Wikipedia:WikiProject Chemistry/IRC discussions/19 Feb 2008

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<Physchim62> be quiet! the boss is here!

<Physchim62> ;)

<Rifleman_82> ;)

<Rifleman_82> heya martin

<walkerma> Hi there!

<walkerma> Just talking with our biochemist

<walkerma> To get his thoughts

<walkerma> Is there anyone else due to come today?

<walkerma> Dirk? DMacks?

<walkerma> OK, maybe we should start. I'll keep a log in case DMacks can't come

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<walkerma> Hi Axiosaurus! Glad you could join us

<Rifleman_82> hi there axiosaurus!

<Rifleman_82> :)

<Physchim62> Dirk seems to be hiding somewhere on Freenode, can't find him

<Physchim62> I will have to disappear in about an hour, so apologies in advance

<Physchim62> (car problems)

<ChemSpiderMan> Hi..ChemSpiderMan back..

<Physchim62> hi CSM

<walkerma> Not already - you just bought the car! Welcome CSM! Anyway, item 1 on the agenda is....

<walkerma> How do we deal with compounds such as Geranyl pyrophosphate which may exist in various conjugate acid/base forms under physiological conditions? See comment here. What about drugs such as Ranitidine, which may be produced in a salt form, yet which are often written as a neutral compound?

<walkerma> The "comment here" is from CSM: "A decision needs to be made about charged state/protonation state The structure does not coincide with the SMILES or the PubChem link"

<walkerma> (On the GPP page)

<Physchim62> what about pH indicators, whose main chemical interest is the difference between two colored form which have the same common name

<walkerma> Yes, we definitely have a lot of different things to consider!

<Rifleman_82> to answer walkerma, i think the article should always be the free acid/base; supplementary chemboxes for various salts should be used

<Rifleman_82> that means all xxx hydrochloride articles should redirect to the "parent"

<itub> to try to put everything in one place, I started writing a page about the different kinds of articles about "ambiguous substances" here: http://en.wikipedia.org/wiki/User:Itub/Ambiguous_chemical_identifiers

<Physchim62> how many chemboxes are we going to have? do we have accurate data to put in them?

<Rifleman_82> if the free acid/base is not known or commonly available, the very least we will have the FW and formula

<ChemSpiderMan> let's try and get an 80-90% solution for the majority. Exclusions need to be delat with then

<walkerma> There's certainly a lot of logic in your suggestion RF 82. Against that, our biochemist argued for representations at physiological pH

<walkerma> CSM is right, though, there are always exceptions!

<ChemSpiderMan> pH7.4?

<ChemSpiderMan> And who's going to know what the right charge state is at pH7.4? BTW , it's a distribution..

<Rifleman_82> agree with csm

<Rifleman_82> how about a simple model to focus on?

<walkerma> Yes, but with the phosphates he preferred O- to OH, but he admitted that the biochem community is divided on the issue

<Rifleman_82> glycine? should it be the fre-acid/free base? or the zwitterion?

<ChemSpiderMan> I think it's WAY too complex to try and determine what the form is at phys pH

<ChemSpiderMan> Rifleman...the answer is "YES"

<Rifleman_82> i would prefer the free acid/free base at the same time because it might not be "realistic" but it is a good working model

<Rifleman_82> yes = ?

<ChemSpiderMan> What do I mean...the answer is what we decuide it is.

<ChemSpiderMan> So, we need to decide on standard forms for classes of compounds... for example, amino acids should be shown as "X"

<walkerma> OK, I get a sense that people like the "parent form" as the solution to this - is that right? Draw the acid, not the salt.

<ChemSpiderMan> fill in the blank

<ChemSpiderMan> I certainly do...

<itub> I'm not sure about the aminoacids

<Physchim62> I think we should standardise on neutral molecules where possible

<ChemSpiderMan> I believe the majority would draw as uncharged

<ChemSpiderMan> yes...agree

<walkerma> I think, then, that we should propose this as the "default" policy, but we should also state that a "structure" (or structure and properties) section be included to clarify the equilibrium at physiological pH

<Rifleman_82> that should be discussed in text

<Rifleman_82> or at least, a link to the appropriate article

<Physchim62> anyone who knows enough chemistry to know that the neutral form is "wrong" under normal conditions also knows enough chemistry to correct for that fact

<walkerma> Rifleman_82: Exactly, in the article

<Physchim62> how would we choose which molecules to describe at physiological pH and which to describe under standard conditions (pH 0)

<ChemSpiderMan> pH 0?

<walkerma> Is pH 0 standard? Or pH7? (Excuse me, I was never good at standard X)

<Physchim62> yes, standard thermochemical data are quoted for pH 0

<itub> if it helps, the main CAS number for glycine (56-40-6) shows the unionized form in scifinder

<Physchim62> activity of H+ = 1 mol/L

<walkerma> OK

<itub> the biochemists have their own standard at pH 7

<Physchim62> and t=37¡C

<walkerma> I think with the proposed policy, we state that compounds will be shown in the neutral form, no matter what is their "standard form"

<ChemSpiderMan> good

<Physchim62> agree

<walkerma> That way we're consistent, and we can clarify the details in the article

<ChemSpiderMan> exceelent

<itub> I think there will be resistance in articles such as ATP

<Physchim62> which is where complicated things should go - in text, not tables

<itub> it is universally called a "triphosphate"

<itub> so if we deptict it as a phosphoric acid it will look inconsistent

<ChemSpiderMan> and there's an exclusion...

<Physchim62> yes, but no single structure can represent ATP under physiological conditions

<ChemSpiderMan> it is where we want the name to be the phosphate and it should be drawn as such

<ChemSpiderMan> our primary key is the article name

<ChemSpiderMan> If the article name is the phosphate then the structure should be a phosphate

<ChemSpiderMan> the article name for glycine is glycine...so we have a choice

<Physchim62> disagree there, I don't think there is anything wrong with displaying a fully protonated ATP. It is no less correct than the fully deprotonated form which would be implied by "triphosphate"

<ChemSpiderMan> citric acid and citrate are clear

<Physchim62> are they?

<itub> it is always shown deprotonated in the textbooks

<Rifleman_82> i'm looking at http://en.wikipedia.org/wiki/Adenosine_triphosphate

<Rifleman_82> and i don't think we can call it a molecule

<Rifleman_82> at best an ion or a fragment

<Physchim62> but we would be no more wrong than the textbooks in showing it fully protonated

<Rifleman_82> (i refer to the image in the bo)

<itub> sure, but we'd be going against the convention

<Rifleman_82> and i think our policy has been that if it is not a molecule (used loosely), it shouldn't have a box

<itub> and that's generally not a good thing

<ChemSpiderMan> Personally I'd prefer protonating it

<walkerma> I think triphosphate is an ester, hence the ate at the end - the protonation aspect isn't relevant, surely? Or am I missing something?

<Rifleman_82> the saem way citrate shouldn't have a box

<walkerma> Like ethyl acetate etc

<Physchim62> at any pH high enough to fully deprotonate the phosphate groups, you would also hydrolyse much of the structure of ATP. The textbook form *cannot* exist

<ChemSpiderMan> yes...Walkerma...you are right

<ChemSpiderMan> and check the IUPAC name...

<ChemSpiderMan> and is the CAS for the neutral form

<ChemSpiderMan> I say leave it neutral

<itub> I suspect you'd also hydrolize it if you lower the pH enough to protonate everything ;-)

<ChemSpiderMan> Walkerma...citrate was an example ...I think there are examples on WP where the name is specific to the the charged form

<Physchim62> I agree. We cannot win on this one, we cannot represent complex equilibria in a single structure diagram, so we have to have a conventional form

<Physchim62> itub, me too ;)

<walkerma> CSM: We certainly have exceptions like hydroxide, which is different from water (molecule)

<Physchim62> we have article for common anions

<itub> BTW, I don't agree with not adding infoboxes to ions

<itub> while they don't have a melting point, they usually do have CAS numbers, molar masses and many other properties

<Physchim62> if we add them, I think we should come up with a separate infobox, not chembox

<Physchim62> ionbox, lets call it

<itub> I suppose that could work

<walkerma> Sounds reasonable, as long as I don't have to write it!

<ChemSpiderMan> so, back to the standard then....neutral

<axiosaurus> what about func. groups e.g. amide?

<Rifleman_82> itub: we can give them an infobox, just not chembox. maybe chembox ion?

<Rifleman_82> change the color scheme a bit to make it clear it is not a chemical per se

<walkerma> Axiosaurus: That would make a good topic for a future discussion, I think! Once Rifleman has his rough draft figured out

<Rifleman_82> actually, my draft is sitting there waiting for more comments

<Rifleman_82> there haven't been many so i've interpreted it as a lack fo consensus

<itub> so, basically chembox means "it is something you can put in a bottle"?

<Rifleman_82> i'm a bit lost because i feel there's "no feedback"

<Physchim62> it seems pretty uncontroversial to me

<Rifleman_82> itub: that's how i look at it

<walkerma> itub: Yes, that;s always been the polocy

<Physchim62> itub, chembox is complicated enough already without adapting it once again to fit in ions and functional groups

<walkerma> axiosaurus: Please look and review RF82's page at

<walkerma> http://en.wikipedia.org/wiki/User:Rifleman_82/Functional_groups_style_guidelines

<axiosaurus> sorry RM- missed that just looking at it

<walkerma> OK, I'd like to get back to the main track.

<itub> I'd not add functional groups. It's just that so many organic compounds are ionic and people often only care about the organic part, that the ion is treated as a chemical in practice. ATP is the perfect example.

<walkerma> Are we agreed that zwitterions should also be presented in their neutral forms, for consistency?

<walkerma> That means amino acids, plus cases like betanin

<ChemSpiderMan> works for me

<walkerma> http://en.wikipedia.org/wiki/Betanin

<walkerma> Again, with clarification in the article

<Rifleman_82> about anions: DCA - dichloroacetate

<walkerma> Example: http://en.wikipedia.org/wiki/Wittig_reagent#Structure_of_the_ylide

<Rifleman_82> popularized by the potentail as a cancer cure

<Physchim62> Martin, yes, zwitterions sould only be shown as zwitterions in exceptional cases (such as the article zwitterion)

<ChemSpiderMan> DCA...the name of the article is Dichloroacetic acid

<Physchim62> "happy spam target" as Dirk would put it

<ChemSpiderMan> the structue is for that too...

<ChemSpiderMan> what's the issue?

<ChemSpiderMan> http://en.wikipedia.org/wiki/Dichloroacetate points to the acid

<Physchim62> the policy up until now has been to redirect the names of organic anions to the parent acid, except for *very* common cases such as acetate

<ChemSpiderMan> that works

<Rifleman_82> about DCA: forget what i said...

<ChemSpiderMan> :-) Forgotten

<Physchim62> the rational is that we almost never have enough to say about the anion on its own to justify a separate article

<Rifleman_82> i'm having difficulty articulating myself :P

<Rifleman_82> there's some amount of overlap between acetate as the anion and acetate as part of the ester

<Physchim62> whereas for inorganic anions, we can often talk about minerals, solubility trends, redox properties etc

<walkerma> I would say that there will always be exceptions, but we can probably handle those OK as they arise. If an anion becomes really important in its own right, it will get a separate article anyway

<walkerma> Are there any objections on the zwitterion issue? Can we move onto the next topic?

<itub> ok

<ChemSpiderMan> nothing from me

<Physchim62> can we discuss internal consistency in chemboxes?

<Rifleman_82> ok

<ChemSpiderMan> y

<Physchim62> several people, both WPians and other users, have complained that some data doesn't match the structure shown

<walkerma> Physchim62: Yes, certainly

<ChemSpiderMan> CSM raises hand as a "me too"

<Physchim62> there is a philosophical point as to "how accurate is chemical data?" (nobody seems to complain loudly about inaccuracies in the Rubber Bible...)

<itub> well, ideally every datum should have a traceable source, so you can blame it on someone else ;-)

<Physchim62> but if we are going to accept that the structure shown is just a representation of the title substance (and I don't think we can do otherwise), we cannot insist that all the data shown correspond to the /structure/ rather than to the /title/

<itub> the data needs to be annotated more often

<Physchim62> itub, see Talk:Cyclohexanone ;)

<Rifleman_82> hmmm

<Rifleman_82> maybe someone can just measure the damn melting point...

<Rifleman_82> but that will be WP:OR

<Rifleman_82> if it's not known for certain, we can just leave it blank or put something somewhat verifiable, and add footnotes saying what problems there are with this figure

<itub> I've found several errors in the NIST chemistry webbook too

<walkerma> Or give several figures

<Physchim62> any large collection of data will have errors

<itub> databases always have errors, and papers often have errors. We have to live with it. But whatever data we list should be traceable ideally

<walkerma> This seems to be YET ANOTHER manifestation of the molecule vs substance, microscopic vs macroscopic. That's surely your point, isn't it, PC?

<walkerma> Sorry, I meant the PROBLEM of molecule vs substance, etc

<Physchim62> you could see it that way, yes. I meant it more as a prophylactic warning against excessive pedantry ;)

<walkerma> We're never pedantic here, are we?

<walkerma> :)

<Physchim62> *prophylactic* warning :)

<ChemSpiderMan> are we back to the Rubber book again?

<ChemSpiderMan> are we finishing in 5 mins?

<Physchim62> there are at least three people here with access to the equipment to measure the mp of cyclohexanone and the skills to carry out the experiment. none of them are going to do it, because it wouldn't be worth their time, and even if they did WP couldn't publish their results

<Physchim62> I've got to dash in a couple of minutes

<walkerma> Well, I think we should raise this general topic in another IRC, since we will not agree anything today

<Physchim62> I'll check on the logs if there's anything else to discuss

<ChemSpiderMan> Walkerma...I am keeping the curation project on hold until we have some of these decisions made

<walkerma> I'd like to finish off with one other topic: How do we handle tautomers in cases such as 1,3-cyclopentanedione, where the structure may vary depending on conditions?

<Physchim62> ChemSpiderMan, yes, I think that's wise for the time being

<ChemSpiderMan> Draw thr structure for the name

<ChemSpiderMan> and note the possible tautomers in the article

<itub> agree, if its called a dienone draw a dienone

<ChemSpiderMan> yup

<ChemSpiderMan> else it's 3-hydroxycyclopent-3-en-1-one for example

<walkerma> How do we choose the "correct" name? DOn't we need a policy for that?

<ChemSpiderMan> name the drawn structure

<ChemSpiderMan> this is the consistency issue

<itub> we already have one

<itub> use the systematic name, or the most common name, or the consensus name ;-)

<ChemSpiderMan> you gave the name

<walkerma> itub: Can we be more specific?

<ChemSpiderMan> 1,3-cyclopentanedione

<ChemSpiderMan> is the name

<ChemSpiderMan> the structure is for that name

<ChemSpiderMan> sorry Walkerma..

<Rifleman_82> hmmm

<ChemSpiderMan> maybe I am missing something?

<Rifleman_82> not cyclopentan-1,3-dione?

<ChemSpiderMan> ah-ha...gotcha

<Rifleman_82> i understand that as an american habit

<walkerma> ChemSpiderMan: What if someone writes an article on 2-hydroxypyridine

<Rifleman_82> of putting the numbers in the front

<walkerma> As well as the one we have on 2-pyridone

<itub> they should be merged

<walkerma> Who is "right"? (Stone, of course, he did his PhD on it)

<itub> unless each tautomer is independently notable

<Rifleman_82> http://www.yanuo.com/products/2-Hydroxypyridine_142-08-5.htm

<walkerma> http://en.wikipedia.org/wiki/2-Pyridone

<itub> as in acetaldehyde/vinyl alcohol

<ChemSpiderMan> merge them

<Rifleman_82> tautomerism is discused

<Rifleman_82> sorry for the typos, it's cold in hong kong and my fingers are stiff

<ChemSpiderMan> actually...2-hydroxypyridine is already merged with a redirect

<walkerma> ChemSpiderMan: Yes, but where should they be merged TO?

<ChemSpiderMan> to 2-pyridone

<walkerma> With some things like pyridones there is a consensus. With some there may not be

<itub> that's a case-by-case decision

<ChemSpiderMan> exactly

<Rifleman_82> as long as redirects exist, no biggie?

<ChemSpiderMan> decisions will be made... :-)

<itub> we can see what CAS does

<ChemSpiderMan> agreed

<ChemSpiderMan> 2-Pyridone

<ChemSpiderMan> From Wikipedia, the free encyclopedia

<ChemSpiderMan> (Redirected from 2-Hydroxypyridine)

<ChemSpiderMan> someone decided....

<Physchim62> we have managed to decide between carbon tetrachloride and tetrachloromethane, for example ;)

<walkerma> OK, so maybe our policy should be open-ended on this. If a clear consensus exists, we go with that; if not, we debate it as a single case.

<walkerma> I think this could work

<Physchim62> both are acceptable IUPAC names, but the article can only have one title

<Rifleman_82> methylene chloride versus dichloromethane??

<itub> CAS has them "merged" as pyridone

<Physchim62> RM, that's a simple case ;)

<Rifleman_82> haha, true

<Rifleman_82> but both can be seen as part of a series... chloromethanes

<itub> 2-hydroxypyridine is under "other names"

<ChemSpiderMan> The IUPAC name appears to be 1,3-Cyclopentanedione

<Rifleman_82> but the two articles aren't synched

<ChemSpiderMan> for the previous structure

<walkerma> CSM: I believe the "correct" structure - representing the solid state - is in fact a hydroxy-enone

<walkerma> But everyone always calls it a dione

<itub> but what about gas phase, and solution in various solvents. Under some conditions the pyridone dominates

<ChemSpiderMan> then again, a decision is required on this one...leave it a dione and draw it as such or draw the hydroxy-enone and name it as such with a redirect and note the solid state form

<itub> actually the wp article already has a good discussion of this ;)

<ChemSpiderMan> it's how people will use the system and query it..

<ChemSpiderMan> redirects are great for this...

<ChemSpiderMan> I prefer the dione...but I guess a vote would work?

<walkerma> I think if the usual name is the dione name, we should leave it as that

<walkerma> That's the usual policy

<walkerma> With things like IUPAC names

<walkerma> We still allow isopropyl alcohol

<walkerma> OK, I think we're about finished for today, is there any last minute business we need to cover urgently?

<ChemSpiderMan> no

<walkerma> I'm very pleased, we seem to have resolved several thorny problems fairly easily

<ChemSpiderMan> not for me

<Rifleman_82> if there are no violent objections for the chemical classes style guidelines, i'll find a few articles to write toward this guideline

<Rifleman_82> that's all for me

<itub> please look at http://en.wikipedia.org/wiki/User:Itub/Ambiguous_chemical_identifiers and feel free to edit

<Rifleman_82> if there are objections in detail, we can of course dicsuss ;)

<walkerma> I wonder if we can use itub's page as the starting point of a Manual of Style section on this?

<ChemSpiderMan> it's a GREAT foundation

<Rifleman_82> good idea

<walkerma> OK, Thanks everyone! Please post your suggestions for future meetings on the IRC discussions page - we have several issues hanging

<walkerma> Is that OK? Shall we end there?

<Rifleman_82> thanks martin

<itub> ok

<ChemSpiderMan> bye all

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<Rifleman_82> night night :)

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<walkerma> Good luck with the car, PC!

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<itub> bye

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