Wikipedia:WikiProject Chemistry/IRC discussions/18 Mar 2008

--- Log opened Tue Mar 18 12:01:47 DST 2008

12:01 &lt;walkerma&gt; Rifleman 82 will not be here, he is on a plane right now. ChemSpiderMan will arrive later

12:02 -!- dmacks [n=dmacks@pdpc/supporter/active/dmacks] has joined #wikichem

12:02 -!- mode/#wikichem [+v dmacks] by ChanServ

12:02 &lt;+dmacks_logging&gt; Ah, there I am.

12:02 &lt;walkerma&gt; Talking to yourself is the first sign of madness!

12:03 &lt;+dmacks&gt; It's only a problem when you start ignoring yourself.

12:04 &lt;walkerma&gt; I wonder if we should start anyway, even though it's pretty quiet?

12:04 &lt;walkerma&gt; Traveler6, can you introduce yourself?

12:05 &lt;Traveler6&gt; I would if I could master this contraption

12:06 * dmacks hears you, seems like you've got it well enough so far...

12:09 &lt;walkerma&gt; I saw the comment too. OK, please try and give comments when you can, let's get started.

12:09 &lt;walkerma&gt; Unless you have something already written out about yourself

12:10 &lt;walkerma&gt; In which case just post it when you have it ready, and we'll still be able to follow the thread anyway. I often keep MS Word open as a notepad to get posts ready.

12:10 &lt;walkerma&gt; Welcome!

12:11 &lt;walkerma&gt; The first item - carbohydrates - I'd like to hold off on until Antony gets here.

12:11 &lt;+dmacks&gt; Makes sense.

12:11 &lt;walkerma&gt; The second involves implementing some of the style issues we've agreed on

12:11 &lt;Traveler6&gt; At last I get it, so what am I to say, I am user:LouisBB with intersts mainly in the organic field. I translate a bit, get people's back up sometimes, as I hate being 'conventional', definitely not a 'bandwaggon' type. I appreciate logic and originality, and questioning auhority (sorry if you belong to them lot)

12:13 &lt;walkerma&gt; Well, here I would say we have a rule by the non-apathetic

12:13 &lt;walkerma&gt; So if you want to help, you get to make the rules too!

12:14 &lt;+dmacks&gt; heh...nice summary:)

12:14 &lt;walkerma&gt; Welcome to our little group! Unfortunately we have some drudge work to do.

12:14 &lt;Traveler6&gt; What is the situation on carbohydrates so far ? Is there a log on it?

12:15 &lt;+dmacks&gt; WikiProject_Chemistry/IRC_discussions is the master page for these IRC discussions, including agenda/summaries and full transcripts.

12:16 &lt;walkerma&gt; All we have is some unresolved discussion (http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Chemistry/IRC_discussions/5_Feb_2008)

12:16 &lt;Traveler6&gt; Many thnks

12:16 &lt;walkerma&gt; 5th Feb is when we discussed this before

12:17 &lt;walkerma&gt; And later, sorry: Wikipedia:WikiProject Chemistry/IRC discussions/19 Feb 2008

12:18 &lt;+dmacks&gt; It's a case where we need to figure out what we mean by "compound" in a chemical-data sense and a wikipedia-article sense. open-chain vs various closed-chains, anomeric forms, etc.

12:18 &lt;walkerma&gt; We never resolved the issue, but we HAVE to address it before we hand over the file to CAS

12:18 &lt;Traveler6&gt; I'll better look it up now and keep a copy handy here

12:19 &lt;walkerma&gt; In case you're not familiar, CAS will be validating our collection of CAS nos. over the next few weeks, we have agreed to work together

12:19 &lt;walkerma&gt; Item 2: We have around 5000 compounds that Antony has checked by hand, but we need to go back and check and see if we have charged forms of these

12:20 &lt;walkerma&gt; For example Geranyl pyrophosphate

12:20 &lt;walkerma&gt; We agreed that the structures and associated terms in the chemboxes would show electrically neutral forms

12:21 &lt;walkerma&gt; We have to (a) identify which of the 5000 are a problem in this regard and

12:21 &lt;+dmacks&gt; Aw geeze, image there is charged but SMILES isn't...self-inconsistency is a pain:(

12:21 &lt;walkerma&gt; (b) Fix them

12:22 &lt;+dmacks&gt; That sqalene color-coding looks pretty suspicious.

12:22 &lt;walkerma&gt; The good thing, they should be easy to spot. Now, I'm willing to take on 2000 for starters, to work. Can someone help me?

12:23 &lt;+dmacks&gt; Got a list or WP catagory of 'em?

12:23 &lt;walkerma&gt; Antony has an SDF file, which is a connected collection of structures with annotations

12:24 &lt;walkerma&gt; The annotations being InChI, InChIKey, IUPAC name and CAS no.

12:25 &lt;walkerma&gt; He will send the file to whoever wants it, and (if need be) the tools to work with it

12:26 &lt;+dmacks&gt; Wonder if that could be massaged into a WP page, so that we can say "here are the compound pages we're working on".

12:26 &lt;walkerma&gt; I believe that some of the ChemAxon tools I mentioned also work with these things.

12:27 &lt;walkerma&gt; We can certainly ask Antony, though someone ( dmacks ??) may need to write a script.

12:27 &lt;+dmacks&gt; Or are we best just using the list of pages that transclude the chembox

12:27 &lt;walkerma&gt; No, the list is taken from a much bigger collection

12:28 &lt;walkerma&gt; I believe some articles don't have boxes at all - these have been noted

12:29 &lt;walkerma&gt; Beetstra: Are you around?

12:31 &lt;walkerma&gt; I had hoped that Axiosaurus would be here, because the other remaining item is the inorganics and organometallics

12:32 &lt;walkerma&gt; For those, we often only have an article name, IUPAC name and a molecular formula that we can rely on.

12:32 &lt;walkerma&gt; InChIs don't work well with inorganics

12:33 &lt;walkerma&gt; dmacks: Would you be able to write a script to upload things to WP?

12:34 &lt;walkerma&gt; Or should we stick to working with the SDF?

12:35 &lt;+dmacks&gt; I've never scripted uploads before, but could give it a try. I see some examples in user-space of code.

12:36 &lt;walkerma&gt; If it's a lot of work, don't bother, but if it's something interesting to you and easy, then by all means have a go!

12:36 &lt;+dmacks&gt; okidoke

12:36 &lt;walkerma&gt; Would you have any time to check structures for charged forms?

12:37 &lt;+dmacks&gt; Sure.

12:37 &lt;+dmacks&gt; *anything* to avoid grading lab reports!

12:38 &lt;walkerma&gt; I concur with that! We have spring break coming up, and although I'll be away, this is something I can work on.

12:38 &lt;walkerma&gt; I think it should be fairly quick to do, and if the structures are editable from within the file the fixing should be fast too.

12:39 &lt;walkerma&gt; Well, do you have any thoughts on the carbohydrates issue?

12:39 &lt;walkerma&gt; (Hopefully Antony will arrive soon)

12:40 &lt;Traveler6&gt; I've been trying to get to the transcripts, but it ia imposs whilst the meeting is on. I'll have to look at it later. So far my contribution can only be "ear-lending"...but your work sounds interesting

12:40 &lt;+dmacks&gt; If we're trying to have infoboxes be self-consistent, then "whatever the lovingly-validated CAS# represents"

12:40 &lt;+dmacks&gt; Do CAS represent specific forms (furanose vs open-chain)?

12:41 &lt;walkerma&gt; I believe they do; they simply represent whatever an author puts into a paper

12:41 &lt;+dmacks&gt; Traveler6: no problem...glad to hear any thoughts you have later too.

12:41 &lt;walkerma&gt; Traveler6: I agree with dmacks there

12:42 &lt;walkerma&gt; But we also need to resolve this issue anyway.

12:42 &lt;+dmacks&gt; Yes. Given the choice (since if CAS is specific and there are multiple specific forms, we can choose which is the main one used in the article/infobox.

12:43 &lt;+dmacks&gt; (vs "related structures" or "other forms" lists/etc)

12:43 &lt;+dmacks&gt; But I don't have a feeling which should be the main one.

12:44 &lt;walkerma&gt; PC would object at this point; I think we may need to have one CAS# for the unspecified form (with correct stereochem) which would go with the article title, then another CAS# to go with the specific structure drawn

12:45 &lt;walkerma&gt; (PC would say the CAS# should match the article name, which is our primary key)

12:46 &lt;+dmacks&gt; Makes sense. "Whatever is no more specific than what the article is"?

12:46 &lt;walkerma&gt; Yes, good definition

12:47 &lt;walkerma&gt; OK: Now the real headache. What should the structure be - open chain or cyclic form?

12:47 &lt;+dmacks&gt; I don't know how to implement that, though. Gotta draw *somethiing*, which is going to be more specific than a non-specific article-name.

12:48 &lt;walkerma&gt; The open chain form has the advantage of simplicity, and is traditional with Fischer projections

12:48 &lt;walkerma&gt; BUT

12:48 &lt;walkerma&gt; The cyclic form seems more appropriate for cases like sucrose

12:48 &lt;walkerma&gt; ie polysaccharides

12:49 &lt;walkerma&gt; With cyclic forms, though, you have to worry about alpha vs beta

12:49 &lt;+dmacks&gt; (sucrose is bad example because it's anomeric ether, not openable, but yeah)

12:50 &lt;walkerma&gt; We also have pyranoses vs furanoses to worry about!

12:50 &lt;+dmacks&gt; closed is probably more familiar to readers other than organikers.

12:51 &lt;walkerma&gt; Do you know how these are handled elsewhere?

12:52 &lt;+dmacks&gt; No:(

12:52 * dmacks hasn't done any sugar chemistry.

12:53 &lt;walkerma&gt; I haven't either, or if I did as an undergrad (<=1981) I've forgotten. I'm thinking that we may need to handle these on a case by case basis.

12:54 &lt;Traveler6&gt; With hexoses is it not easier to draw the di-saccharide shape than the hexagonal one, or is this a silly question ? (one has to start somewhere)

12:55 &lt;walkerma&gt; Do you mean the open chain shape?

12:56 &lt;Traveler6&gt; I thought the linking there is shown by long lines

12:57 &lt;+dmacks&gt; Traveler6: You mean "how to draw" a given structure (example: where to put the bond that closes the ring.

12:57 &lt;+dmacks&gt; ?

12:57 &lt;walkerma&gt; Fischer projections?

12:57 &lt;Traveler6&gt; Whether that could be applied to polys I'd have to reflect upon, that is why I doubted myself

12:58 &lt;+dmacks&gt; Lots of older literature does a linear/condensed structure and then "long bonds" on top to close rings.

12:59 &lt;walkerma&gt; One problem I think is that Fischer projections only really work well for monosaccharides, IMHO

12:59 &lt;+dmacks&gt; But we have a deeper problem on Wikipedia...should we even be having a ring at all.

13:00 &lt;walkerma&gt; As I understand it, pretty much all polysaccharides are based on rings, so I think we will have to go with that

13:00 &lt;+dmacks&gt; It can be done...chain next to another chain. Actually illustrates cross-linking quite well. But annoying as heck to draw it.

13:00 &lt;walkerma&gt; And annoying/ugly to look at, IMHO

13:00 &lt;Traveler6&gt; I think, that that was what I was thinking about, as in the hexagonal repro you generally use thick lines and thin lines to make it look stereo, which can complicate the drawing

13:00 &lt;+dmacks&gt; Concurred.

13:01 &lt;walkerma&gt; In papers I've read on natural products with attached sugars (often poly), they always use cyclic forms

13:01 &lt;walkerma&gt; So I think we need to follow the convention there.

13:01 &lt;walkerma&gt; Perhaps we could have a sub-page of the style guide which defines a "principal form" for each one of the monosaccharides - there is at least a fairly limited (certainly finite) number - and we could handle derivatives (such as phostphates) from those defined structures. With important polysaccharides like sucrose we could have defined structures too. Could that work?

13:02 &lt;Traveler6&gt; The hexagonal repro is definitely prettier

13:02 &lt;+dmacks&gt; Yeah.

13:02 &lt;+dmacks&gt; I think in *most* cases (maybe all except mono-sacc's themselves), the ring is closed by definition (not free anomeric OH), so may as well standardize on it.

13:03 &lt;walkerma&gt; Yes

13:05 &lt;walkerma&gt; Traveler6: Does that sound viable?

13:06 &lt;+dmacks&gt; (The issue of *how* to draw it (hexagon with straight lines, hexagon with wedge/dot, etc) is separate)

13:06 * Beetstra 'enters' the room ..

13:08 &lt;walkerma&gt; Hello! We're trying to resolve the old carbohydrate problem. I made a proposal just a couple of minutes ago that is "on the table"

13:08 &lt;+dmacks&gt; Speaking of confusingly drawn, /me looks at Sucrose, makes plea that all representations try to have consistent perspective unless "good reason" for a different one.

13:09 * Beetstra tries to read back ..

13:09 &lt;+dmacks&gt; (...for any given compound, not "globally on WP)

13:09 &lt;+Beetstra&gt; Hi LouisBB, welcome here!

13:09 &lt;Traveler6&gt; Certainly. I concur. I also just thought, that there are some nucleic acid structures involving sugars. Would that be too complicated to include here, and should we draw in biochem as well, or is that outside our scope?

13:10 &lt;Traveler6&gt; Hello Beetstra, nice to meet you again

13:10 &lt;walkerma&gt; There is no formal biochem project, though there is a molecular biology group that sometimes gets involved.

13:11 &lt;walkerma&gt; I think sucrose uses the [Haworth projection]], which is a traditional way of drawing these things.

13:11 &lt;+Beetstra&gt; Can someone summarise the carbohydrate problem for me, please?

13:12 &lt;walkerma&gt; (The project is [Wikipedia:WikiProject Molecular and Cellular Biology]])

13:12 &lt;walkerma&gt; WikiProject Molecular and Cellular Biology

13:12 &lt;walkerma&gt; The problem is which form to use in the structure box

13:12 &lt;walkerma&gt; open or cyclic; alpha or beta; furanose or pyranose

13:14 &lt;+Beetstra&gt; OK, that is what I guessed

13:14 &lt;+Beetstra&gt; What would IUPAC recommend?

13:14 &lt;walkerma&gt; We seem to be agreeing that a cyclic form will be needed. I'm proposing that we pick a "principal form" for each monosaccharide, and use that as our choice for derivatives too

13:14 &lt;Traveler6&gt; As there is an "alternative names" entry there could be an "alternative notations" entry as well

13:15 &lt;walkerma&gt; I think IUPAC doesn't need to worry about such things

13:15 &lt;+Beetstra&gt; oh

13:15 &lt;+Beetstra&gt; This problem is similar to the amino acid problem .. where to put the protons ..

13:15 &lt;walkerma&gt; More complex than that, IMHO

13:16 &lt;+Beetstra&gt; Yes, indeed

13:16 &lt;Traveler6&gt; Alternative "representation"" I mean

13:16 &lt;+Beetstra&gt; I think that wikipedia starts to need an "IUPAC" guideline of itself ..

13:16 &lt;+Beetstra&gt; I think that subpage of the chem styleguide is a good one

13:17 &lt;+Beetstra&gt; That could include other problem molecules as well ..

13:18 &lt;walkerma&gt; I just think that if we try to say, "Let's go with alpha pyranoses" someone will say, "But fooanose is NEVER in that form" and we could argue till the cows come home

13:18 &lt;walkerma&gt; So we should just accept that this requires a case by case basis

13:19 &lt;+Beetstra&gt; That is also an exception that you can write into a rule .. if the pyranose form is reasonably stable, then draw that one, otherwise draw the normal form.

13:20 &lt;+dmacks&gt; Makes sense.

13:20 &lt;+dmacks&gt; ("normal"==?)

13:20 &lt;walkerma&gt; But people may still argue about these things - I think we need somewhere where we say, "We have agreed it is THIS form"

13:21 &lt;walkerma&gt; dmacks: Yes!

13:21 &lt;+Beetstra&gt; Well, if it is not the pyranose form which you buy from Aldrich .. which form is it then ..

13:22 &lt;+dmacks&gt; Beetstra: you made a distinction between "pyranose" and "normal"...what specifically did you mean?

13:24 &lt;Traveler6&gt; An interjection: Excuse me for a natural break (for Hector, my dog) 'see you later

13:24 &lt;+dmacks&gt; Thanks for joining us, Traveler6!

13:25 &lt;walkerma&gt; Yes, thanks!

13:26 &lt;+Beetstra&gt; See you later, Louis

13:26 &lt;+Beetstra&gt; Well, for most sugars the pyranose is a reasonably normal form .. not always the most stable, but OK

13:26 &lt;+Beetstra&gt; so that is the choice structure

13:27 &lt;+Beetstra&gt; But for those where the pyranose form simply does not occur, then there must be for that one literature on what is the 'more stable' form ..

13:27 &lt;+Beetstra&gt; Or do we want to force the hierarchy .. alpha-pyranose, open form, ...

13:27 * Beetstra has to leave as well .. maybe online later

13:28 &lt;walkerma&gt; This sounds like a plan, anyway

13:29 &lt;walkerma&gt; I think we could say on a subpage: Here are the standard forms; if not listed, then use the pyranose by default, but another form if that is the commonly accepted term

13:29 &lt;walkerma&gt; form, not term

13:29 &lt;+dmacks&gt; yeah...as long as we can get a preference for "something that exists ~stably", and then a preference for what to do when we have choices, don't care too much *what* choice we decide is best.

13:29 &lt;walkerma&gt; As long as we agree to standardise on that one form

13:29 &lt;+dmacks&gt; yeah

13:30 &lt;+Beetstra&gt; sounds good!

13:30 &lt;+Beetstra&gt; later!

13:30 -!- Beetstra [n=djbeetst@Wikimedia/Beetstra] has quit ["Bye Bye"]

13:30 &lt;walkerma&gt; OK, I think we should close things there. I'll speak with Antony about getting the SDF file sent out

13:30 &lt;+dmacks&gt; great

13:30 &lt;walkerma&gt; Thanks a lot!

13:30 &lt;+dmacks&gt; Thanks for hosting the meeting!

--- Log closed Tue Mar 18 13:30:52 DST 2008