a few of them but am not familiar with chemical formulas and am afraid I may do it incorrectly. Also, this article, is all about refining and the chemicals and chemistry of the process. So would certainly appreciate help in other areas as well. Such as, I've been trying to come up with a better way of structuring the article sections but haven't been able to settle on a plan. Input by way of edit or recommendations on the article's talk page are appreciated. Thanks David Condrey ^{log talk} 07:47, 11 September 2015 (UTC)

Top-cited missing journals

WP:JCW has recently updated, and the coverage of chemistry journals is fairly good. There's still a few major journals of chemistry that don't have their articles on Wikipedia, so I've compiled this of chemistry-related/semi-related journals which may or may not be of interest to people in this project.

Top-cited missing journals:

General

Biochemistry

Environmental chemistry

Materials science

Physics

See Wikipedia:WikiProject Physics/Missing journals

See our journal writing guide at WP:JWG for help on writing these articles. Any help you can give is greatly appreciated. Headbomb {talk / contribs / physics / books} 13:31, 25 August 2015 (UTC)

I came back to see if any progress was being made and I have to say I was hoping to see a little bit more blue links If anyone needs any help, just let me know! Headbomb {talk / contribs / physics / books} 12:13, 11 September 2015 (UTC)

I've moved the list to a separate page, linked above, so that it will persist when this page is archived, and can be more easily linked-to. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 12:33, 11 September 2015 (UTC)

"Grain"

The usage of Grain is under discussion, see talk:food grain -- 70.51.202.113 (talk) 05:48, 17 September 2015 (UTC)

Sialon

In the Sialon article is a dead link claiming the invention of sialon for 1984. Here is a work from 1977 dealing with sialon type materials: http://escholarship.org/uc/item/0b26j81z#page-3 Sincerely, Ralph — Preceding unsigned comment added by 194.169.251.10 (talk) 06:42, 17 September 2015 (UTC)

Request help with referencing for Dopamine

I've been working on the dopamine article, with the goal of bringing it to GA and then FA status, but I'm having a bit of difficulty. I wrote a short section on the chemistry of dopamine, by interpolating scraps of information from various places, but none of them are good references. I believe the information can be found in the Merck Index, but I don't have ready access to that book. I wonder if any of the participants in this project could help out by (a) checking the Chemistry section of the article for validity (I'm not very good at chemistry), and (b) checking whether the Merck Index does contain this information, and giving me a page number. (Ideally for the 2013 edition, but I'll take what I can get.)

Let me add that it would be nice to add any important info that is missing, but we don't want to expand the section dramatically -- the dopamine article is very widely read, and ought to stay as accessible as possible. Anyway, thanks for any help you can give me. Looie496 (talk) 13:52, 18 September 2015 (UTC)

Reaction box

I missed any discussion of the "reaction box" as illustrated in Jones oxidation. My slight concern is the link to commercial sources, or ones that have a lot of advertising. Maybe that is not a problem since even journals have advertizing, but not as blatantly as http://www.organic-chemistry.org/namedreactions/jones-oxidation.shtm. But it would be useful to hear views. --Smokefoot (talk) 15:58, 18 September 2015 (UTC)

organic-chemistry.org is listed in Portal:Organic chemistry/Resources and it does have useful information, or at least a summary and lead refs or representative examples. But it fails WP:EL, as it seems to be nothing but that, which means it has nothing that wouldn't be written in a good WP article using those underlying refs (or secondary ones, etc.). I see Smokefoot pinged User:BiomolecularGraphics4All, a new account who is adding {{Reactionbox}} to tons of articles but who has not responded (unless "adding these boxes" is itself a problem, I don't see grounds for administratively acting against that account). Would be good to get User:Beetstra's input, as he worked on that infobox suite back in 2010. At the time (per Template talk:Reactionbox, there was lots of unfinished business, unresolved concerns, or at least discussion that petered out. DMacks (talk) 04:27, 21 September 2015 (UTC)

My apologies in advance if the utility of reactionbox has not yet been settled by the chemistry wikiproject, to the same extent as chembox or drugbox. But I think some of the discussion misses the point. My goal has not been to add external links WP:EL, but to add identifiers and cite sources using a standard template WP:CS. In fact, I agree that the pages referenced on organic-chemistry.org and rsc.org often contain less useful information than a good wikipedia article. It is not the link destination but the identifier that contains the key information that I'm trying to annotate. Consider the equivalent issue of CAS numbers and ChemSpider IDs in a chembox. Both contain links to sites with advertising, and often less information than the original wikipedia page. The important item is the identifier itself, the link purely cites the authority responsible for assigning them. Although I'm not the author of the {{Reactionbox}} nor {{Chembox}}, I do find them extremely useful, and the more consistently they are used the more useful they are. But I'd also like to hear people's views. It never occurred to me that the previous inconsistent state, of some pages with a reactiobox and others without was intentional after 5 years. BiomolecularGraphics4All (talk) 07:44, 21 September 2015 (UTC)

Energy units for chemistry and physics

Please consider commenting at Template talk:Convert#Energy units for chemistry and physics. --John (talk) 20:55, 21 September 2015 (UTC)

Low-barrier hydrogen bond

Hi, I've done a few edits on the low-barrier hydrogen bond page. They're mostly from a protein and enzyme point of view. It would be good for a chemist to have a look through and clarify the causes and detection of LBHBs. (have also notified WP:Physics]]) T.Shafee(Evo﹠Evo)^talk 11:56, 23 September 2015 (UTC)

Newly-revised recommended physical constants

As of June 2015, CODATA has released updated values for the fundamental physical constants. See, for example: NIST CODATA. I have started updating some of the relevant pages and have noticed that some of the pages have already been changed, but these values are so deeply embedded in all of Wikipedia, that it will probably take a while to update them all. To make matters more challenging, updating these values should be done periodically as new values are available. Any help swapping out the new values will be greatly appreciated! JCMPC (talk) 01:42, 25 September 2015 (UTC)

AfC submission

See Draft:II-VI semiconductor compounds. Best, FoCuS contribs; talk to me! 13:14, 29 September 2015 (UTC)

Avermectin structure incorrect

Seeing as this will be important in light of the recently awarded Nobel Prize in physiology and medicine, could we get this corrected? -- the stereochemistry of the three substituents in the upper left disaccharide ring needs reversal. (See http://pubs.acs.org/doi/pdf/10.1021/ja00404a041). The only real difference between Avermectin and Ivermectin is the double bond in the upper right, I think. It is correct at https://pubchem.ncbi.nlm.nih.gov/compound/6434889. Ivermectin is correct. Hansonrstolaf (talk)

Fixed as Avermectin skeletal.svg. I agree it seemed trivially similar to the Ivermectins, so I just cloned and adjusted that one's image. Someone please double-check it against the ref. The sec-butyl on the upper right of B_1a was also problematic because it did not include the stereochemistry of the methyl within it (only had the stereochemistry for the whole alkyl group as attached to the ring). Looks like commons:Category:Avermectins needs a lot of cleanup. DMacks (talk) 21:36, 6 October 2015 (UTC)

Wikipedia:Articles for deletion/Zoltan Hajos

Help with fixing some issues in Zoltan Hajos would be most welcome. --Leyo 08:52, 7 October 2015 (UTC)

Mercury nano-trap water filtration

Hello chemistry experts! This article was copy-pasted out of AfC into mainspace. It hasn't been assessed yet. Perhaps someone from this project should take a look at it. —Anne Delong (talk) 22:52, 15 October 2015 (UTC)

Assembly

I agree with Primefac's assessment, but wanted to double-check Draft:Templating Methods – Use of Metals in Supramolecular Assembly was correctly declined. Best, FoCuS contribs; talk to me! 22:58, 26 October 2015 (UTC)

Well intentioned but a little too amateurish. Anyway we have Template reaction. Will poach some of the declined article and make that title a redirect.--Smokefoot (talk) 23:53, 26 October 2015 (UTC)

Shortcuts

Currently, we have the following redirects to WP:CHEMISTRY

We also have the following redirect to WP:CHEMICALS

There are other redirects as well (and lowercase variants), but they don't matter for this discussion. I put forward the claim that WP:CHEMS/WP:CHEM/WP:CHM are ambiguous and we should do something about it. In particular, when I see 'CHEMS' I'm thinking 'chemicals' as in 'did you order the chems?', and when I hear 'CHEM', I'm thinking chemistry as in 'Chem classes this afternoon?' or 'CHEM3000'. CHM I'd be ??? / leaning chemistry just because sometimes CHM is a class code instead of CHEM. And I'm tired of being brought to the 'wrong' page when I put WP:CHEM in the search box. If figure if this is confusing to me after years of editing and hundreds of thousands of edits, this surely is confusing to newcomers as well.

I suggest we either

1) Re-target WP:CHEM to point to WP:CHEMISTRY, and WP:CHEMS to point to WP:CHEMICALS. Then make WP:CHM point towards a dab page. We can use bot cleanup to 'retroactively enforce' the new convention, so old links still point to the intended target.
2) Endorse a new WP:CHEMIS and WP:CHEMIC. We use bot cleanup to enforce the new convention, so newcomers are only presented with the current shortcuts to reduce confusion.

a) We leave old shortcuts as they are, we just don't mention them anywhere 'visible' (like the front page of WP:CHEMISTRY/WP:CHEMICALS.
b) We retire the old shortcuts, making all of them point to a dab page.
c) We do option 1) as well. We re-target WP:CHEM to point to WP:CHEMISTRY, and WP:CHEMS to point to WP:CHEMICALS. Then make WP:CHM point towards a dab page.

There's also option 3

3) Do nothing.

The downside of 1) is the old fart factor. We have habits, and this would require veterans of these projects familiar with the current convention to change their behavior. There's a transition issue, but it should resolve itself after a month or two.
The downside of 2) depends on the sub-option chosen. Each have their pros and cons.

a) Requires the least amount of change from anyone, at the cost of the old abbreviation slowly creeping back into use over time because nothing is done to warn anyone WP:CHEMS/WP:CHEM/WP:CHM are kinda ambiguous and shouldn't be used.
b) Requires vets to adapt, but there's a dab page to help the 'victims' of those didn't.
c) Requires vets to adapt.

The downside of 3) is the current mess that we have.

My personal preference is option 1 = 2c > 2b > 2a >>>>>>>>>>> 3. Headbomb {talk / contribs / physics / books} 17:56, 22 September 2015 (UTC)

I have encountered this problem before. Kudos for bringing it up. If we go with strategy 1 should probably make a point of alerting the other science/medicine/engineering WikiProjects. Sizeofint (talk) 23:29, 22 September 2015 (UTC)

Anyone else want to comment on this? Headbomb {talk / contribs / physics / books} 03:24, 28 October 2015 (UTC)

I object, and propose some other route. The problem is that to me, I have made mistakes tooo often between the two that I decided never to look at CHEMICALS again (it is a sub-wikiproject, isn't it). It always confuses me into where to look for a talk or argument. It's WP:CHEMISTRY for me. So I propose to remove the sub-shortcuts but one (leave WP:CHEMICALS, obviously). MUltiple other reasonable shortcuts can & should lead to CHEMISTRY. -DePiep (talk) 11:13, 28 October 2015 (UTC) (Well, please read this as an endorsement of your option #2. Especially the deprecation-part, can't be strong enough). -DePiep (talk) 11:15, 28 October 2015 (UTC)

Osmosis

I recently revised osmotic pressure. It became apparent that the subject of osmosis is badly fragmented.

to cite some of the relevant articles. These should surely be merged into one article? Reverse osmosis probably merits the separate article.

Is there an opportunity here for a collaborative project - chemistry and biology - leading to a unified treatment of osmosis? Petergans (talk) 08:46, 30 October 2015 (UTC)

Amino acid Representations

I have noticed that many, if not all, the amino acids on their individual pages and on the amino acid page are represented in their non-ionic form. I feel this is misleading, or misinforming, as it is the form least likely found in nature. The Zwitterionic form would be the best form to include, in my opinion. I would be happy to change the structures if the community doesn't mind. I have noticed there has been some discussion on the amino acid talk page, and on some of the individual pages, but nothing has been changed. I asked about this in the WikiProject: Molecular and Cell Biology as well, but some of the discussion already on talk pages seemed to come from this project as well. So I am asking here also. Htienson (talk) 22:01, 20 October 2015 (UTC)

Seems like a good idea to me. You'd have the opportunity to depict them with uniform drawing settings, in the event that they are not already that way. --Smokefoot (talk) 00:02, 21 October 2015 (UTC)

I think that ideally we'd show both forms. The 'classic' non-ionic depiction is the most commonly used, even in text books, failing to show it may confuse our lay readers. --Project Osprey (talk) 08:29, 21 October 2015 (UTC)
I agree with Project Osprey here - please show both. Showing the zwitterion is more correct, but these compounds are called 'amino acids' and not 'ammonium carboxylates' - a lay reader would/might maybe expect an amino-group and an acid-group, the zwitterionic form might be confusing to them (I presume that this concept is however properly explained in the article). --Dirk Beetstra ^{T C} 09:20, 21 October 2015 (UTC)
In principle, yes. In practice, I am not so sure. I assume you are referring to the graphic in the {{chembox}}. The down side of these graphics is that they cause the size of these already large infoboxes to grow even larger. This is especially a problem when viewing the article on a mobile device. One has to scroll down forever until one reaches the lead. If we include 2D depictions of both the neutral and zwitterionic forms plus the 3D structure, this really starts to get out of hand. In a related issue, I question why we are including 3D depictions at all. These are arbitrary selected conformations and IMHO, the ball and sticks depictions plus dashed lined for aromatic bonds are really ugly. I think these 3D depictions should be removed. Boghog (talk) 11:51, 21 October 2015 (UTC)

While I think a uniform depiction across multiple articles is a good idea, choosing which representation style is not easy. The functional groups in amino acids have different protonation states in different environments (aqueous vs solid, pH dependence, etc). Simple zwitterionic forms (ammonium carboxylates) are not always the accurate form when considering the physiological environment where amino acid ionization states are most relevant. And since 2D representations of chemical compounds already have many simplifications related to structure and bonding built into them, we shouldn't necessarily strive for the highest degree of scientific "accuracy" with them. They are meant as a kind of shorthand. As is done in most text books, I think it makes most sense from an educational perspective to show them in amino acid forms first, then describe zwitterions and more complex biological ionization states in the text. -- Ed (Edgar181) 13:56, 21 October 2015 (UTC)

Thank you for your feedback. As amino acids are biological molecules I think the most relevant form is the proper ionization state under most normal physiological conditions (i.e. pH 7.4). From the discussion it sounds like a good compromise would be showing the physiologically relevant form next to the non-ionic form, without the 3-D structure at the top of the page. I also tend to find these difficult to look at and not very informative except in very specific settings. I will also make sure to add something early on in the introduction that explains the two different structures. Any other suggestions or comments? Htienson (talk) 18:41, 3 November 2015 (UTC)

IUPAC gold book definitions and dihedral angles

Hi I am no chemist but did edit the dihedral angle page, In it i did add the UIPAC goldbook definition. (but i did much more to the geometry part of it.

I would like a chemist to have a look at it.:

also on https://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/Gold_Book_workgroup#A_bit_confused_though.2C_can_I_cite_from_Gold_Book.3F (sorry I don't know hoe to link there in proper wikipedia fashion ) I was wondering can we cite from the gold book or not? WillemienH (talk) 23:04, 2 November 2015 (UTC)

The gold book definition is uneccesarily complicated and too specific to chemistry. A dihedral angle is simply the angle between two intersecting planes. To avoid any ambiguity, it is the angle between any pair of lines, one in each plane, that that have a common point on, and are normal (perpendicular) to, the line of intersection of the planes. For a non-chemical use, there may be a dihedral angle between the two wings of an aircraft. Petergans (talk) 08:06, 3 November 2015 (UTC)

I don't know where that comes from. The IUPAC Gold Book gives the definition of a dihedral angle as follows

The angle between two intersecting planes on a third plane normal to the intersection of the two planes.

I have put this definition in the chemistry section. Petergans (talk) 16:51, 3 November 2015 (UTC)

Thanks for your edit, I am still wondering on 2 points: The previous definition was from torsion angle goldbook torsion angle, torsion angle is a redirect to dihedral angle I am thinking to put it back in but then n a new sub section. I was wondering about the UIPAC torsion angle definition and the description on the page, they do differ. (on clockwise and counterclockwise)

An other point the "Atan2" formula's in the article, they seem strange in $\varphi =\operatorname {atan2} \left(\left([\mathbf {b} _{1}\times \mathbf {b} _{2}]\times [\mathbf {b} _{2}\times \mathbf {b} _{3}]\right)\cdot {\frac {\mathbf {b} _{2}}{|\mathbf {b} _{2}|}},[\mathbf {b} _{1}\times \mathbf {b} _{2}]\cdot [\mathbf {b} _{2}\times \mathbf {b} _{3}]\right).$ atan2 seems to be a function of 2 vectors not of 2 numbers. while the atan2 page says atan2 is a function of 2 numbers. the formula seems to be comming from a book on computational chemistry can you check them out? Maybe best to continiue this discussion on talk:dihedral angle WillemienH (talk) 08:33, 4 November 2015 (UTC)

A torsion (aka twisting) vibration is a term used in vibrational spectroscopy to signify a vibration in which the angle between two planes changes. For example, in ethane, rotation of one CH₃ group with respect to the other, about the C-C bond is part of a torsion vibration. In this context torsion angle and dihedral angle are synonymous. In principle left and right torsions could be distinguished from each other in a chiral molecule, but I don't know if it has ever been done. Petergans (talk) 09:45, 4 November 2015 (UTC)

I have completely revised the article. I have eliminated the section referring to atan2 (comment of WillemienH, above) because I am unable to find a source for it, nor could I see the relevance of a 3-vector formula to an angle that can be defined in terms of the dot product of 2 vectors, as illustrated by the formula : $\cos \varphi =-{\frac {\mathbf {n} _{A}\cdot \mathbf {n} _{B}}{|\mathbf {n} _{A}||\mathbf {n} _{B}|}}$ . Also I have cleaned up the extensive duplication that was present before. Petergans (talk) 09:36, 9 November 2015 (UTC)

Ionosilica

Is this already covered and/or is it notable - Ionosilica Thanks, JMHamo (talk) 23:57, 12 November 2015 (UTC)

@JMHamo: @Peter Hesemann:. Peter Hesemann, the name of the editor who created this article, is also the name of an active researcher on modified silicas. This article appears to be self-promotion of a pretty specialized topic, although one can be sure that Hesemann is convinced that it is very, very important. Why people like this cannot contribute anything more general that does not benefit themselves reveals about how many scientists interacts with Wikipedia, which is seen as a venue for publicity. Aside from WP:COI, a specific concern is the usual one: WP:SECONDARY - it would be nice if the article cited a review. http://www.cmos.icgm.fr/phesemann. Oh well, life goes on. --Smokefoot (talk) 01:46, 13 November 2015 (UTC)

The review is also written by our author. I have done a bit of peacock culling, and fixed refs. Graeme Bartlett (talk) 09:04, 13 November 2015 (UTC)

Ariel Fernandez

Can someone with good chemistry knowledge please evaluate a request posted on behalf of Ariel Fernandez -- here? There's a long history of COI here. We don't want an article that is unduly negative, but I'd like to make sure that the proposed changes are not flawed in terms of the claims we'd add. Is the idea of a dehydron coherent? That article (not the redirect) was originally created by Arifer (talk · contribs) (see [10])... Nomoskedasticity (talk) 16:47, 8 November 2015 (UTC)

The idea of the dehydron is coherent. There is software that can calculate them in a reproducible way. Whether or not the dehydron is a legit concept is not why Fernandez's work is being called into question. Rather, it is due to claims made regarding purported relationships between dehydrons and molecular evolution, for which the reproducibility of the data has been challenged significantly enough to result in three expressions of concern and a fourth article placed on publication hold for around a year now. Molevol1234 (talk) 18:05, 16 November 2015 (UTC)

TfD of interest

A merger has been proposed for three templates that format external links to pubchem in slightly different ways, but the discussion has seen very little participation. Please comment here if you're interested. Thanks! Opabinia regalis (talk) 01:52, 19 November 2015 (UTC)

Slow Science

Slow Science has been requested to be renamed, see talk:Slow Science -- 70.51.44.60 (talk) 04:37, 28 November 2015 (UTC)

Seeking input on a student handbook for chemistry

Hello all! The Wiki Education Foundation is preparing to print a handbook to help student editors working with chemistry articles. You can find the draft text here. I'd really appreciate input from other editors on the Talk page. This WikiProject has already been an invaluable resource in creating this handbook, so thanks! Any feedback is especially helpful prior to Nov. 13 (this Friday). Thanks again! Eryk (Wiki Ed) (talk) 18:17, 9 November 2015 (UTC)

The obsession for editors Wiki-chem is content yet the goal for Wiki Ed is some sort of experience involving learning markup language and communication skills, both admirable. It seems as though Wiki-Ed views student contributions as a recruiting tool, which is debatable. In fact it might be an unrecruiting tool because the students often get beaten up and the instructors pissed off. There are two central problems:

Central problem #1: Wiki-chemistry is now so sophisticated that, with rare exceptions, contributing is beyond any reasonable undergraduate's ability, in the absence of active involvement of a professor. So what we get instead is a lot of safety cruft or hyper-esoterica such as articles on compounds selected seemingly at random from a chem catalogue.
Central problem #2: It is difficult (almost impossible) for students to contribute unless the instructor is an experienced Wikipedian.

Isn't there another venue such as Wikitextbooks that could be used to engage these young editors? --Smokefoot (talk) 18:53, 9 November 2015 (UTC)

Hi Smokefoot! Thanks for your comments. For Wiki Ed, quality content trumps editor recruitment. That's why I think the goals of WikiProject Chem and student assignments are pretty aligned: we want people to contribute good, well-resourced content to Wikipedia (in this case, concerning chemistry). Of course, the majority of this community, like most communities on Wikipedia, has been extremely helpful to new editors, regardless of whether they edit from a classroom or from a living room. As you mentioned, we're working to create a resource that helps students contribute content with the guidance of experienced Wikipedians and instructors. We've specifically highlighted to avoid the "safety cruft," among other advice found in WP:MOSCHEM and other resources. Other guidance you'd have for editors who are students would be well appreciated on the Talk page of the handbook itself, so we can make sure the content of the handbook reflects the concerns of the Chemistry community on Wikipedia. Thanks again for the feedback! Eryk (Wiki Ed) (talk) 21:39, 9 November 2015 (UTC)

There perhaps should be some information on notability — how to determine whether Wikipedia should have an article written on the topic. Sometimes students write about a very narrow topic, that could be a title for a journal article, but could be much broader in an encyclopedia. Also we sometimes get useless stubs that say almost nothing about a substance. So there should be some review about what subjects are suitable for the first time writers. For student assignments I find that plagiarism is a serious problem, even though there is warning against it. Perhaps there should be negative marks if it is detected. Another problem I have seen recently is registering user accounts for groups, rather than individuals. Make sure that each individual has their own user on Wikipedia. (not a Chemistry problem however.) Graeme Bartlett (talk) 00:58, 10 November 2015 (UTC)

Thanks for the feedback, Graeme Bartlett! We expect plagiarism enforcement from instructors, and we're actively searching for plagiarism. It's a top priority for us - if you see plagiarism, please notify us! We do address plagiarism on the first page, and in the complementary online training and student editing brochure, but I'll see about reiterating it elsewhere in the handbook as I agree it is critically important. And we agree that registering group accounts doesn't work. That's why Wiki Ed requires each student to have a distinct username. You shouldn't find group accounts coming from the instructors we work with. The last point, on notability, is also a concern that's addressed outside the specific chemistry handbook. We work with the instructor to steer students away from overly narrow topics and find articles that are backed by significant literature. Thanks again for the feedback! Eryk (Wiki Ed) (talk) 20:39, 10 November 2015 (UTC)

@Eryk (Wiki Ed): Recently I came across an Extinction course which has added plagiarism. I suspect this is not assisted by Wiki Ed. I made a list of users at User:Graeme Bartlett/ext2015 but have not yet checked much of the contributions. (Nothing to do with Chemistry). Graeme Bartlett (talk) 21:44, 10 November 2015 (UTC)

Graeme Bartlett, thanks for flagging that. You're correct that it isn't a Wiki Ed-supported course, but we'll be reaching out to this instructor. Eryk (Wiki Ed) (talk) 00:23, 11 November 2015 (UTC)

Other places to help out could be Wikiversity, Wikisource or Simple English Wikipedia. These will also have Chemistry work that needs to be done, but will have their own rules. Graeme Bartlett (talk) 01:09, 10 November 2015 (UTC)

Eryk (Wiki Ed) , and Graeme, I can see one clear avenue of approach: notable people not yet covered. According to WP:PROF, anyone holding a named chair in a major university is notable. We probably have many of the present holders of these positions, but the earlier ones remain notable. Every president of the American Chemical Society is notable; we are missing about 50% of the ones after 2007. Every present and past member of the chemistry section of the National Academy of Sciences is notable--we probably have most of the present, but not the past. Every editor in chief of a major journal is notable, present and past. We lack most of them. Such articles are quite straightforward to write. And the students will learn a little chemistry as the work on the articles. DGG ( talk ) 01:46, 2 December 2015 (UTC)

Great ideas for student projects. We might even think outside of the US (horrors!). --Smokefoot (talk) 13:06, 2 December 2015 (UTC)

Copyright question: Lists of isomers of Alkanes

(originally a help-me request at my user talk page)

Short question: Are the sources used by the Lists of isomers of (n)-alkanes articles copyrighted, or do the lists of isomers fall under fair use?

Background

This question pertains to the following 6 list articles:

Prior to 28 November 2015, only the first 4 articles existed (-nonane — -docane). I created the -tridecane and -tetradecane articles on 28 Nov, by copying the data from http://www.scribd.com/doc/56047899/Constitutional-Isomers-of-Alkanes#scribd. I neglected to cite my sources when I committed, and @User:Seagull123 helpfully asked me to do so. (see also initial discussion of the issue).

I am only able to find 3 such lists of isomers of alkanes up to tetradecane on the internet, and they all seem to be exact copies of each other:

http://www.scribd.com/doc/56047899/Constitutional-Isomers-of-Alkanes#scribd (the one I cited in -tridecane and -tetradecane)
http://www.chemicalland21.com/info/Constitutional%20Isomers%20Of%20Alkanes.htm
http://www.kentchemistry.com/links/organic/isomersofalkanes.htm (the one cited in -nonane)

I have reversed my thinking from the original discussion on @User:Seagull123's talk page. I believe the lists of isomers is non-copyrightable, much as a list of States in the United States is simply statement of fact. The sequence of the number of isomers for the first n alkanes is, in more general terms, the number of n-node unrooted quartic trees (graph theory)<ref name= OEIS >On-Line Encyclopedia of Integer Sequences (sequence A000602 in the OEIS)</ref>. The naming of the isomers is formulaic, following IUPAC rules.

While Wikipedia:Copyright in lists is an essay, not policy, I think it and its talk page are very instructive in the conversation.

sbb (talk) 13:18, 30 November 2015 (UTC)

No I think there will be no copyright in the list of names. It will be public domain. Fair use is not required, and if it was, then it probably would not be justified. The way it is presented with the subheadings, could add some creative content though. The scribd list is poorly presented, and normally I would not consider this a reliable source either.

Agreed, the Scribd list is poor, and it's not what I'd call a decent source citation. I used it because it had the most permissive copyright/license. But, as you noted, if it's something that cannot be copyrighted, no claim of copyright or licensing will restrict that. I'm moving forward with the assumption that any list of isomers of alkanes cannot be copyrighted.

I checked some of the combinations, and they looked OK. But do you know if there are no duplicates (same shape with two different names) in the list?

No, I don't know there are no duplicates, but the length of the list matches the known number(s) of isomers for a particular n-alkane.

Is there a computer program around that will generate all the isomers? (http://hrcak.srce.hr/file/151228 http://pubs.acs.org/doi/abs/10.1021/ed048p675) Also chirality does not seem to make any appearance in the list. At which point is the isomer impossible due to being overcrowded? Graeme Bartlett (talk) 21:28, 30 November 2015 (UTC)

The number of known isomers for a particular alkane ignores stereoisomers, and does not take into account unstable, overcrowded, or otherwise unrealistic actual isomer molecules. The number is identical to the number of n-node unrooted quartic trees (see reference to OEIS above).

http://www.pmf.kg.ac.rs/KJS/volumes/kjs25/kjs25lukovits73.pdf does the job for tetradecane but does not give the names, and it also refers to a dodecane list in another paper. It says this was worked out in the 1930s. Graeme Bartlett (talk) 21:43, 30 November 2015 (UTC)

Interesting paper, thank you for the link. I'll look into generating IUPAC names from compressed adjacency matrices. sbb (talk) 00:05, 4 December 2015 (UTC)

Halogenation halohydrins

While they fail the IUPAC definition would editors here concider compounds such as 2,2,2-trichloroethanol (structure shown) to be halohydrins or not? I ask because we seem to have quite a lot of compounds like this and I'm trying to figure out how to categorise them. --Project Osprey (talk) 08:19, 8 October 2015 (UTC)

I think that category will do. The definition looks like there should be only one halogen atom though. Graeme Bartlett (talk) 05:07, 16 October 2015 (UTC)

Indeed it does. However I expect they share a similar chemistry, intramolecular cyclisation to give the dichloroepoxide is known and forms the basis of the Corey-Link Reaction. On the other hand some editors do feel strongly about us deviating from IUPAC definitions. --Project Osprey (talk) 09:00, 16 October 2015 (UTC)

No idea about the categorization, but Corey–Link reaction now exists (we didn't seem to have it in any WP language). DMacks (talk) 20:31, 16 October 2015 (UTC)

The definitions are always difficult to read, mainly because of the misunderstanding of what these definitions define. 1,1,2,2-tetrachloroethene is an alkene, despite alkenes being defined as "Acyclic branched or unbranched hydrocarbons having one carbon–carbon double bond and the general formula CnH2n". It is the core part that defines the functionality (the basic carbon-fragment), in which nothing to everything can be substituted (the hydrogens, and even the carbons). Here in 2,2,2-trichloroethanol we have a halohydrin ('Cl-C-C-OH'), where 2 hydrogens on the chlorine-bearing carbon are replaced by chlorides. --Dirk Beetstra ^{T C} 06:42, 21 October 2015 (UTC)(changed typo --Dirk Beetstra ^{T C} 10:54, 6 December 2015 (UTC))

@Beetstra: I am confused by "1,1,2,2-tetrachloroethane is an alkene" as it is not an alkene but a substituted alkane. Did you mean 1,1,2,2-tetrachloroethene is an alkene (ie. that your post has a typo), which would make sense, or am I missing something? I concur that 2,2,2-trichloroethanol is definitely a halohydrin, though. :) EdChem (talk) 04:17, 5 December 2015 (UTC)

@EdChem: typo. I meant 1,1,2,2-tetrachloroethene. Now repaired. --Dirk Beetstra ^{T C} 10:54, 6 December 2015 (UTC)

@Beetstra: Thanks, I am glad that was all it was and I wasn't missing something. :) EdChem (talk) 10:58, 6 December 2015 (UTC)

Fundamental error in chemboxes

Whenever an equilibrium constant value (pKa etc.) is cited it is essential to give the temperature at which the value was determined. It cannot be simply assumed that the value relates to 25°C, though many values do so. See acid dissociation constant#temperature dependence for details concenrning the thermodynamics. Where it is known, temperature vaiation (or standard enthalpy and and standard entropy) could be displayed.

Strictly speaking, the ionic strength should also be stated. If the data are availble, values extrapolated to zero ionic strength should be cited, as otherwise values depend also on the nature and strength of the ionic medium. Petergans (talk) 16:36, 23 December 2015 (UTC)

So, when the given value is at 25 °C, there is no error at all. If not 25 °C, then that's called an omission. -DePiep (talk) 16:51, 23 December 2015 (UTC)