User:Walkerma/SandboxB

Wikipedia:WikiProject Stargate

Contacted April 08, 2006. 8 articles suggested so far.

As with Star Trek, a common criticism of our pages is that they start from a fictional rather than nonfictional point of view; however most agree that this is ridiculous considering the subject matter is inherently fictional. Nevertheless, an effort has been made to look at articles from a nonfictional perspective.

Contact with WP Stargate
Assessment	Article	Date	Comments
These are article drugboxes and chemboxes checked by User:ChemSpiderMan, using PubChem, CAS no. checks, ChemSpider, ACD/Name. See this paper for a recent paper on errors in IUPAC name generators; ACD/Name is clearly the best. The original PDF includes the actual structures, and also lists a few that have been fixed. You can leave comments below. Thanks for helping! Note: entries that have been fixed for more than two weeks have been removed from this list, assuming they have no residual problem associated with them. Xylulose_5-phosphate As drawn this is not a phosphate. This is a dihydrogen phosphate. EDIT: Redraw the structure. Comments Done. Most databases show it as the dihydrogen phosphate, though. Fvasconcellos (t·c) 14:02, 9 January 2008 (UTC) We should probably discuss this in our IRC on Tuesday. Yellow_2G ChemSpider suggests the CAS NUMBER is for the free acid but I am not sure. Can anyone confirm? Beta-hydroxybutyryl-CoA I believe that coenzyme A should be fully protonated yet the majority of sites are charged. A WP-CHEM needs to be made about all CoEnZA compounds for consistency EDIT: WP-CHEM decision required Comments Betanin The structure on ChemSpider is [1] EDIT: Decision to be made about what the structure is , WP-CHEM decision Comments As a betalain, I'm pretty sure betanin exists as a zwitterion. Fvasconcellos (t·c) 14:10, 9 January 2008 (UTC) Bis(2,4,5-trichlorophenyl-6-carbopentoxyphenyl)oxalate The CAS number is listed below as 1165-91-9 ChemSpider lists the structure below for that number: [2] Also…ChemExper says [3] I DON’T know which structure is associated with that CAS Number. Can it be confirmed? The structure as drawn is: EDIT: Someone confirm the CAS Number. Also, the molecular formula is INCORRECT Comments CAS 1165-91-9 is bis(2,4,6-trichlorophenyl)oxalate (TCPO). This compound (CPPO) is, according to eMolecules, 30431-54-0 and 102579-84-0 ... Molecular formula fixed. Fvasconcellos (t·c) 00:10, 9 January 2008 (UTC) Bis(triphenylphosphine)iminium_chloride Ugly structure . I prefer… EDIT: WP-CHEM choose to replace structure Comments I disagree, I like the fact that the structure shows how the P is tetrahedral. Walkerma (talk) 05:42, 8 January 2008 (UTC) I agree that it communicates the Tetrahedral nature better but the overlap, for me, looks confusing. The question is whether to reduce confusion or communicate tetrahedral nature. I'll leave the decision to WP:Chem of course.--ChemSpiderMan (talk) 05:56, 8 January 2008 (UTC) Why not replace the phenyl rings with C6H5 or Ph? And note Ph = (benzene ring) in the image? --Rifleman 82 (talk) 17:51, 14 February 2008 (UTC) Bismarck_brown_Y Insert Chembox Insert IUPAC Name = 4,4'-[1,3-phenylenedi(E)diazene-2,1-diyl]dibenzene-1,3-diamine CONFIRM E/Z Comments For CAS#10114-58-6, Chemical Abstracts gives the 2HCl salt and has undefined double-bond geometry. For the neutral structure in the image Chemical Abstracts has CAS#1052-38-6, again with undefined double-bond geometry, but lists Basic brown G as a synonym, but not Bismark brown Y. -- Ed (Edgar181) 17:07, 10 January 2008 (UTC) Bistriflimide I disagree with the systematic name EDIT: Replace name if agreed. Comments This is being debated by IUPAC, see [4]. Walkerma (talk) 05:42, 8 January 2008 (UTC) Now...you are a wealth of information Walkerma! --ChemSpiderMan (talk) 05:51, 8 January 2008 (UTC) Bromocresol_purple The InChI String has been generated with the wrong settings and therefore generates the WRONG structure. The correct InChI is: InChI=1/C21H17BrO5S/c1-12-9-14(7-8-18(12)23)21(15-10-13(2)20(24)17(22)11-15)16-5-3-4-6-19(16)28(25,26)27-21/h3-11,23-24H,1-2H3 Comments FIXED: SORT OF. I replaced the InChI from the ChemBox with Physchim62's {{InChI}}, but now the InChI intrudes slightly into the Chembox. I've requested a modification which (if doable) should fix this. Walkerma (talk) 07:09, 9 January 2008 (UTC) The WP:CHEM team should be interested in this email send out today for comments. This is from the InChI team and is encouraging the adoption of standard settings. This was the issue with Bromocresol Purple...settings were chosen. If and when these standards were adopted then these problems should go away. We will be making these settings on our [ http://www.chemspider.com/InChI.asmx InChI Web service] for everyone to use. --ChemSpiderMan (talk) 22:02, 10 January 2008 (UTC) Calcium_carbimide The name says it’s a TRIcarboxylate but it is only doubly charged. Assuming it is then you need a 2:3 stoichiometry with Calcium Pubchem shows the neutral compound http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6335910 ChemSpider suggests it’s a 1:1 ratio. So, I think just the name is wrong? calcium 2-(carboxymethyl)-2-hydroxysuccinate - methylcyanamide (1:1) EDIT: Change the name? Comments Carthamin ChemSpider says: [5] The masses and the formulae are different. Which one is correct??? The name is: 3-[(Z)-{5-(β-L-Glucopyranosyloxy)-4,5-dihydroxy-3-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-2,6-dioxo-3-cyclohexen-1-ylidene}methyl]-1,2,6-trihydroxy-5-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-4-oxo-2,5-cyclohexadien-1-yl β-D-glucopyranoside Comments The mass and formula in the Wikipedia article are consistent with those reported in Chemical Abstracts, PubChem, EINECS and the Merck Index. ChemSpider appears to be the outlier.-- Ed (Edgar181) 16:07, 9 January 2008 (UTC) I click on the emolecules link and find three compounds...two of mass of 910.78 but with different logP values (so they should be different molecules since they were calculated by the same algorithm) and one with a mass of 450. Then I click on the PubChem link and got a structure of mass 562 and a TOTALLY different structure..so, at least the PubChem link needs changing. The PubChem link is http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=11968069. I checked for the PubChem based InChi and found the structure on ChemSpider here but under the name Carthamine not Carthamin. Thanks to this work I have now curated out the INCORRECT names associated with the structure on ChemSpider.. All carmathine related names are removed from [here http://www.chemspider.com/Chemical-Structure.16736410.html]. I'll take CAS as the definitive call on this one. Ed..thanks for the help on this one.--ChemSpiderMan (talk) 05:24, 10 January 2008 (UTC) One more comment on this. Ed commented on the Carmathin record "I don't understand why emolecules has inconsistent data." This is in regards to linking the CAS number from Carmathin to eMolecules and seeing three different structures. This is not a comment against eMolecules as the same issue WILL exist on PubChem and CHemSPider in theory. NONE of these databases should be the primary reprepsentatives for CAS Numbers. I don't think the CAS Number should be linked to ANY external database in the way implemented now...that is doing a CAS number search. Why? The record on Wikipedia has the structures already. What is the value of linking the CAS Number. It's fine to link the PubChem ID, the eMolecules ID or even the ChemSpider ID but this will go directly to a record. However, a CAS Number search can take you to many structures with the same CAS number and create confusion.--ChemSpiderMan (talk) 05:08, 11 January 2008 (UTC) Coenzyme_F420 Add the structure : http://www.chemspider.com/Search.aspx?q=coenzyme+F420 13,16,17,18-tetrahydroxy-11-methyl-5,10-dioxo-19-(2,4,8-trioxo-1,3,4,8-tetrahydropyrimido[4,5-b]quinolin-10(2H)-yl)-12,14-dioxa-4,9-diaza-13-phosphanonadecane-1,3,8-tricarboxylic acid 13-oxide Comments Ethocybin Should the molecule in Wikipedia be drawn as charged or as above with the name 3-[2-(diethylamino)ethyl]-1H-indol-4-yl dihydrogen phosphate Comments F430 Please confirm my representation below. The SMILES string is: [Ni].O=C(O)CC[C@@H]1C\6=N/[C@]2(NC(=O)C[C@@]12C)C[C@@H]3/N=C (\[C@](CC(=O)N)(C)[C@@H]3CCC(=O)O)C[C@H]5/N=C4/C(C(=O)CC[C@H ]4[C@@H]5CC(=O)O)=C7\[N-]/C(=C/6)[C@@H](CC(=O)O)[C@@H]7CCC(=O)O From http://www.chemspider.com/Chemical-Structure.4573710.html I find: 73145-13-8 (can someone check the CAS number) Coenzyme F430 factor 430 Factor F430 Comments FADH2 Confirm the structure I have drawn and add the name. [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate Comments Fructose-1-phosphate Problems with this one…. The name does not have stereochemistry The name converts to the cyclic form: The PubCHem link is to the cyclic form [6] Is there a WP:CHEM policy about sugars in linear, cyclized form? The CAS number links to both linear and cyclic forms. Compare it to: Fructose_1,6-bisphosphate which is cyclic Comments (Also see below) Fructose_1,6-bisphosphate I think there needs to be a WP:CHEM statement on sugar representations. Also, protonation states ESPECIALLY if InChIKeys are going to be generated… [(2S,3S,4S,5R)-2,3,4-trihydroxytetrahydrofuran-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)] RNBGYGVWRKECFJ-CERMHHMHBJ is for the structure above RNBGYGVWRKECFJ-GSMOWLIGBO is for the structure in the ChemBox Consistency Issues Record to Record There needs to be consistency around linear vs cyclic, charged versus uncharged, named with stereo or not. Comments Fructose_6-phosphate The structure as drawn is not consistent with the name…which is right? [(2R,3S,4S,5S)-3,4,5-trihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate Comments Fumonisin_B2 Formatting issues: From ChemSpider: [7] I have not proven the structure to be correct though. But it is consistent with PubChem. Comments Gamma-amanitin No structure. This structure is in ChemSpider… [8] It has no stereochemistry Comments Geranyl_pyrophosphate A decision needs to be made about charged state/protonation state. The structure does not coincide with the SMILES or the PubChem link. (2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate Comments Geranylgeranyl_pyrophosphate Same issue with protonated/charged states – the MF and Mass do not match the structure Comments Glycerate_3-phosphate Name does not match the structure. Glycerate phosphate, (2R)-2-hydroxy-3-phosphonooxy-propanoate, (2R)-2-hydroxy-3-(phosphonooxy)propanoic acid. EDIT: Decide what the structure should be and name appropriately Comments Guanosine_diphosphate_mannose I think a better image is at: [[9]] IUPAC NAME [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate Comments I added the IUPAC name, but a suitable structure needs to be drawn (with clear copyright) Redrawn from Chemspider's SMILES. Please let me know if I made a mistake! --Rifleman 82 (talk) 17:59, 14 February 2008 (UTC) HMG-CoA Add IUPAC Name and add stereochemistry to the structure. (9R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8,21-trimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide Comments I added the IUPAC name, structure still needs to be done. Comments Heme_b Compare the Wikipedia structure with the PubChem structure and notice the difference in MF. Also, what is the best representation for the structure? WP or PubChem? I'd like to know the consensus to reproduce it in ChemSpider since there are THREE representations in CS [10] Comments Heme c The link in PubChem goes to the identifiers HEC or Hem. PubChem has heme c as [11] What is the correct structure? Hippuristanol No structure. I suggest validating the full stereochemistry here: but the structure is available on ChemSpider here Comments I've uploaded a structure based on that found at the discoverer's website; does it match the one currently at CS? It also needs an IUPAC name; I use the free version of ChemSketch (only names compounds up to 50 atoms or 3 cycles), and my skills aren't up to that :) Fvasconcellos (t·c) 00:33, 21 January 2008 (UTC) ChemDraw 11 cannot generate a name either. A minor remark: IUPAC recommends not to attach wedged bonds to each other like in this structure but to use a wedged H. Сасусlе 00:53, 21 January 2008 (UTC) ACD/Name CAN generate a name "(2R,2'R,4S,4a'S,4b'S,5'S,6a'S,6b'R,7'R,9a'S,10a'S,10b'S,12a'S)-4,4a',5,5,6a',7'-Hexamethylicosahydro-3H-spiro[furan-2,8'-naphtho[2',1':4,5]indeno[2,1-b]furan]-2',5',7'-triol" The structure as drawn is incorrect I believe since a number of stereocenters are not defined. I will submit the actual structure with full stereo onto ChemSpider and send you the link.--ChemSpiderMan (talk) 02:56, 22 January 2008 (UTC) Chemical Abstracts gives a structure for hippuristanol with all the stereocenters defined. CAS#80442-78-0. I've added a corresponding image and SMILES to the article. I'm unable to generate and IUPAC name. -- Ed (Edgar181) 14:10, 22 January 2008 (UTC) The structure is consistent with the one on ChemSpider now http://www.chemspider.com/Chemical-Structure.21105577.html. The IUPAC Name is above in the text...--ChemSpiderMan (talk) 17:02, 22 January 2008 (UTC) Thanks, and sorry about that; I've updated the SVG. Is there any way to break the SMILES string? Fvasconcellos (t·c) 19:21, 22 January 2008 (UTC) Hydrastine Hydrastine is lacking stereochemistry. Suggested structure is here. Suggested name is (3S)-6,7-dimethoxy-3-[(5R)-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-2-benzofuran-1(3H)-one Comments Should it be (+)-hydrastine or (−)-hydrastine? (+)-Hydrastine is (3R, 5S), not the other way round; (−)-hydrastine is all-R.[12] Fvasconcellos (t·c) 12:29, 20 January 2008 (UTC) Inositol_pentakisphosphate No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE As host of ChemSpider I grant Copyright to you...However, I don't think the images are of sufficient quality for you. I had started a conversation on Wikipedia previously about the possibility to generate PNG images off of ChemSpider but I don't think I received any feedback and we cannot do this right now because of the list of other things to do. It would be many weeks now before we could do it. i would suggest downloading the structure from ChemSPider into an appropriate package at the desktop and generate the PNG or SVG image from that package. I am opening the discussion here again about whether or not there is interest in us generating PNG/SVG images of the structures from ChemSpider for use on Wikipedia?--ChemSpiderMan (talk) 16:33, 20 January 2008 (UTC) Kallidin No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE Laminarin No structure. One is listed on ChemSpider that needs validating here. Comments MTSL The structure shown is: (an N-oxide) It says the name is: S-(2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate This converts to: (different structure, the corresponding amine) Comments Neocarzinostatin There is no structure on the record. This record is on ChemSpider for validation and inclusion here. Comments Looks like it's lacking a stereo descriptor? See reference 5 here and this, which also appear to show the most common orientation. Interestingly, PDB has plenty of crystal structures deposited for it, such as PDB: 1NCO​. Fvasconcellos (t·c) 12:49, 22 January 2008 (UTC) The structure at ChemSpider and the structure at "reference 5" linked above seem to be missing a double bond (exocyclic from the cyclopentane ring). Although Chemical Abstracts lists the structure as "No structure diagram available", I found a J. Org. Chem. reference from someone who actually made the compound and filled the chembox with the structure and data they report. That structure is the same as the one shown in 3 or 4 other recent journal articles I looked at. Our article refers to it as a "dienediyne" which is consistent with the structure I've added, but not the ChemSpider one. If anyone can double check me with other references, that would be nice. -- Ed (Edgar181) 12:29, 25 January 2008 (UTC) I have done some additional literature research but remain confused. An examination of PubChem shows the structure Edgar181 has drawn as the Neocarzinostatin chromophore rather than Neocarzinostatin itself. The difference is the one exocyclic bond. Since it has a MeSH annotation I am going to contact MeSH directly and get their comments. I DO agree that there are publications out there with the exocyclic double bond and labeled as Neocarzinostatin. For example 1. So, I'm not sure we're there yet.--ChemSpiderMan (talk) 15:15, 25 January 2008 (UTC) I've done a bit more reading too, and here's what I can tell. Neocarzinostatin is a complex of a small molecule (properly referred to as neocarzinostatin chromophore) bound to an amino acid, but the term neocarzinostatin sometimes gets used to refer to just the chromophore part. I think Wikipedia just needs a single article for neocarzinostatin and neocarzinostatin chromophore so I've tried to reword the article a bit to reflect this. The chembox is titled "neocarzinostatin chromophore" and the data in the box is for just this part (except that it now has two CAS numbers, each denoting what it corresponds to). The structure associated with CAS#79633-18-4, which I just added to the article, does indeed have the exocyclic double bond. Hopefully, this helps reduce the confusion instead of creating more. 15:37, 25 January 2008 (UTC) Yes, neocarzinostatin (properly holo-neocarzinostatin) is a protein-chromophore complex; see the PDB link I provided above. The protein alone would be "apo-neocarzinostatin", and the small molecule (prosthetic group) is the "neocarzinostatin chromophore", as Ed mentioned in the chembox. Fvasconcellos (t·c) 15:40, 25 January 2008 (UTC) Then it looks like we are dealing with an error of the absence of the double bond in other multiple databases? This includes KEGG and PubChem. I couldn't find it in eMolecules. ChemSpider is now corrected. The IUPAC Name (software generated) is: (1aS,5R,6R,6aE)-6-{[(2R,3R,4R,5R,6R)-4,5-Dihydroxy-6-methyl-3-(methylamino)tetrahydro-2H-pyran-2-yl]oxy}-1a-(2-oxo-1,3-dioxolan-4-yl)-2,3,8,9-tetradehydro-1a,5,6,9a-tetrahydrocyclopenta[5,6]cyclonona[1,2-b]oxiren-5-yl 2-hydroxy-7-methoxy-5-methyl-1-naphthoate. If you accept it either insert or let me know and I will.--ChemSpiderMan (talk) 16:01, 25 January 2008 (UTC) OK, I added it. -- Ed (Edgar181) 16:12, 25 January 2008 (UTC) Apparently, holo-neocarzinostatin has the proposed INN "zinostatin". Proposed INN list 74 has the structure as Ed drew it, with the double bond—so yes, it appears other databases are in error :) Fvasconcellos (t·c) 16:19, 25 January 2008 (UTC) Nile_blue The formula and the SMILES include chlorine. Should the image be a chloride salt ? EDIT: Decide on salt or not and make modifications Comments Norbaeocystin I think it’s a bad idea to hook a ChemBox to a PubChem or eMolecules search. When you click PubChem you get this: 45 HITS! http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=HistorySearch&WebEnvRq=1&db=pccompound&query_key=4&WebEnv=0WZ72yTPcueOePRfvFnsns4pyG6_yXI3zQjko-Hmmo0niFnKvuq0kSzEag9oycHVtGsi4aAsh5IvYR%40264662E1739B1F60_0066SID When you click eMolecules you get this: 0 hits http://www.emolecules.com/cgi-bin/search?t=ex&q=%5BNH3%2B%5DCCC1%3DCNC2%3DC1C%28OP%28%5BO-%5D%29%28O%29%3DO%29%3DCC%3DC2 The connections should be real to a 1:1 record. Same here: http://en.wikipedia.org/wiki/O-Acetylpsilocin Comments Pectic_acid No structure on Wikipedia/ The structure is here]. Comments Phosphopantetheine Structure needs stereochemistry and a IUPAC Name. ChemSpider says the structure is this. (3R)-3-hydroxy-4-({3-[(2-mercaptoethyl)amino]-3-oxopropyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen phosphate Comments Plicatic_acid I believe the structure might be wrong. The structure shown here should be validated. (1S,2S,3R)-1-(3,4-dihydroxy-5-methoxyphenyl)-2,3,7-trihydroxy-3-(hydroxymethyl)-6-methoxy-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid The ChemSpider record is here. Comments Pyrrolizidine Is Pyrrolizidine itself a naturally occurring alkaloid? It appears to be a fragment of the alkaloid. [13] Comments Pyrrolysine Should the carboxylic acid and amine be charged or neutral. The name suggests neutral N6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine Comments QS21 No structure on the record. Confirm this as the structure and add: (structure) Also see this. Comments Quaternium-15 Drawn as a cis-compound. Should it be a trans compound: [14] Comments Quercitron The label on the structure image suggests the structure is wrong…shouldn’t it be replaced.? Comments Quinoline_Yellow SS version is: [15] WS version is: Comments Ristocetin No structure on Wikipedia. Suggested structure is on ChemSpider [here]. Comments Roseophilin No structure on Wikipedia. Suggested structure on ChemSpider here. Comments S-Adenosyl_methionine Structure is not charge balanced because of the NH3 plus charge. Is there a counterion? Comments S-Allyl_cysteine The IUPAC name is not consistent with the structure. Actual IUPAC name should be: (2R)-3-(allylthio)-2-aminopropane-1,1-diol Comments No! No way is this a 1,1-diol! I think perhaps the current name is a little wrong, I suspect the person meant S-{2-propenyl}-L-cysteine - is this IUPAC though? Walkerma (talk) 05:03, 7 February 2008 (UTC) Comments back..no, clearly it is NOT a diol. I don't where this association came from. I checked back in my files and could not see why I said this. This is why we need eyes checking my comments. After 4800 structures they are tired eyes.--ChemSpiderMan (talk) 23:25, 7 February 2008 (UTC) Spirotryprostatin_A WP says mass is 365.43. Actual mass is 395.43. Comments The Chembox originally went with a different image, Image:Spirotryprostatin A.JPG, which is missing the methoxy group (Note, the Edmondson/Danishefsky paper draws this demethoxy compound too, as an analogue). Someone fixed the structure but not the formula or the mass. The formula should be C22H25N3O4 (mass 395), not C21H23N3O3 (mass 365), which was "correct" for the original structure. Now fixed. Sulforhodamine_B No structure for this article Structure is here]/ Comments Now done (More to follow) Status of Wikipedia Curation Project I am taking some downtime from the curation project for a few days to finish some other projects (publications, book chapter etc.) I will provide Walkerma with the latest report for him to post into this Sandbox for discussion. I am up to the letter "P", have already knocked out "X,Y,Z". I think it will be another couple of weeks before I return to the project. --ChemSpiderMan (talk) 14:22, 18 January 2008 (UTC) That's fine! I'm running around trying to get ready for the new semester (Monday), so I'm behind in transferring things over to here. We really appreciate the immense amount of work done so far! Look at the no. of daily hits on a typical page and you can see the importance of the work. Hope you can get caught up - though don't forget about us! Walkerma (talk) 14:58, 18 January 2008 (UTC) The link to the updated copy of the report issued on 011808 is here--ChemSpiderMan (talk) 13:37, 19 January 2008 (UTC) Another update to the curation report is here--ChemSpiderMan (talk) 05:21, 4 February 2008 (UTC) The link above has been updated to allow login without a password.--ChemSpiderMan (talk) 01:39, 6 February 2008 (UTC)
These are article drugboxes and chemboxes checked by User:ChemSpiderMan, using PubChem, CAS no. checks, ChemSpider, ACD/Name. See this paper for a recent paper on errors in IUPAC name generators; ACD/Name is clearly the best. The original PDF includes the actual structures, and also lists a few that have been fixed. You can leave comments below. Thanks for helping! Note: entries that have been fixed for more than two weeks have been removed from this list, assuming they have no residual problem associated with them. Xylulose_5-phosphate As drawn this is not a phosphate. This is a dihydrogen phosphate. EDIT: Redraw the structure. Comments Done. Most databases show it as the dihydrogen phosphate, though. Fvasconcellos (t·c) 14:02, 9 January 2008 (UTC) We should probably discuss this in our IRC on Tuesday. Yellow_2G ChemSpider suggests the CAS NUMBER is for the free acid but I am not sure. Can anyone confirm? Beta-hydroxybutyryl-CoA I believe that coenzyme A should be fully protonated yet the majority of sites are charged. A WP-CHEM needs to be made about all CoEnZA compounds for consistency EDIT: WP-CHEM decision required Comments Betanin The structure on ChemSpider is [16] EDIT: Decision to be made about what the structure is , WP-CHEM decision Comments As a betalain, I'm pretty sure betanin exists as a zwitterion. Fvasconcellos (t·c) 14:10, 9 January 2008 (UTC) Bis(2,4,5-trichlorophenyl-6-carbopentoxyphenyl)oxalate The CAS number is listed below as 1165-91-9 ChemSpider lists the structure below for that number: [17] Also…ChemExper says [18] I DON’T know which structure is associated with that CAS Number. Can it be confirmed? The structure as drawn is: EDIT: Someone confirm the CAS Number. Also, the molecular formula is INCORRECT Comments CAS 1165-91-9 is bis(2,4,6-trichlorophenyl)oxalate (TCPO). This compound (CPPO) is, according to eMolecules, 30431-54-0 and 102579-84-0 ... Molecular formula fixed. Fvasconcellos (t·c) 00:10, 9 January 2008 (UTC) Bis(triphenylphosphine)iminium_chloride Ugly structure . I prefer… EDIT: WP-CHEM choose to replace structure Comments I disagree, I like the fact that the structure shows how the P is tetrahedral. Walkerma (talk) 05:42, 8 January 2008 (UTC) I agree that it communicates the Tetrahedral nature better but the overlap, for me, looks confusing. The question is whether to reduce confusion or communicate tetrahedral nature. I'll leave the decision to WP:Chem of course.--ChemSpiderMan (talk) 05:56, 8 January 2008 (UTC) Why not replace the phenyl rings with C6H5 or Ph? And note Ph = (benzene ring) in the image? --Rifleman 82 (talk) 17:51, 14 February 2008 (UTC) Bismarck_brown_Y Insert Chembox Insert IUPAC Name = 4,4'-[1,3-phenylenedi(E)diazene-2,1-diyl]dibenzene-1,3-diamine CONFIRM E/Z Comments For CAS#10114-58-6, Chemical Abstracts gives the 2HCl salt and has undefined double-bond geometry. For the neutral structure in the image Chemical Abstracts has CAS#1052-38-6, again with undefined double-bond geometry, but lists Basic brown G as a synonym, but not Bismark brown Y. -- Ed (Edgar181) 17:07, 10 January 2008 (UTC) Bistriflimide I disagree with the systematic name EDIT: Replace name if agreed. Comments This is being debated by IUPAC, see [19]. Walkerma (talk) 05:42, 8 January 2008 (UTC) Now...you are a wealth of information Walkerma! --ChemSpiderMan (talk) 05:51, 8 January 2008 (UTC) Bromocresol_purple The InChI String has been generated with the wrong settings and therefore generates the WRONG structure. The correct InChI is: InChI=1/C21H17BrO5S/c1-12-9-14(7-8-18(12)23)21(15-10-13(2)20(24)17(22)11-15)16-5-3-4-6-19(16)28(25,26)27-21/h3-11,23-24H,1-2H3 Comments FIXED: SORT OF. I replaced the InChI from the ChemBox with Physchim62's {{InChI}}, but now the InChI intrudes slightly into the Chembox. I've requested a modification which (if doable) should fix this. Walkerma (talk) 07:09, 9 January 2008 (UTC) The WP:CHEM team should be interested in this email send out today for comments. This is from the InChI team and is encouraging the adoption of standard settings. This was the issue with Bromocresol Purple...settings were chosen. If and when these standards were adopted then these problems should go away. We will be making these settings on our [ http://www.chemspider.com/InChI.asmx InChI Web service] for everyone to use. --ChemSpiderMan (talk) 22:02, 10 January 2008 (UTC) Calcium_carbimide The name says it’s a TRIcarboxylate but it is only doubly charged. Assuming it is then you need a 2:3 stoichiometry with Calcium Pubchem shows the neutral compound http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6335910 ChemSpider suggests it’s a 1:1 ratio. So, I think just the name is wrong? calcium 2-(carboxymethyl)-2-hydroxysuccinate - methylcyanamide (1:1) EDIT: Change the name? Comments Carthamin ChemSpider says: [20] The masses and the formulae are different. Which one is correct??? The name is: 3-[(Z)-{5-(β-L-Glucopyranosyloxy)-4,5-dihydroxy-3-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-2,6-dioxo-3-cyclohexen-1-ylidene}methyl]-1,2,6-trihydroxy-5-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-4-oxo-2,5-cyclohexadien-1-yl β-D-glucopyranoside Comments The mass and formula in the Wikipedia article are consistent with those reported in Chemical Abstracts, PubChem, EINECS and the Merck Index. ChemSpider appears to be the outlier.-- Ed (Edgar181) 16:07, 9 January 2008 (UTC) I click on the emolecules link and find three compounds...two of mass of 910.78 but with different logP values (so they should be different molecules since they were calculated by the same algorithm) and one with a mass of 450. Then I click on the PubChem link and got a structure of mass 562 and a TOTALLY different structure..so, at least the PubChem link needs changing. The PubChem link is http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=11968069. I checked for the PubChem based InChi and found the structure on ChemSpider here but under the name Carthamine not Carthamin. Thanks to this work I have now curated out the INCORRECT names associated with the structure on ChemSpider.. All carmathine related names are removed from [here http://www.chemspider.com/Chemical-Structure.16736410.html]. I'll take CAS as the definitive call on this one. Ed..thanks for the help on this one.--ChemSpiderMan (talk) 05:24, 10 January 2008 (UTC) One more comment on this. Ed commented on the Carmathin record "I don't understand why emolecules has inconsistent data." This is in regards to linking the CAS number from Carmathin to eMolecules and seeing three different structures. This is not a comment against eMolecules as the same issue WILL exist on PubChem and CHemSPider in theory. NONE of these databases should be the primary reprepsentatives for CAS Numbers. I don't think the CAS Number should be linked to ANY external database in the way implemented now...that is doing a CAS number search. Why? The record on Wikipedia has the structures already. What is the value of linking the CAS Number. It's fine to link the PubChem ID, the eMolecules ID or even the ChemSpider ID but this will go directly to a record. However, a CAS Number search can take you to many structures with the same CAS number and create confusion.--ChemSpiderMan (talk) 05:08, 11 January 2008 (UTC) Coenzyme_F420 Add the structure : http://www.chemspider.com/Search.aspx?q=coenzyme+F420 13,16,17,18-tetrahydroxy-11-methyl-5,10-dioxo-19-(2,4,8-trioxo-1,3,4,8-tetrahydropyrimido[4,5-b]quinolin-10(2H)-yl)-12,14-dioxa-4,9-diaza-13-phosphanonadecane-1,3,8-tricarboxylic acid 13-oxide Comments Ethocybin Should the molecule in Wikipedia be drawn as charged or as above with the name 3-[2-(diethylamino)ethyl]-1H-indol-4-yl dihydrogen phosphate Comments F430 Please confirm my representation below. The SMILES string is: [Ni].O=C(O)CC[C@@H]1C\6=N/[C@]2(NC(=O)C[C@@]12C)C[C@@H]3/N=C (\[C@](CC(=O)N)(C)[C@@H]3CCC(=O)O)C[C@H]5/N=C4/C(C(=O)CC[C@H ]4[C@@H]5CC(=O)O)=C7\[N-]/C(=C/6)[C@@H](CC(=O)O)[C@@H]7CCC(=O)O From http://www.chemspider.com/Chemical-Structure.4573710.html I find: 73145-13-8 (can someone check the CAS number) Coenzyme F430 factor 430 Factor F430 Comments FADH2 Confirm the structure I have drawn and add the name. [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate Comments Fructose-1-phosphate Problems with this one…. The name does not have stereochemistry The name converts to the cyclic form: The PubCHem link is to the cyclic form [21] Is there a WP:CHEM policy about sugars in linear, cyclized form? The CAS number links to both linear and cyclic forms. Compare it to: Fructose_1,6-bisphosphate which is cyclic Comments (Also see below) Fructose_1,6-bisphosphate I think there needs to be a WP:CHEM statement on sugar representations. Also, protonation states ESPECIALLY if InChIKeys are going to be generated… [(2S,3S,4S,5R)-2,3,4-trihydroxytetrahydrofuran-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)] RNBGYGVWRKECFJ-CERMHHMHBJ is for the structure above RNBGYGVWRKECFJ-GSMOWLIGBO is for the structure in the ChemBox Consistency Issues Record to Record There needs to be consistency around linear vs cyclic, charged versus uncharged, named with stereo or not. Comments Fructose_6-phosphate The structure as drawn is not consistent with the name…which is right? [(2R,3S,4S,5S)-3,4,5-trihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate Comments Fumonisin_B2 Formatting issues: From ChemSpider: [22] I have not proven the structure to be correct though. But it is consistent with PubChem. Comments Gamma-amanitin No structure. This structure is in ChemSpider… [23] It has no stereochemistry Comments Geranyl_pyrophosphate A decision needs to be made about charged state/protonation state. The structure does not coincide with the SMILES or the PubChem link. (2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate Comments Geranylgeranyl_pyrophosphate Same issue with protonated/charged states – the MF and Mass do not match the structure Comments Glycerate_3-phosphate Name does not match the structure. Glycerate phosphate, (2R)-2-hydroxy-3-phosphonooxy-propanoate, (2R)-2-hydroxy-3-(phosphonooxy)propanoic acid. EDIT: Decide what the structure should be and name appropriately Comments Guanosine_diphosphate_mannose I think a better image is at: [[24]] IUPAC NAME [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate Comments I added the IUPAC name, but a suitable structure needs to be drawn (with clear copyright) Redrawn from Chemspider's SMILES. Please let me know if I made a mistake! --Rifleman 82 (talk) 17:59, 14 February 2008 (UTC) HMG-CoA Add IUPAC Name and add stereochemistry to the structure. (9R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8,21-trimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide Comments I added the IUPAC name, structure still needs to be done. Comments Heme_b Compare the Wikipedia structure with the PubChem structure and notice the difference in MF. Also, what is the best representation for the structure? WP or PubChem? I'd like to know the consensus to reproduce it in ChemSpider since there are THREE representations in CS [25] Comments Heme c The link in PubChem goes to the identifiers HEC or Hem. PubChem has heme c as [26] What is the correct structure? Hippuristanol No structure. I suggest validating the full stereochemistry here: but the structure is available on ChemSpider here Comments I've uploaded a structure based on that found at the discoverer's website; does it match the one currently at CS? It also needs an IUPAC name; I use the free version of ChemSketch (only names compounds up to 50 atoms or 3 cycles), and my skills aren't up to that :) Fvasconcellos (t·c) 00:33, 21 January 2008 (UTC) ChemDraw 11 cannot generate a name either. A minor remark: IUPAC recommends not to attach wedged bonds to each other like in this structure but to use a wedged H. Сасусlе 00:53, 21 January 2008 (UTC) ACD/Name CAN generate a name "(2R,2'R,4S,4a'S,4b'S,5'S,6a'S,6b'R,7'R,9a'S,10a'S,10b'S,12a'S)-4,4a',5,5,6a',7'-Hexamethylicosahydro-3H-spiro[furan-2,8'-naphtho[2',1':4,5]indeno[2,1-b]furan]-2',5',7'-triol" The structure as drawn is incorrect I believe since a number of stereocenters are not defined. I will submit the actual structure with full stereo onto ChemSpider and send you the link.--ChemSpiderMan (talk) 02:56, 22 January 2008 (UTC) Chemical Abstracts gives a structure for hippuristanol with all the stereocenters defined. CAS#80442-78-0. I've added a corresponding image and SMILES to the article. I'm unable to generate and IUPAC name. -- Ed (Edgar181) 14:10, 22 January 2008 (UTC) The structure is consistent with the one on ChemSpider now http://www.chemspider.com/Chemical-Structure.21105577.html. The IUPAC Name is above in the text...--ChemSpiderMan (talk) 17:02, 22 January 2008 (UTC) Thanks, and sorry about that; I've updated the SVG. Is there any way to break the SMILES string? Fvasconcellos (t·c) 19:21, 22 January 2008 (UTC) Hydrastine Hydrastine is lacking stereochemistry. Suggested structure is here. Suggested name is (3S)-6,7-dimethoxy-3-[(5R)-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-2-benzofuran-1(3H)-one Comments Should it be (+)-hydrastine or (−)-hydrastine? (+)-Hydrastine is (3R, 5S), not the other way round; (−)-hydrastine is all-R.[27] Fvasconcellos (t·c) 12:29, 20 January 2008 (UTC) Inositol_pentakisphosphate No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE As host of ChemSpider I grant Copyright to you...However, I don't think the images are of sufficient quality for you. I had started a conversation on Wikipedia previously about the possibility to generate PNG images off of ChemSpider but I don't think I received any feedback and we cannot do this right now because of the list of other things to do. It would be many weeks now before we could do it. i would suggest downloading the structure from ChemSPider into an appropriate package at the desktop and generate the PNG or SVG image from that package. I am opening the discussion here again about whether or not there is interest in us generating PNG/SVG images of the structures from ChemSpider for use on Wikipedia?--ChemSpiderMan (talk) 16:33, 20 January 2008 (UTC) Kallidin No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE Laminarin No structure. One is listed on ChemSpider that needs validating here. Comments MTSL The structure shown is: (an N-oxide) It says the name is: S-(2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate This converts to: (different structure, the corresponding amine) Comments Neocarzinostatin There is no structure on the record. This record is on ChemSpider for validation and inclusion here. Comments Looks like it's lacking a stereo descriptor? See reference 5 here and this, which also appear to show the most common orientation. Interestingly, PDB has plenty of crystal structures deposited for it, such as PDB: 1NCO​. Fvasconcellos (t·c) 12:49, 22 January 2008 (UTC) The structure at ChemSpider and the structure at "reference 5" linked above seem to be missing a double bond (exocyclic from the cyclopentane ring). Although Chemical Abstracts lists the structure as "No structure diagram available", I found a J. Org. Chem. reference from someone who actually made the compound and filled the chembox with the structure and data they report. That structure is the same as the one shown in 3 or 4 other recent journal articles I looked at. Our article refers to it as a "dienediyne" which is consistent with the structure I've added, but not the ChemSpider one. If anyone can double check me with other references, that would be nice. -- Ed (Edgar181) 12:29, 25 January 2008 (UTC) I have done some additional literature research but remain confused. An examination of PubChem shows the structure Edgar181 has drawn as the Neocarzinostatin chromophore rather than Neocarzinostatin itself. The difference is the one exocyclic bond. Since it has a MeSH annotation I am going to contact MeSH directly and get their comments. I DO agree that there are publications out there with the exocyclic double bond and labeled as Neocarzinostatin. For example 1. So, I'm not sure we're there yet.--ChemSpiderMan (talk) 15:15, 25 January 2008 (UTC) I've done a bit more reading too, and here's what I can tell. Neocarzinostatin is a complex of a small molecule (properly referred to as neocarzinostatin chromophore) bound to an amino acid, but the term neocarzinostatin sometimes gets used to refer to just the chromophore part. I think Wikipedia just needs a single article for neocarzinostatin and neocarzinostatin chromophore so I've tried to reword the article a bit to reflect this. The chembox is titled "neocarzinostatin chromophore" and the data in the box is for just this part (except that it now has two CAS numbers, each denoting what it corresponds to). The structure associated with CAS#79633-18-4, which I just added to the article, does indeed have the exocyclic double bond. Hopefully, this helps reduce the confusion instead of creating more. 15:37, 25 January 2008 (UTC) Yes, neocarzinostatin (properly holo-neocarzinostatin) is a protein-chromophore complex; see the PDB link I provided above. The protein alone would be "apo-neocarzinostatin", and the small molecule (prosthetic group) is the "neocarzinostatin chromophore", as Ed mentioned in the chembox. Fvasconcellos (t·c) 15:40, 25 January 2008 (UTC) Then it looks like we are dealing with an error of the absence of the double bond in other multiple databases? This includes KEGG and PubChem. I couldn't find it in eMolecules. ChemSpider is now corrected. The IUPAC Name (software generated) is: (1aS,5R,6R,6aE)-6-{[(2R,3R,4R,5R,6R)-4,5-Dihydroxy-6-methyl-3-(methylamino)tetrahydro-2H-pyran-2-yl]oxy}-1a-(2-oxo-1,3-dioxolan-4-yl)-2,3,8,9-tetradehydro-1a,5,6,9a-tetrahydrocyclopenta[5,6]cyclonona[1,2-b]oxiren-5-yl 2-hydroxy-7-methoxy-5-methyl-1-naphthoate. If you accept it either insert or let me know and I will.--ChemSpiderMan (talk) 16:01, 25 January 2008 (UTC) OK, I added it. -- Ed (Edgar181) 16:12, 25 January 2008 (UTC) Apparently, holo-neocarzinostatin has the proposed INN "zinostatin". Proposed INN list 74 has the structure as Ed drew it, with the double bond—so yes, it appears other databases are in error :) Fvasconcellos (t·c) 16:19, 25 January 2008 (UTC) Nile_blue The formula and the SMILES include chlorine. Should the image be a chloride salt ? EDIT: Decide on salt or not and make modifications Comments Norbaeocystin I think it’s a bad idea to hook a ChemBox to a PubChem or eMolecules search. When you click PubChem you get this: 45 HITS! http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=HistorySearch&WebEnvRq=1&db=pccompound&query_key=4&WebEnv=0WZ72yTPcueOePRfvFnsns4pyG6_yXI3zQjko-Hmmo0niFnKvuq0kSzEag9oycHVtGsi4aAsh5IvYR%40264662E1739B1F60_0066SID When you click eMolecules you get this: 0 hits http://www.emolecules.com/cgi-bin/search?t=ex&q=%5BNH3%2B%5DCCC1%3DCNC2%3DC1C%28OP%28%5BO-%5D%29%28O%29%3DO%29%3DCC%3DC2 The connections should be real to a 1:1 record. Same here: http://en.wikipedia.org/wiki/O-Acetylpsilocin Comments Pectic_acid No structure on Wikipedia/ The structure is here]. Comments Phosphopantetheine Structure needs stereochemistry and a IUPAC Name. ChemSpider says the structure is this. (3R)-3-hydroxy-4-({3-[(2-mercaptoethyl)amino]-3-oxopropyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen phosphate Comments Plicatic_acid I believe the structure might be wrong. The structure shown here should be validated. (1S,2S,3R)-1-(3,4-dihydroxy-5-methoxyphenyl)-2,3,7-trihydroxy-3-(hydroxymethyl)-6-methoxy-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid The ChemSpider record is here. Comments Pyrrolizidine Is Pyrrolizidine itself a naturally occurring alkaloid? It appears to be a fragment of the alkaloid. [28] Comments Pyrrolysine Should the carboxylic acid and amine be charged or neutral. The name suggests neutral N6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine Comments QS21 No structure on the record. Confirm this as the structure and add: (structure) Also see this. Comments Quaternium-15 Drawn as a cis-compound. Should it be a trans compound: [29] Comments Quercitron The label on the structure image suggests the structure is wrong…shouldn’t it be replaced.? Comments Quinoline_Yellow SS version is: [30] WS version is: Comments Ristocetin No structure on Wikipedia. Suggested structure is on ChemSpider [here]. Comments Roseophilin No structure on Wikipedia. Suggested structure on ChemSpider here. Comments S-Adenosyl_methionine Structure is not charge balanced because of the NH3 plus charge. Is there a counterion? Comments S-Allyl_cysteine The IUPAC name is not consistent with the structure. Actual IUPAC name should be: (2R)-3-(allylthio)-2-aminopropane-1,1-diol Comments No! No way is this a 1,1-diol! I think perhaps the current name is a little wrong, I suspect the person meant S-{2-propenyl}-L-cysteine - is this IUPAC though? Walkerma (talk) 05:03, 7 February 2008 (UTC) Comments back..no, clearly it is NOT a diol. I don't where this association came from. I checked back in my files and could not see why I said this. This is why we need eyes checking my comments. After 4800 structures they are tired eyes.--ChemSpiderMan (talk) 23:25, 7 February 2008 (UTC) Spirotryprostatin_A WP says mass is 365.43. Actual mass is 395.43. Comments The Chembox originally went with a different image, Image:Spirotryprostatin A.JPG, which is missing the methoxy group (Note, the Edmondson/Danishefsky paper draws this demethoxy compound too, as an analogue). Someone fixed the structure but not the formula or the mass. The formula should be C22H25N3O4 (mass 395), not C21H23N3O3 (mass 365), which was "correct" for the original structure. Now fixed. Sulforhodamine_B No structure for this article Structure is here]/ Comments Now done (More to follow) Status of Wikipedia Curation Project I am taking some downtime from the curation project for a few days to finish some other projects (publications, book chapter etc.) I will provide Walkerma with the latest report for him to post into this Sandbox for discussion. I am up to the letter "P", have already knocked out "X,Y,Z". I think it will be another couple of weeks before I return to the project. --ChemSpiderMan (talk) 14:22, 18 January 2008 (UTC) That's fine! I'm running around trying to get ready for the new semester (Monday), so I'm behind in transferring things over to here. We really appreciate the immense amount of work done so far! Look at the no. of daily hits on a typical page and you can see the importance of the work. Hope you can get caught up - though don't forget about us! Walkerma (talk) 14:58, 18 January 2008 (UTC) The link to the updated copy of the report issued on 011808 is here--ChemSpiderMan (talk) 13:37, 19 January 2008 (UTC) Another update to the curation report is here--ChemSpiderMan (talk) 05:21, 4 February 2008 (UTC) The link above has been updated to allow login without a password.--ChemSpiderMan (talk) 01:39, 6 February 2008 (UTC)
These are article drugboxes and chemboxes checked by User:ChemSpiderMan, using PubChem, CAS no. checks, ChemSpider, ACD/Name. See this paper for a recent paper on errors in IUPAC name generators; ACD/Name is clearly the best. The original PDF includes the actual structures, and also lists a few that have been fixed. You can leave comments below. Thanks for helping! Note: entries that have been fixed for more than two weeks have been removed from this list, assuming they have no residual problem associated with them. Xylulose_5-phosphate As drawn this is not a phosphate. This is a dihydrogen phosphate. EDIT: Redraw the structure. Comments Done. Most databases show it as the dihydrogen phosphate, though. Fvasconcellos (t·c) 14:02, 9 January 2008 (UTC) We should probably discuss this in our IRC on Tuesday. Yellow_2G ChemSpider suggests the CAS NUMBER is for the free acid but I am not sure. Can anyone confirm? Beta-hydroxybutyryl-CoA I believe that coenzyme A should be fully protonated yet the majority of sites are charged. A WP-CHEM needs to be made about all CoEnZA compounds for consistency EDIT: WP-CHEM decision required Comments Betanin The structure on ChemSpider is [31] EDIT: Decision to be made about what the structure is , WP-CHEM decision Comments As a betalain, I'm pretty sure betanin exists as a zwitterion. Fvasconcellos (t·c) 14:10, 9 January 2008 (UTC) Bis(2,4,5-trichlorophenyl-6-carbopentoxyphenyl)oxalate The CAS number is listed below as 1165-91-9 ChemSpider lists the structure below for that number: [32] Also…ChemExper says [33] I DON’T know which structure is associated with that CAS Number. Can it be confirmed? The structure as drawn is: EDIT: Someone confirm the CAS Number. Also, the molecular formula is INCORRECT Comments CAS 1165-91-9 is bis(2,4,6-trichlorophenyl)oxalate (TCPO). This compound (CPPO) is, according to eMolecules, 30431-54-0 and 102579-84-0 ... Molecular formula fixed. Fvasconcellos (t·c) 00:10, 9 January 2008 (UTC) Bis(triphenylphosphine)iminium_chloride Ugly structure . I prefer… EDIT: WP-CHEM choose to replace structure Comments I disagree, I like the fact that the structure shows how the P is tetrahedral. Walkerma (talk) 05:42, 8 January 2008 (UTC) I agree that it communicates the Tetrahedral nature better but the overlap, for me, looks confusing. The question is whether to reduce confusion or communicate tetrahedral nature. I'll leave the decision to WP:Chem of course.--ChemSpiderMan (talk) 05:56, 8 January 2008 (UTC) Why not replace the phenyl rings with C6H5 or Ph? And note Ph = (benzene ring) in the image? --Rifleman 82 (talk) 17:51, 14 February 2008 (UTC) Bismarck_brown_Y Insert Chembox Insert IUPAC Name = 4,4'-[1,3-phenylenedi(E)diazene-2,1-diyl]dibenzene-1,3-diamine CONFIRM E/Z Comments For CAS#10114-58-6, Chemical Abstracts gives the 2HCl salt and has undefined double-bond geometry. For the neutral structure in the image Chemical Abstracts has CAS#1052-38-6, again with undefined double-bond geometry, but lists Basic brown G as a synonym, but not Bismark brown Y. -- Ed (Edgar181) 17:07, 10 January 2008 (UTC) Bistriflimide I disagree with the systematic name EDIT: Replace name if agreed. Comments This is being debated by IUPAC, see [34]. Walkerma (talk) 05:42, 8 January 2008 (UTC) Now...you are a wealth of information Walkerma! --ChemSpiderMan (talk) 05:51, 8 January 2008 (UTC) Bromocresol_purple The InChI String has been generated with the wrong settings and therefore generates the WRONG structure. The correct InChI is: InChI=1/C21H17BrO5S/c1-12-9-14(7-8-18(12)23)21(15-10-13(2)20(24)17(22)11-15)16-5-3-4-6-19(16)28(25,26)27-21/h3-11,23-24H,1-2H3 Comments FIXED: SORT OF. I replaced the InChI from the ChemBox with Physchim62's {{InChI}}, but now the InChI intrudes slightly into the Chembox. I've requested a modification which (if doable) should fix this. Walkerma (talk) 07:09, 9 January 2008 (UTC) The WP:CHEM team should be interested in this email send out today for comments. This is from the InChI team and is encouraging the adoption of standard settings. This was the issue with Bromocresol Purple...settings were chosen. If and when these standards were adopted then these problems should go away. We will be making these settings on our [ http://www.chemspider.com/InChI.asmx InChI Web service] for everyone to use. --ChemSpiderMan (talk) 22:02, 10 January 2008 (UTC) Calcium_carbimide The name says it’s a TRIcarboxylate but it is only doubly charged. Assuming it is then you need a 2:3 stoichiometry with Calcium Pubchem shows the neutral compound http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6335910 ChemSpider suggests it’s a 1:1 ratio. So, I think just the name is wrong? calcium 2-(carboxymethyl)-2-hydroxysuccinate - methylcyanamide (1:1) EDIT: Change the name? Comments Carthamin ChemSpider says: [35] The masses and the formulae are different. Which one is correct??? The name is: 3-[(Z)-{5-(β-L-Glucopyranosyloxy)-4,5-dihydroxy-3-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-2,6-dioxo-3-cyclohexen-1-ylidene}methyl]-1,2,6-trihydroxy-5-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-4-oxo-2,5-cyclohexadien-1-yl β-D-glucopyranoside Comments The mass and formula in the Wikipedia article are consistent with those reported in Chemical Abstracts, PubChem, EINECS and the Merck Index. ChemSpider appears to be the outlier.-- Ed (Edgar181) 16:07, 9 January 2008 (UTC) I click on the emolecules link and find three compounds...two of mass of 910.78 but with different logP values (so they should be different molecules since they were calculated by the same algorithm) and one with a mass of 450. Then I click on the PubChem link and got a structure of mass 562 and a TOTALLY different structure..so, at least the PubChem link needs changing. The PubChem link is http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=11968069. I checked for the PubChem based InChi and found the structure on ChemSpider here but under the name Carthamine not Carthamin. Thanks to this work I have now curated out the INCORRECT names associated with the structure on ChemSpider.. All carmathine related names are removed from [here http://www.chemspider.com/Chemical-Structure.16736410.html]. I'll take CAS as the definitive call on this one. Ed..thanks for the help on this one.--ChemSpiderMan (talk) 05:24, 10 January 2008 (UTC) One more comment on this. Ed commented on the Carmathin record "I don't understand why emolecules has inconsistent data." This is in regards to linking the CAS number from Carmathin to eMolecules and seeing three different structures. This is not a comment against eMolecules as the same issue WILL exist on PubChem and CHemSPider in theory. NONE of these databases should be the primary reprepsentatives for CAS Numbers. I don't think the CAS Number should be linked to ANY external database in the way implemented now...that is doing a CAS number search. Why? The record on Wikipedia has the structures already. What is the value of linking the CAS Number. It's fine to link the PubChem ID, the eMolecules ID or even the ChemSpider ID but this will go directly to a record. However, a CAS Number search can take you to many structures with the same CAS number and create confusion.--ChemSpiderMan (talk) 05:08, 11 January 2008 (UTC) Coenzyme_F420 Add the structure : http://www.chemspider.com/Search.aspx?q=coenzyme+F420 13,16,17,18-tetrahydroxy-11-methyl-5,10-dioxo-19-(2,4,8-trioxo-1,3,4,8-tetrahydropyrimido[4,5-b]quinolin-10(2H)-yl)-12,14-dioxa-4,9-diaza-13-phosphanonadecane-1,3,8-tricarboxylic acid 13-oxide Comments Ethocybin Should the molecule in Wikipedia be drawn as charged or as above with the name 3-[2-(diethylamino)ethyl]-1H-indol-4-yl dihydrogen phosphate Comments F430 Please confirm my representation below. The SMILES string is: [Ni].O=C(O)CC[C@@H]1C\6=N/[C@]2(NC(=O)C[C@@]12C)C[C@@H]3/N=C (\[C@](CC(=O)N)(C)[C@@H]3CCC(=O)O)C[C@H]5/N=C4/C(C(=O)CC[C@H ]4[C@@H]5CC(=O)O)=C7\[N-]/C(=C/6)[C@@H](CC(=O)O)[C@@H]7CCC(=O)O From http://www.chemspider.com/Chemical-Structure.4573710.html I find: 73145-13-8 (can someone check the CAS number) Coenzyme F430 factor 430 Factor F430 Comments FADH2 Confirm the structure I have drawn and add the name. [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate Comments Fructose-1-phosphate Problems with this one…. The name does not have stereochemistry The name converts to the cyclic form: The PubCHem link is to the cyclic form [36] Is there a WP:CHEM policy about sugars in linear, cyclized form? The CAS number links to both linear and cyclic forms. Compare it to: Fructose_1,6-bisphosphate which is cyclic Comments (Also see below) Fructose_1,6-bisphosphate I think there needs to be a WP:CHEM statement on sugar representations. Also, protonation states ESPECIALLY if InChIKeys are going to be generated… [(2S,3S,4S,5R)-2,3,4-trihydroxytetrahydrofuran-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)] RNBGYGVWRKECFJ-CERMHHMHBJ is for the structure above RNBGYGVWRKECFJ-GSMOWLIGBO is for the structure in the ChemBox Consistency Issues Record to Record There needs to be consistency around linear vs cyclic, charged versus uncharged, named with stereo or not. Comments Fructose_6-phosphate The structure as drawn is not consistent with the name…which is right? [(2R,3S,4S,5S)-3,4,5-trihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate Comments Fumonisin_B2 Formatting issues: From ChemSpider: [37] I have not proven the structure to be correct though. But it is consistent with PubChem. Comments Gamma-amanitin No structure. This structure is in ChemSpider… [38] It has no stereochemistry Comments Geranyl_pyrophosphate A decision needs to be made about charged state/protonation state. The structure does not coincide with the SMILES or the PubChem link. (2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate Comments Geranylgeranyl_pyrophosphate Same issue with protonated/charged states – the MF and Mass do not match the structure Comments Glycerate_3-phosphate Name does not match the structure. Glycerate phosphate, (2R)-2-hydroxy-3-phosphonooxy-propanoate, (2R)-2-hydroxy-3-(phosphonooxy)propanoic acid. EDIT: Decide what the structure should be and name appropriately Comments Guanosine_diphosphate_mannose I think a better image is at: [[39]] IUPAC NAME [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate Comments I added the IUPAC name, but a suitable structure needs to be drawn (with clear copyright) Redrawn from Chemspider's SMILES. Please let me know if I made a mistake! --Rifleman 82 (talk) 17:59, 14 February 2008 (UTC) HMG-CoA Add IUPAC Name and add stereochemistry to the structure. (9R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8,21-trimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide Comments I added the IUPAC name, structure still needs to be done. Comments Heme_b Compare the Wikipedia structure with the PubChem structure and notice the difference in MF. Also, what is the best representation for the structure? WP or PubChem? I'd like to know the consensus to reproduce it in ChemSpider since there are THREE representations in CS [40] Comments Heme c The link in PubChem goes to the identifiers HEC or Hem. PubChem has heme c as [41] What is the correct structure? Hippuristanol No structure. I suggest validating the full stereochemistry here: but the structure is available on ChemSpider here Comments I've uploaded a structure based on that found at the discoverer's website; does it match the one currently at CS? It also needs an IUPAC name; I use the free version of ChemSketch (only names compounds up to 50 atoms or 3 cycles), and my skills aren't up to that :) Fvasconcellos (t·c) 00:33, 21 January 2008 (UTC) ChemDraw 11 cannot generate a name either. A minor remark: IUPAC recommends not to attach wedged bonds to each other like in this structure but to use a wedged H. Сасусlе 00:53, 21 January 2008 (UTC) ACD/Name CAN generate a name "(2R,2'R,4S,4a'S,4b'S,5'S,6a'S,6b'R,7'R,9a'S,10a'S,10b'S,12a'S)-4,4a',5,5,6a',7'-Hexamethylicosahydro-3H-spiro[furan-2,8'-naphtho[2',1':4,5]indeno[2,1-b]furan]-2',5',7'-triol" The structure as drawn is incorrect I believe since a number of stereocenters are not defined. I will submit the actual structure with full stereo onto ChemSpider and send you the link.--ChemSpiderMan (talk) 02:56, 22 January 2008 (UTC) Chemical Abstracts gives a structure for hippuristanol with all the stereocenters defined. CAS#80442-78-0. I've added a corresponding image and SMILES to the article. I'm unable to generate and IUPAC name. -- Ed (Edgar181) 14:10, 22 January 2008 (UTC) The structure is consistent with the one on ChemSpider now http://www.chemspider.com/Chemical-Structure.21105577.html. The IUPAC Name is above in the text...--ChemSpiderMan (talk) 17:02, 22 January 2008 (UTC) Thanks, and sorry about that; I've updated the SVG. Is there any way to break the SMILES string? Fvasconcellos (t·c) 19:21, 22 January 2008 (UTC) Hydrastine Hydrastine is lacking stereochemistry. Suggested structure is here. Suggested name is (3S)-6,7-dimethoxy-3-[(5R)-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-2-benzofuran-1(3H)-one Comments Should it be (+)-hydrastine or (−)-hydrastine? (+)-Hydrastine is (3R, 5S), not the other way round; (−)-hydrastine is all-R.[42] Fvasconcellos (t·c) 12:29, 20 January 2008 (UTC) Inositol_pentakisphosphate No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE As host of ChemSpider I grant Copyright to you...However, I don't think the images are of sufficient quality for you. I had started a conversation on Wikipedia previously about the possibility to generate PNG images off of ChemSpider but I don't think I received any feedback and we cannot do this right now because of the list of other things to do. It would be many weeks now before we could do it. i would suggest downloading the structure from ChemSPider into an appropriate package at the desktop and generate the PNG or SVG image from that package. I am opening the discussion here again about whether or not there is interest in us generating PNG/SVG images of the structures from ChemSpider for use on Wikipedia?--ChemSpiderMan (talk) 16:33, 20 January 2008 (UTC) Kallidin No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE Laminarin No structure. One is listed on ChemSpider that needs validating here. Comments MTSL The structure shown is: (an N-oxide) It says the name is: S-(2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate This converts to: (different structure, the corresponding amine) Comments Neocarzinostatin There is no structure on the record. This record is on ChemSpider for validation and inclusion here. Comments Looks like it's lacking a stereo descriptor? See reference 5 here and this, which also appear to show the most common orientation. Interestingly, PDB has plenty of crystal structures deposited for it, such as PDB: 1NCO​. Fvasconcellos (t·c) 12:49, 22 January 2008 (UTC) The structure at ChemSpider and the structure at "reference 5" linked above seem to be missing a double bond (exocyclic from the cyclopentane ring). Although Chemical Abstracts lists the structure as "No structure diagram available", I found a J. Org. Chem. reference from someone who actually made the compound and filled the chembox with the structure and data they report. That structure is the same as the one shown in 3 or 4 other recent journal articles I looked at. Our article refers to it as a "dienediyne" which is consistent with the structure I've added, but not the ChemSpider one. If anyone can double check me with other references, that would be nice. -- Ed (Edgar181) 12:29, 25 January 2008 (UTC) I have done some additional literature research but remain confused. An examination of PubChem shows the structure Edgar181 has drawn as the Neocarzinostatin chromophore rather than Neocarzinostatin itself. The difference is the one exocyclic bond. Since it has a MeSH annotation I am going to contact MeSH directly and get their comments. I DO agree that there are publications out there with the exocyclic double bond and labeled as Neocarzinostatin. For example 1. So, I'm not sure we're there yet.--ChemSpiderMan (talk) 15:15, 25 January 2008 (UTC) I've done a bit more reading too, and here's what I can tell. Neocarzinostatin is a complex of a small molecule (properly referred to as neocarzinostatin chromophore) bound to an amino acid, but the term neocarzinostatin sometimes gets used to refer to just the chromophore part. I think Wikipedia just needs a single article for neocarzinostatin and neocarzinostatin chromophore so I've tried to reword the article a bit to reflect this. The chembox is titled "neocarzinostatin chromophore" and the data in the box is for just this part (except that it now has two CAS numbers, each denoting what it corresponds to). The structure associated with CAS#79633-18-4, which I just added to the article, does indeed have the exocyclic double bond. Hopefully, this helps reduce the confusion instead of creating more. 15:37, 25 January 2008 (UTC) Yes, neocarzinostatin (properly holo-neocarzinostatin) is a protein-chromophore complex; see the PDB link I provided above. The protein alone would be "apo-neocarzinostatin", and the small molecule (prosthetic group) is the "neocarzinostatin chromophore", as Ed mentioned in the chembox. Fvasconcellos (t·c) 15:40, 25 January 2008 (UTC) Then it looks like we are dealing with an error of the absence of the double bond in other multiple databases? This includes KEGG and PubChem. I couldn't find it in eMolecules. ChemSpider is now corrected. The IUPAC Name (software generated) is: (1aS,5R,6R,6aE)-6-{[(2R,3R,4R,5R,6R)-4,5-Dihydroxy-6-methyl-3-(methylamino)tetrahydro-2H-pyran-2-yl]oxy}-1a-(2-oxo-1,3-dioxolan-4-yl)-2,3,8,9-tetradehydro-1a,5,6,9a-tetrahydrocyclopenta[5,6]cyclonona[1,2-b]oxiren-5-yl 2-hydroxy-7-methoxy-5-methyl-1-naphthoate. If you accept it either insert or let me know and I will.--ChemSpiderMan (talk) 16:01, 25 January 2008 (UTC) OK, I added it. -- Ed (Edgar181) 16:12, 25 January 2008 (UTC) Apparently, holo-neocarzinostatin has the proposed INN "zinostatin". Proposed INN list 74 has the structure as Ed drew it, with the double bond—so yes, it appears other databases are in error :) Fvasconcellos (t·c) 16:19, 25 January 2008 (UTC) Nile_blue The formula and the SMILES include chlorine. Should the image be a chloride salt ? EDIT: Decide on salt or not and make modifications Comments Norbaeocystin I think it’s a bad idea to hook a ChemBox to a PubChem or eMolecules search. When you click PubChem you get this: 45 HITS! http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=HistorySearch&WebEnvRq=1&db=pccompound&query_key=4&WebEnv=0WZ72yTPcueOePRfvFnsns4pyG6_yXI3zQjko-Hmmo0niFnKvuq0kSzEag9oycHVtGsi4aAsh5IvYR%40264662E1739B1F60_0066SID When you click eMolecules you get this: 0 hits http://www.emolecules.com/cgi-bin/search?t=ex&q=%5BNH3%2B%5DCCC1%3DCNC2%3DC1C%28OP%28%5BO-%5D%29%28O%29%3DO%29%3DCC%3DC2 The connections should be real to a 1:1 record. Same here: http://en.wikipedia.org/wiki/O-Acetylpsilocin Comments Pectic_acid No structure on Wikipedia/ The structure is here]. Comments Phosphopantetheine Structure needs stereochemistry and a IUPAC Name. ChemSpider says the structure is this. (3R)-3-hydroxy-4-({3-[(2-mercaptoethyl)amino]-3-oxopropyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen phosphate Comments Plicatic_acid I believe the structure might be wrong. The structure shown here should be validated. (1S,2S,3R)-1-(3,4-dihydroxy-5-methoxyphenyl)-2,3,7-trihydroxy-3-(hydroxymethyl)-6-methoxy-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid The ChemSpider record is here. Comments Pyrrolizidine Is Pyrrolizidine itself a naturally occurring alkaloid? It appears to be a fragment of the alkaloid. [43] Comments Pyrrolysine Should the carboxylic acid and amine be charged or neutral. The name suggests neutral N6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine Comments QS21 No structure on the record. Confirm this as the structure and add: (structure) Also see this. Comments Quaternium-15 Drawn as a cis-compound. Should it be a trans compound: [44] Comments Quercitron The label on the structure image suggests the structure is wrong…shouldn’t it be replaced.? Comments Quinoline_Yellow SS version is: [45] WS version is: Comments Ristocetin No structure on Wikipedia. Suggested structure is on ChemSpider [here]. Comments Roseophilin No structure on Wikipedia. Suggested structure on ChemSpider here. Comments S-Adenosyl_methionine Structure is not charge balanced because of the NH3 plus charge. Is there a counterion? Comments S-Allyl_cysteine The IUPAC name is not consistent with the structure. Actual IUPAC name should be: (2R)-3-(allylthio)-2-aminopropane-1,1-diol Comments No! No way is this a 1,1-diol! I think perhaps the current name is a little wrong, I suspect the person meant S-{2-propenyl}-L-cysteine - is this IUPAC though? Walkerma (talk) 05:03, 7 February 2008 (UTC) Comments back..no, clearly it is NOT a diol. I don't where this association came from. I checked back in my files and could not see why I said this. This is why we need eyes checking my comments. After 4800 structures they are tired eyes.--ChemSpiderMan (talk) 23:25, 7 February 2008 (UTC) Spirotryprostatin_A WP says mass is 365.43. Actual mass is 395.43. Comments The Chembox originally went with a different image, Image:Spirotryprostatin A.JPG, which is missing the methoxy group (Note, the Edmondson/Danishefsky paper draws this demethoxy compound too, as an analogue). Someone fixed the structure but not the formula or the mass. The formula should be C22H25N3O4 (mass 395), not C21H23N3O3 (mass 365), which was "correct" for the original structure. Now fixed. Sulforhodamine_B No structure for this article Structure is here]/ Comments Now done (More to follow) Status of Wikipedia Curation Project I am taking some downtime from the curation project for a few days to finish some other projects (publications, book chapter etc.) I will provide Walkerma with the latest report for him to post into this Sandbox for discussion. I am up to the letter "P", have already knocked out "X,Y,Z". I think it will be another couple of weeks before I return to the project. --ChemSpiderMan (talk) 14:22, 18 January 2008 (UTC) That's fine! I'm running around trying to get ready for the new semester (Monday), so I'm behind in transferring things over to here. We really appreciate the immense amount of work done so far! Look at the no. of daily hits on a typical page and you can see the importance of the work. Hope you can get caught up - though don't forget about us! Walkerma (talk) 14:58, 18 January 2008 (UTC) The link to the updated copy of the report issued on 011808 is here--ChemSpiderMan (talk) 13:37, 19 January 2008 (UTC) Another update to the curation report is here--ChemSpiderMan (talk) 05:21, 4 February 2008 (UTC) The link above has been updated to allow login without a password.--ChemSpiderMan (talk) 01:39, 6 February 2008 (UTC)
These are article drugboxes and chemboxes checked by User:ChemSpiderMan, using PubChem, CAS no. checks, ChemSpider, ACD/Name. See this paper for a recent paper on errors in IUPAC name generators; ACD/Name is clearly the best. The original PDF includes the actual structures, and also lists a few that have been fixed. You can leave comments below. Thanks for helping! Note: entries that have been fixed for more than two weeks have been removed from this list, assuming they have no residual problem associated with them. Xylulose_5-phosphate As drawn this is not a phosphate. This is a dihydrogen phosphate. EDIT: Redraw the structure. Comments Done. Most databases show it as the dihydrogen phosphate, though. Fvasconcellos (t·c) 14:02, 9 January 2008 (UTC) We should probably discuss this in our IRC on Tuesday. Yellow_2G ChemSpider suggests the CAS NUMBER is for the free acid but I am not sure. Can anyone confirm? Beta-hydroxybutyryl-CoA I believe that coenzyme A should be fully protonated yet the majority of sites are charged. A WP-CHEM needs to be made about all CoEnZA compounds for consistency EDIT: WP-CHEM decision required Comments Betanin The structure on ChemSpider is [46] EDIT: Decision to be made about what the structure is , WP-CHEM decision Comments As a betalain, I'm pretty sure betanin exists as a zwitterion. Fvasconcellos (t·c) 14:10, 9 January 2008 (UTC) Bis(2,4,5-trichlorophenyl-6-carbopentoxyphenyl)oxalate The CAS number is listed below as 1165-91-9 ChemSpider lists the structure below for that number: [47] Also…ChemExper says [48] I DON’T know which structure is associated with that CAS Number. Can it be confirmed? The structure as drawn is: EDIT: Someone confirm the CAS Number. Also, the molecular formula is INCORRECT Comments CAS 1165-91-9 is bis(2,4,6-trichlorophenyl)oxalate (TCPO). This compound (CPPO) is, according to eMolecules, 30431-54-0 and 102579-84-0 ... Molecular formula fixed. Fvasconcellos (t·c) 00:10, 9 January 2008 (UTC) Bis(triphenylphosphine)iminium_chloride Ugly structure . I prefer… EDIT: WP-CHEM choose to replace structure Comments I disagree, I like the fact that the structure shows how the P is tetrahedral. Walkerma (talk) 05:42, 8 January 2008 (UTC) I agree that it communicates the Tetrahedral nature better but the overlap, for me, looks confusing. The question is whether to reduce confusion or communicate tetrahedral nature. I'll leave the decision to WP:Chem of course.--ChemSpiderMan (talk) 05:56, 8 January 2008 (UTC) Why not replace the phenyl rings with C6H5 or Ph? And note Ph = (benzene ring) in the image? --Rifleman 82 (talk) 17:51, 14 February 2008 (UTC) Bismarck_brown_Y Insert Chembox Insert IUPAC Name = 4,4'-[1,3-phenylenedi(E)diazene-2,1-diyl]dibenzene-1,3-diamine CONFIRM E/Z Comments For CAS#10114-58-6, Chemical Abstracts gives the 2HCl salt and has undefined double-bond geometry. For the neutral structure in the image Chemical Abstracts has CAS#1052-38-6, again with undefined double-bond geometry, but lists Basic brown G as a synonym, but not Bismark brown Y. -- Ed (Edgar181) 17:07, 10 January 2008 (UTC) Bistriflimide I disagree with the systematic name EDIT: Replace name if agreed. Comments This is being debated by IUPAC, see [49]. Walkerma (talk) 05:42, 8 January 2008 (UTC) Now...you are a wealth of information Walkerma! --ChemSpiderMan (talk) 05:51, 8 January 2008 (UTC) Bromocresol_purple The InChI String has been generated with the wrong settings and therefore generates the WRONG structure. The correct InChI is: InChI=1/C21H17BrO5S/c1-12-9-14(7-8-18(12)23)21(15-10-13(2)20(24)17(22)11-15)16-5-3-4-6-19(16)28(25,26)27-21/h3-11,23-24H,1-2H3 Comments FIXED: SORT OF. I replaced the InChI from the ChemBox with Physchim62's {{InChI}}, but now the InChI intrudes slightly into the Chembox. I've requested a modification which (if doable) should fix this. Walkerma (talk) 07:09, 9 January 2008 (UTC) The WP:CHEM team should be interested in this email send out today for comments. This is from the InChI team and is encouraging the adoption of standard settings. This was the issue with Bromocresol Purple...settings were chosen. If and when these standards were adopted then these problems should go away. We will be making these settings on our [ http://www.chemspider.com/InChI.asmx InChI Web service] for everyone to use. --ChemSpiderMan (talk) 22:02, 10 January 2008 (UTC) Calcium_carbimide The name says it’s a TRIcarboxylate but it is only doubly charged. Assuming it is then you need a 2:3 stoichiometry with Calcium Pubchem shows the neutral compound http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6335910 ChemSpider suggests it’s a 1:1 ratio. So, I think just the name is wrong? calcium 2-(carboxymethyl)-2-hydroxysuccinate - methylcyanamide (1:1) EDIT: Change the name? Comments Carthamin ChemSpider says: [50] The masses and the formulae are different. Which one is correct??? The name is: 3-[(Z)-{5-(β-L-Glucopyranosyloxy)-4,5-dihydroxy-3-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-2,6-dioxo-3-cyclohexen-1-ylidene}methyl]-1,2,6-trihydroxy-5-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-4-oxo-2,5-cyclohexadien-1-yl β-D-glucopyranoside Comments The mass and formula in the Wikipedia article are consistent with those reported in Chemical Abstracts, PubChem, EINECS and the Merck Index. ChemSpider appears to be the outlier.-- Ed (Edgar181) 16:07, 9 January 2008 (UTC) I click on the emolecules link and find three compounds...two of mass of 910.78 but with different logP values (so they should be different molecules since they were calculated by the same algorithm) and one with a mass of 450. Then I click on the PubChem link and got a structure of mass 562 and a TOTALLY different structure..so, at least the PubChem link needs changing. The PubChem link is http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=11968069. I checked for the PubChem based InChi and found the structure on ChemSpider here but under the name Carthamine not Carthamin. Thanks to this work I have now curated out the INCORRECT names associated with the structure on ChemSpider.. All carmathine related names are removed from [here http://www.chemspider.com/Chemical-Structure.16736410.html]. I'll take CAS as the definitive call on this one. Ed..thanks for the help on this one.--ChemSpiderMan (talk) 05:24, 10 January 2008 (UTC) One more comment on this. Ed commented on the Carmathin record "I don't understand why emolecules has inconsistent data." This is in regards to linking the CAS number from Carmathin to eMolecules and seeing three different structures. This is not a comment against eMolecules as the same issue WILL exist on PubChem and CHemSPider in theory. NONE of these databases should be the primary reprepsentatives for CAS Numbers. I don't think the CAS Number should be linked to ANY external database in the way implemented now...that is doing a CAS number search. Why? The record on Wikipedia has the structures already. What is the value of linking the CAS Number. It's fine to link the PubChem ID, the eMolecules ID or even the ChemSpider ID but this will go directly to a record. However, a CAS Number search can take you to many structures with the same CAS number and create confusion.--ChemSpiderMan (talk) 05:08, 11 January 2008 (UTC) Coenzyme_F420 Add the structure : http://www.chemspider.com/Search.aspx?q=coenzyme+F420 13,16,17,18-tetrahydroxy-11-methyl-5,10-dioxo-19-(2,4,8-trioxo-1,3,4,8-tetrahydropyrimido[4,5-b]quinolin-10(2H)-yl)-12,14-dioxa-4,9-diaza-13-phosphanonadecane-1,3,8-tricarboxylic acid 13-oxide Comments Ethocybin Should the molecule in Wikipedia be drawn as charged or as above with the name 3-[2-(diethylamino)ethyl]-1H-indol-4-yl dihydrogen phosphate Comments F430 Please confirm my representation below. The SMILES string is: [Ni].O=C(O)CC[C@@H]1C\6=N/[C@]2(NC(=O)C[C@@]12C)C[C@@H]3/N=C (\[C@](CC(=O)N)(C)[C@@H]3CCC(=O)O)C[C@H]5/N=C4/C(C(=O)CC[C@H ]4[C@@H]5CC(=O)O)=C7\[N-]/C(=C/6)[C@@H](CC(=O)O)[C@@H]7CCC(=O)O From http://www.chemspider.com/Chemical-Structure.4573710.html I find: 73145-13-8 (can someone check the CAS number) Coenzyme F430 factor 430 Factor F430 Comments FADH2 Confirm the structure I have drawn and add the name. [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate Comments Fructose-1-phosphate Problems with this one…. The name does not have stereochemistry The name converts to the cyclic form: The PubCHem link is to the cyclic form [51] Is there a WP:CHEM policy about sugars in linear, cyclized form? The CAS number links to both linear and cyclic forms. Compare it to: Fructose_1,6-bisphosphate which is cyclic Comments (Also see below) Fructose_1,6-bisphosphate I think there needs to be a WP:CHEM statement on sugar representations. Also, protonation states ESPECIALLY if InChIKeys are going to be generated… [(2S,3S,4S,5R)-2,3,4-trihydroxytetrahydrofuran-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)] RNBGYGVWRKECFJ-CERMHHMHBJ is for the structure above RNBGYGVWRKECFJ-GSMOWLIGBO is for the structure in the ChemBox Consistency Issues Record to Record There needs to be consistency around linear vs cyclic, charged versus uncharged, named with stereo or not. Comments Fructose_6-phosphate The structure as drawn is not consistent with the name…which is right? [(2R,3S,4S,5S)-3,4,5-trihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate Comments Fumonisin_B2 Formatting issues: From ChemSpider: [52] I have not proven the structure to be correct though. But it is consistent with PubChem. Comments Gamma-amanitin No structure. This structure is in ChemSpider… [53] It has no stereochemistry Comments Geranyl_pyrophosphate A decision needs to be made about charged state/protonation state. The structure does not coincide with the SMILES or the PubChem link. (2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate Comments Geranylgeranyl_pyrophosphate Same issue with protonated/charged states – the MF and Mass do not match the structure Comments Glycerate_3-phosphate Name does not match the structure. Glycerate phosphate, (2R)-2-hydroxy-3-phosphonooxy-propanoate, (2R)-2-hydroxy-3-(phosphonooxy)propanoic acid. EDIT: Decide what the structure should be and name appropriately Comments Guanosine_diphosphate_mannose I think a better image is at: [[54]] IUPAC NAME [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate Comments I added the IUPAC name, but a suitable structure needs to be drawn (with clear copyright) Redrawn from Chemspider's SMILES. Please let me know if I made a mistake! --Rifleman 82 (talk) 17:59, 14 February 2008 (UTC) HMG-CoA Add IUPAC Name and add stereochemistry to the structure. (9R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8,21-trimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide Comments I added the IUPAC name, structure still needs to be done. Comments Heme_b Compare the Wikipedia structure with the PubChem structure and notice the difference in MF. Also, what is the best representation for the structure? WP or PubChem? I'd like to know the consensus to reproduce it in ChemSpider since there are THREE representations in CS [55] Comments Heme c The link in PubChem goes to the identifiers HEC or Hem. PubChem has heme c as [56] What is the correct structure? Hippuristanol No structure. I suggest validating the full stereochemistry here: but the structure is available on ChemSpider here Comments I've uploaded a structure based on that found at the discoverer's website; does it match the one currently at CS? It also needs an IUPAC name; I use the free version of ChemSketch (only names compounds up to 50 atoms or 3 cycles), and my skills aren't up to that :) Fvasconcellos (t·c) 00:33, 21 January 2008 (UTC) ChemDraw 11 cannot generate a name either. A minor remark: IUPAC recommends not to attach wedged bonds to each other like in this structure but to use a wedged H. Сасусlе 00:53, 21 January 2008 (UTC) ACD/Name CAN generate a name "(2R,2'R,4S,4a'S,4b'S,5'S,6a'S,6b'R,7'R,9a'S,10a'S,10b'S,12a'S)-4,4a',5,5,6a',7'-Hexamethylicosahydro-3H-spiro[furan-2,8'-naphtho[2',1':4,5]indeno[2,1-b]furan]-2',5',7'-triol" The structure as drawn is incorrect I believe since a number of stereocenters are not defined. I will submit the actual structure with full stereo onto ChemSpider and send you the link.--ChemSpiderMan (talk) 02:56, 22 January 2008 (UTC) Chemical Abstracts gives a structure for hippuristanol with all the stereocenters defined. CAS#80442-78-0. I've added a corresponding image and SMILES to the article. I'm unable to generate and IUPAC name. -- Ed (Edgar181) 14:10, 22 January 2008 (UTC) The structure is consistent with the one on ChemSpider now http://www.chemspider.com/Chemical-Structure.21105577.html. The IUPAC Name is above in the text...--ChemSpiderMan (talk) 17:02, 22 January 2008 (UTC) Thanks, and sorry about that; I've updated the SVG. Is there any way to break the SMILES string? Fvasconcellos (t·c) 19:21, 22 January 2008 (UTC) Hydrastine Hydrastine is lacking stereochemistry. Suggested structure is here. Suggested name is (3S)-6,7-dimethoxy-3-[(5R)-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-2-benzofuran-1(3H)-one Comments Should it be (+)-hydrastine or (−)-hydrastine? (+)-Hydrastine is (3R, 5S), not the other way round; (−)-hydrastine is all-R.[57] Fvasconcellos (t·c) 12:29, 20 January 2008 (UTC) Inositol_pentakisphosphate No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE As host of ChemSpider I grant Copyright to you...However, I don't think the images are of sufficient quality for you. I had started a conversation on Wikipedia previously about the possibility to generate PNG images off of ChemSpider but I don't think I received any feedback and we cannot do this right now because of the list of other things to do. It would be many weeks now before we could do it. i would suggest downloading the structure from ChemSPider into an appropriate package at the desktop and generate the PNG or SVG image from that package. I am opening the discussion here again about whether or not there is interest in us generating PNG/SVG images of the structures from ChemSpider for use on Wikipedia?--ChemSpiderMan (talk) 16:33, 20 January 2008 (UTC) Kallidin No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE Laminarin No structure. One is listed on ChemSpider that needs validating here. Comments MTSL The structure shown is: (an N-oxide) It says the name is: S-(2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate This converts to: (different structure, the corresponding amine) Comments Neocarzinostatin There is no structure on the record. This record is on ChemSpider for validation and inclusion here. Comments Looks like it's lacking a stereo descriptor? See reference 5 here and this, which also appear to show the most common orientation. Interestingly, PDB has plenty of crystal structures deposited for it, such as PDB: 1NCO​. Fvasconcellos (t·c) 12:49, 22 January 2008 (UTC) The structure at ChemSpider and the structure at "reference 5" linked above seem to be missing a double bond (exocyclic from the cyclopentane ring). Although Chemical Abstracts lists the structure as "No structure diagram available", I found a J. Org. Chem. reference from someone who actually made the compound and filled the chembox with the structure and data they report. That structure is the same as the one shown in 3 or 4 other recent journal articles I looked at. Our article refers to it as a "dienediyne" which is consistent with the structure I've added, but not the ChemSpider one. If anyone can double check me with other references, that would be nice. -- Ed (Edgar181) 12:29, 25 January 2008 (UTC) I have done some additional literature research but remain confused. An examination of PubChem shows the structure Edgar181 has drawn as the Neocarzinostatin chromophore rather than Neocarzinostatin itself. The difference is the one exocyclic bond. Since it has a MeSH annotation I am going to contact MeSH directly and get their comments. I DO agree that there are publications out there with the exocyclic double bond and labeled as Neocarzinostatin. For example 1. So, I'm not sure we're there yet.--ChemSpiderMan (talk) 15:15, 25 January 2008 (UTC) I've done a bit more reading too, and here's what I can tell. Neocarzinostatin is a complex of a small molecule (properly referred to as neocarzinostatin chromophore) bound to an amino acid, but the term neocarzinostatin sometimes gets used to refer to just the chromophore part. I think Wikipedia just needs a single article for neocarzinostatin and neocarzinostatin chromophore so I've tried to reword the article a bit to reflect this. The chembox is titled "neocarzinostatin chromophore" and the data in the box is for just this part (except that it now has two CAS numbers, each denoting what it corresponds to). The structure associated with CAS#79633-18-4, which I just added to the article, does indeed have the exocyclic double bond. Hopefully, this helps reduce the confusion instead of creating more. 15:37, 25 January 2008 (UTC) Yes, neocarzinostatin (properly holo-neocarzinostatin) is a protein-chromophore complex; see the PDB link I provided above. The protein alone would be "apo-neocarzinostatin", and the small molecule (prosthetic group) is the "neocarzinostatin chromophore", as Ed mentioned in the chembox. Fvasconcellos (t·c) 15:40, 25 January 2008 (UTC) Then it looks like we are dealing with an error of the absence of the double bond in other multiple databases? This includes KEGG and PubChem. I couldn't find it in eMolecules. ChemSpider is now corrected. The IUPAC Name (software generated) is: (1aS,5R,6R,6aE)-6-{[(2R,3R,4R,5R,6R)-4,5-Dihydroxy-6-methyl-3-(methylamino)tetrahydro-2H-pyran-2-yl]oxy}-1a-(2-oxo-1,3-dioxolan-4-yl)-2,3,8,9-tetradehydro-1a,5,6,9a-tetrahydrocyclopenta[5,6]cyclonona[1,2-b]oxiren-5-yl 2-hydroxy-7-methoxy-5-methyl-1-naphthoate. If you accept it either insert or let me know and I will.--ChemSpiderMan (talk) 16:01, 25 January 2008 (UTC) OK, I added it. -- Ed (Edgar181) 16:12, 25 January 2008 (UTC) Apparently, holo-neocarzinostatin has the proposed INN "zinostatin". Proposed INN list 74 has the structure as Ed drew it, with the double bond—so yes, it appears other databases are in error :) Fvasconcellos (t·c) 16:19, 25 January 2008 (UTC) Nile_blue The formula and the SMILES include chlorine. Should the image be a chloride salt ? EDIT: Decide on salt or not and make modifications Comments Norbaeocystin I think it’s a bad idea to hook a ChemBox to a PubChem or eMolecules search. When you click PubChem you get this: 45 HITS! http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=HistorySearch&WebEnvRq=1&db=pccompound&query_key=4&WebEnv=0WZ72yTPcueOePRfvFnsns4pyG6_yXI3zQjko-Hmmo0niFnKvuq0kSzEag9oycHVtGsi4aAsh5IvYR%40264662E1739B1F60_0066SID When you click eMolecules you get this: 0 hits http://www.emolecules.com/cgi-bin/search?t=ex&q=%5BNH3%2B%5DCCC1%3DCNC2%3DC1C%28OP%28%5BO-%5D%29%28O%29%3DO%29%3DCC%3DC2 The connections should be real to a 1:1 record. Same here: http://en.wikipedia.org/wiki/O-Acetylpsilocin Comments Pectic_acid No structure on Wikipedia/ The structure is here]. Comments Phosphopantetheine Structure needs stereochemistry and a IUPAC Name. ChemSpider says the structure is this. (3R)-3-hydroxy-4-({3-[(2-mercaptoethyl)amino]-3-oxopropyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen phosphate Comments Plicatic_acid I believe the structure might be wrong. The structure shown here should be validated. (1S,2S,3R)-1-(3,4-dihydroxy-5-methoxyphenyl)-2,3,7-trihydroxy-3-(hydroxymethyl)-6-methoxy-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid The ChemSpider record is here. Comments Pyrrolizidine Is Pyrrolizidine itself a naturally occurring alkaloid? It appears to be a fragment of the alkaloid. [58] Comments Pyrrolysine Should the carboxylic acid and amine be charged or neutral. The name suggests neutral N6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine Comments QS21 No structure on the record. Confirm this as the structure and add: (structure) Also see this. Comments Quaternium-15 Drawn as a cis-compound. Should it be a trans compound: [59] Comments Quercitron The label on the structure image suggests the structure is wrong…shouldn’t it be replaced.? Comments Quinoline_Yellow SS version is: [60] WS version is: Comments Ristocetin No structure on Wikipedia. Suggested structure is on ChemSpider [here]. Comments Roseophilin No structure on Wikipedia. Suggested structure on ChemSpider here. Comments S-Adenosyl_methionine Structure is not charge balanced because of the NH3 plus charge. Is there a counterion? Comments S-Allyl_cysteine The IUPAC name is not consistent with the structure. Actual IUPAC name should be: (2R)-3-(allylthio)-2-aminopropane-1,1-diol Comments No! No way is this a 1,1-diol! I think perhaps the current name is a little wrong, I suspect the person meant S-{2-propenyl}-L-cysteine - is this IUPAC though? Walkerma (talk) 05:03, 7 February 2008 (UTC) Comments back..no, clearly it is NOT a diol. I don't where this association came from. I checked back in my files and could not see why I said this. This is why we need eyes checking my comments. After 4800 structures they are tired eyes.--ChemSpiderMan (talk) 23:25, 7 February 2008 (UTC) Spirotryprostatin_A WP says mass is 365.43. Actual mass is 395.43. Comments The Chembox originally went with a different image, Image:Spirotryprostatin A.JPG, which is missing the methoxy group (Note, the Edmondson/Danishefsky paper draws this demethoxy compound too, as an analogue). Someone fixed the structure but not the formula or the mass. The formula should be C22H25N3O4 (mass 395), not C21H23N3O3 (mass 365), which was "correct" for the original structure. Now fixed. Sulforhodamine_B No structure for this article Structure is here]/ Comments Now done (More to follow) Status of Wikipedia Curation Project I am taking some downtime from the curation project for a few days to finish some other projects (publications, book chapter etc.) I will provide Walkerma with the latest report for him to post into this Sandbox for discussion. I am up to the letter "P", have already knocked out "X,Y,Z". I think it will be another couple of weeks before I return to the project. --ChemSpiderMan (talk) 14:22, 18 January 2008 (UTC) That's fine! I'm running around trying to get ready for the new semester (Monday), so I'm behind in transferring things over to here. We really appreciate the immense amount of work done so far! Look at the no. of daily hits on a typical page and you can see the importance of the work. Hope you can get caught up - though don't forget about us! Walkerma (talk) 14:58, 18 January 2008 (UTC) The link to the updated copy of the report issued on 011808 is here--ChemSpiderMan (talk) 13:37, 19 January 2008 (UTC) Another update to the curation report is here--ChemSpiderMan (talk) 05:21, 4 February 2008 (UTC) The link above has been updated to allow login without a password.--ChemSpiderMan (talk) 01:39, 6 February 2008 (UTC)
These are article drugboxes and chemboxes checked by User:ChemSpiderMan, using PubChem, CAS no. checks, ChemSpider, ACD/Name. See this paper for a recent paper on errors in IUPAC name generators; ACD/Name is clearly the best. The original PDF includes the actual structures, and also lists a few that have been fixed. You can leave comments below. Thanks for helping! Note: entries that have been fixed for more than two weeks have been removed from this list, assuming they have no residual problem associated with them. Xylulose_5-phosphate As drawn this is not a phosphate. This is a dihydrogen phosphate. EDIT: Redraw the structure. Comments Done. Most databases show it as the dihydrogen phosphate, though. Fvasconcellos (t·c) 14:02, 9 January 2008 (UTC) We should probably discuss this in our IRC on Tuesday. Yellow_2G ChemSpider suggests the CAS NUMBER is for the free acid but I am not sure. Can anyone confirm? Beta-hydroxybutyryl-CoA I believe that coenzyme A should be fully protonated yet the majority of sites are charged. A WP-CHEM needs to be made about all CoEnZA compounds for consistency EDIT: WP-CHEM decision required Comments Betanin The structure on ChemSpider is [61] EDIT: Decision to be made about what the structure is , WP-CHEM decision Comments As a betalain, I'm pretty sure betanin exists as a zwitterion. Fvasconcellos (t·c) 14:10, 9 January 2008 (UTC) Bis(2,4,5-trichlorophenyl-6-carbopentoxyphenyl)oxalate The CAS number is listed below as 1165-91-9 ChemSpider lists the structure below for that number: [62] Also…ChemExper says [63] I DON’T know which structure is associated with that CAS Number. Can it be confirmed? The structure as drawn is: EDIT: Someone confirm the CAS Number. Also, the molecular formula is INCORRECT Comments CAS 1165-91-9 is bis(2,4,6-trichlorophenyl)oxalate (TCPO). This compound (CPPO) is, according to eMolecules, 30431-54-0 and 102579-84-0 ... Molecular formula fixed. Fvasconcellos (t·c) 00:10, 9 January 2008 (UTC) Bis(triphenylphosphine)iminium_chloride Ugly structure . I prefer… EDIT: WP-CHEM choose to replace structure Comments I disagree, I like the fact that the structure shows how the P is tetrahedral. Walkerma (talk) 05:42, 8 January 2008 (UTC) I agree that it communicates the Tetrahedral nature better but the overlap, for me, looks confusing. The question is whether to reduce confusion or communicate tetrahedral nature. I'll leave the decision to WP:Chem of course.--ChemSpiderMan (talk) 05:56, 8 January 2008 (UTC) Why not replace the phenyl rings with C6H5 or Ph? And note Ph = (benzene ring) in the image? --Rifleman 82 (talk) 17:51, 14 February 2008 (UTC) Bismarck_brown_Y Insert Chembox Insert IUPAC Name = 4,4'-[1,3-phenylenedi(E)diazene-2,1-diyl]dibenzene-1,3-diamine CONFIRM E/Z Comments For CAS#10114-58-6, Chemical Abstracts gives the 2HCl salt and has undefined double-bond geometry. For the neutral structure in the image Chemical Abstracts has CAS#1052-38-6, again with undefined double-bond geometry, but lists Basic brown G as a synonym, but not Bismark brown Y. -- Ed (Edgar181) 17:07, 10 January 2008 (UTC) Bistriflimide I disagree with the systematic name EDIT: Replace name if agreed. Comments This is being debated by IUPAC, see [64]. Walkerma (talk) 05:42, 8 January 2008 (UTC) Now...you are a wealth of information Walkerma! --ChemSpiderMan (talk) 05:51, 8 January 2008 (UTC) Bromocresol_purple The InChI String has been generated with the wrong settings and therefore generates the WRONG structure. The correct InChI is: InChI=1/C21H17BrO5S/c1-12-9-14(7-8-18(12)23)21(15-10-13(2)20(24)17(22)11-15)16-5-3-4-6-19(16)28(25,26)27-21/h3-11,23-24H,1-2H3 Comments FIXED: SORT OF. I replaced the InChI from the ChemBox with Physchim62's {{InChI}}, but now the InChI intrudes slightly into the Chembox. I've requested a modification which (if doable) should fix this. Walkerma (talk) 07:09, 9 January 2008 (UTC) The WP:CHEM team should be interested in this email send out today for comments. This is from the InChI team and is encouraging the adoption of standard settings. This was the issue with Bromocresol Purple...settings were chosen. If and when these standards were adopted then these problems should go away. We will be making these settings on our [ http://www.chemspider.com/InChI.asmx InChI Web service] for everyone to use. --ChemSpiderMan (talk) 22:02, 10 January 2008 (UTC) Calcium_carbimide The name says it’s a TRIcarboxylate but it is only doubly charged. Assuming it is then you need a 2:3 stoichiometry with Calcium Pubchem shows the neutral compound http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6335910 ChemSpider suggests it’s a 1:1 ratio. So, I think just the name is wrong? calcium 2-(carboxymethyl)-2-hydroxysuccinate - methylcyanamide (1:1) EDIT: Change the name? Comments Carthamin ChemSpider says: [65] The masses and the formulae are different. Which one is correct??? The name is: 3-[(Z)-{5-(β-L-Glucopyranosyloxy)-4,5-dihydroxy-3-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-2,6-dioxo-3-cyclohexen-1-ylidene}methyl]-1,2,6-trihydroxy-5-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-4-oxo-2,5-cyclohexadien-1-yl β-D-glucopyranoside Comments The mass and formula in the Wikipedia article are consistent with those reported in Chemical Abstracts, PubChem, EINECS and the Merck Index. ChemSpider appears to be the outlier.-- Ed (Edgar181) 16:07, 9 January 2008 (UTC) I click on the emolecules link and find three compounds...two of mass of 910.78 but with different logP values (so they should be different molecules since they were calculated by the same algorithm) and one with a mass of 450. Then I click on the PubChem link and got a structure of mass 562 and a TOTALLY different structure..so, at least the PubChem link needs changing. The PubChem link is http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=11968069. I checked for the PubChem based InChi and found the structure on ChemSpider here but under the name Carthamine not Carthamin. Thanks to this work I have now curated out the INCORRECT names associated with the structure on ChemSpider.. All carmathine related names are removed from [here http://www.chemspider.com/Chemical-Structure.16736410.html]. I'll take CAS as the definitive call on this one. Ed..thanks for the help on this one.--ChemSpiderMan (talk) 05:24, 10 January 2008 (UTC) One more comment on this. Ed commented on the Carmathin record "I don't understand why emolecules has inconsistent data." This is in regards to linking the CAS number from Carmathin to eMolecules and seeing three different structures. This is not a comment against eMolecules as the same issue WILL exist on PubChem and CHemSPider in theory. NONE of these databases should be the primary reprepsentatives for CAS Numbers. I don't think the CAS Number should be linked to ANY external database in the way implemented now...that is doing a CAS number search. Why? The record on Wikipedia has the structures already. What is the value of linking the CAS Number. It's fine to link the PubChem ID, the eMolecules ID or even the ChemSpider ID but this will go directly to a record. However, a CAS Number search can take you to many structures with the same CAS number and create confusion.--ChemSpiderMan (talk) 05:08, 11 January 2008 (UTC) Coenzyme_F420 Add the structure : http://www.chemspider.com/Search.aspx?q=coenzyme+F420 13,16,17,18-tetrahydroxy-11-methyl-5,10-dioxo-19-(2,4,8-trioxo-1,3,4,8-tetrahydropyrimido[4,5-b]quinolin-10(2H)-yl)-12,14-dioxa-4,9-diaza-13-phosphanonadecane-1,3,8-tricarboxylic acid 13-oxide Comments Ethocybin Should the molecule in Wikipedia be drawn as charged or as above with the name 3-[2-(diethylamino)ethyl]-1H-indol-4-yl dihydrogen phosphate Comments F430 Please confirm my representation below. The SMILES string is: [Ni].O=C(O)CC[C@@H]1C\6=N/[C@]2(NC(=O)C[C@@]12C)C[C@@H]3/N=C (\[C@](CC(=O)N)(C)[C@@H]3CCC(=O)O)C[C@H]5/N=C4/C(C(=O)CC[C@H ]4[C@@H]5CC(=O)O)=C7\[N-]/C(=C/6)[C@@H](CC(=O)O)[C@@H]7CCC(=O)O From http://www.chemspider.com/Chemical-Structure.4573710.html I find: 73145-13-8 (can someone check the CAS number) Coenzyme F430 factor 430 Factor F430 Comments FADH2 Confirm the structure I have drawn and add the name. [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate Comments Fructose-1-phosphate Problems with this one…. The name does not have stereochemistry The name converts to the cyclic form: The PubCHem link is to the cyclic form [66] Is there a WP:CHEM policy about sugars in linear, cyclized form? The CAS number links to both linear and cyclic forms. Compare it to: Fructose_1,6-bisphosphate which is cyclic Comments (Also see below) Fructose_1,6-bisphosphate I think there needs to be a WP:CHEM statement on sugar representations. Also, protonation states ESPECIALLY if InChIKeys are going to be generated… [(2S,3S,4S,5R)-2,3,4-trihydroxytetrahydrofuran-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)] RNBGYGVWRKECFJ-CERMHHMHBJ is for the structure above RNBGYGVWRKECFJ-GSMOWLIGBO is for the structure in the ChemBox Consistency Issues Record to Record There needs to be consistency around linear vs cyclic, charged versus uncharged, named with stereo or not. Comments Fructose_6-phosphate The structure as drawn is not consistent with the name…which is right? [(2R,3S,4S,5S)-3,4,5-trihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate Comments Fumonisin_B2 Formatting issues: From ChemSpider: [67] I have not proven the structure to be correct though. But it is consistent with PubChem. Comments Gamma-amanitin No structure. This structure is in ChemSpider… [68] It has no stereochemistry Comments Geranyl_pyrophosphate A decision needs to be made about charged state/protonation state. The structure does not coincide with the SMILES or the PubChem link. (2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate Comments Geranylgeranyl_pyrophosphate Same issue with protonated/charged states – the MF and Mass do not match the structure Comments Glycerate_3-phosphate Name does not match the structure. Glycerate phosphate, (2R)-2-hydroxy-3-phosphonooxy-propanoate, (2R)-2-hydroxy-3-(phosphonooxy)propanoic acid. EDIT: Decide what the structure should be and name appropriately Comments Guanosine_diphosphate_mannose I think a better image is at: [[69]] IUPAC NAME [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate Comments I added the IUPAC name, but a suitable structure needs to be drawn (with clear copyright) Redrawn from Chemspider's SMILES. Please let me know if I made a mistake! --Rifleman 82 (talk) 17:59, 14 February 2008 (UTC) HMG-CoA Add IUPAC Name and add stereochemistry to the structure. (9R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8,21-trimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide Comments I added the IUPAC name, structure still needs to be done. Comments Heme_b Compare the Wikipedia structure with the PubChem structure and notice the difference in MF. Also, what is the best representation for the structure? WP or PubChem? I'd like to know the consensus to reproduce it in ChemSpider since there are THREE representations in CS [70] Comments Heme c The link in PubChem goes to the identifiers HEC or Hem. PubChem has heme c as [71] What is the correct structure? Hippuristanol No structure. I suggest validating the full stereochemistry here: but the structure is available on ChemSpider here Comments I've uploaded a structure based on that found at the discoverer's website; does it match the one currently at CS? It also needs an IUPAC name; I use the free version of ChemSketch (only names compounds up to 50 atoms or 3 cycles), and my skills aren't up to that :) Fvasconcellos (t·c) 00:33, 21 January 2008 (UTC) ChemDraw 11 cannot generate a name either. A minor remark: IUPAC recommends not to attach wedged bonds to each other like in this structure but to use a wedged H. Сасусlе 00:53, 21 January 2008 (UTC) ACD/Name CAN generate a name "(2R,2'R,4S,4a'S,4b'S,5'S,6a'S,6b'R,7'R,9a'S,10a'S,10b'S,12a'S)-4,4a',5,5,6a',7'-Hexamethylicosahydro-3H-spiro[furan-2,8'-naphtho[2',1':4,5]indeno[2,1-b]furan]-2',5',7'-triol" The structure as drawn is incorrect I believe since a number of stereocenters are not defined. I will submit the actual structure with full stereo onto ChemSpider and send you the link.--ChemSpiderMan (talk) 02:56, 22 January 2008 (UTC) Chemical Abstracts gives a structure for hippuristanol with all the stereocenters defined. CAS#80442-78-0. I've added a corresponding image and SMILES to the article. I'm unable to generate and IUPAC name. -- Ed (Edgar181) 14:10, 22 January 2008 (UTC) The structure is consistent with the one on ChemSpider now http://www.chemspider.com/Chemical-Structure.21105577.html. The IUPAC Name is above in the text...--ChemSpiderMan (talk) 17:02, 22 January 2008 (UTC) Thanks, and sorry about that; I've updated the SVG. Is there any way to break the SMILES string? Fvasconcellos (t·c) 19:21, 22 January 2008 (UTC) Hydrastine Hydrastine is lacking stereochemistry. Suggested structure is here. Suggested name is (3S)-6,7-dimethoxy-3-[(5R)-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-2-benzofuran-1(3H)-one Comments Should it be (+)-hydrastine or (−)-hydrastine? (+)-Hydrastine is (3R, 5S), not the other way round; (−)-hydrastine is all-R.[72] Fvasconcellos (t·c) 12:29, 20 January 2008 (UTC) Inositol_pentakisphosphate No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE As host of ChemSpider I grant Copyright to you...However, I don't think the images are of sufficient quality for you. I had started a conversation on Wikipedia previously about the possibility to generate PNG images off of ChemSpider but I don't think I received any feedback and we cannot do this right now because of the list of other things to do. It would be many weeks now before we could do it. i would suggest downloading the structure from ChemSPider into an appropriate package at the desktop and generate the PNG or SVG image from that package. I am opening the discussion here again about whether or not there is interest in us generating PNG/SVG images of the structures from ChemSpider for use on Wikipedia?--ChemSpiderMan (talk) 16:33, 20 January 2008 (UTC) Kallidin No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE Laminarin No structure. One is listed on ChemSpider that needs validating here. Comments MTSL The structure shown is: (an N-oxide) It says the name is: S-(2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate This converts to: (different structure, the corresponding amine) Comments Neocarzinostatin There is no structure on the record. This record is on ChemSpider for validation and inclusion here. Comments Looks like it's lacking a stereo descriptor? See reference 5 here and this, which also appear to show the most common orientation. Interestingly, PDB has plenty of crystal structures deposited for it, such as PDB: 1NCO​. Fvasconcellos (t·c) 12:49, 22 January 2008 (UTC) The structure at ChemSpider and the structure at "reference 5" linked above seem to be missing a double bond (exocyclic from the cyclopentane ring). Although Chemical Abstracts lists the structure as "No structure diagram available", I found a J. Org. Chem. reference from someone who actually made the compound and filled the chembox with the structure and data they report. That structure is the same as the one shown in 3 or 4 other recent journal articles I looked at. Our article refers to it as a "dienediyne" which is consistent with the structure I've added, but not the ChemSpider one. If anyone can double check me with other references, that would be nice. -- Ed (Edgar181) 12:29, 25 January 2008 (UTC) I have done some additional literature research but remain confused. An examination of PubChem shows the structure Edgar181 has drawn as the Neocarzinostatin chromophore rather than Neocarzinostatin itself. The difference is the one exocyclic bond. Since it has a MeSH annotation I am going to contact MeSH directly and get their comments. I DO agree that there are publications out there with the exocyclic double bond and labeled as Neocarzinostatin. For example 1. So, I'm not sure we're there yet.--ChemSpiderMan (talk) 15:15, 25 January 2008 (UTC) I've done a bit more reading too, and here's what I can tell. Neocarzinostatin is a complex of a small molecule (properly referred to as neocarzinostatin chromophore) bound to an amino acid, but the term neocarzinostatin sometimes gets used to refer to just the chromophore part. I think Wikipedia just needs a single article for neocarzinostatin and neocarzinostatin chromophore so I've tried to reword the article a bit to reflect this. The chembox is titled "neocarzinostatin chromophore" and the data in the box is for just this part (except that it now has two CAS numbers, each denoting what it corresponds to). The structure associated with CAS#79633-18-4, which I just added to the article, does indeed have the exocyclic double bond. Hopefully, this helps reduce the confusion instead of creating more. 15:37, 25 January 2008 (UTC) Yes, neocarzinostatin (properly holo-neocarzinostatin) is a protein-chromophore complex; see the PDB link I provided above. The protein alone would be "apo-neocarzinostatin", and the small molecule (prosthetic group) is the "neocarzinostatin chromophore", as Ed mentioned in the chembox. Fvasconcellos (t·c) 15:40, 25 January 2008 (UTC) Then it looks like we are dealing with an error of the absence of the double bond in other multiple databases? This includes KEGG and PubChem. I couldn't find it in eMolecules. ChemSpider is now corrected. The IUPAC Name (software generated) is: (1aS,5R,6R,6aE)-6-{[(2R,3R,4R,5R,6R)-4,5-Dihydroxy-6-methyl-3-(methylamino)tetrahydro-2H-pyran-2-yl]oxy}-1a-(2-oxo-1,3-dioxolan-4-yl)-2,3,8,9-tetradehydro-1a,5,6,9a-tetrahydrocyclopenta[5,6]cyclonona[1,2-b]oxiren-5-yl 2-hydroxy-7-methoxy-5-methyl-1-naphthoate. If you accept it either insert or let me know and I will.--ChemSpiderMan (talk) 16:01, 25 January 2008 (UTC) OK, I added it. -- Ed (Edgar181) 16:12, 25 January 2008 (UTC) Apparently, holo-neocarzinostatin has the proposed INN "zinostatin". Proposed INN list 74 has the structure as Ed drew it, with the double bond—so yes, it appears other databases are in error :) Fvasconcellos (t·c) 16:19, 25 January 2008 (UTC) Nile_blue The formula and the SMILES include chlorine. Should the image be a chloride salt ? EDIT: Decide on salt or not and make modifications Comments Norbaeocystin I think it’s a bad idea to hook a ChemBox to a PubChem or eMolecules search. When you click PubChem you get this: 45 HITS! http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=HistorySearch&WebEnvRq=1&db=pccompound&query_key=4&WebEnv=0WZ72yTPcueOePRfvFnsns4pyG6_yXI3zQjko-Hmmo0niFnKvuq0kSzEag9oycHVtGsi4aAsh5IvYR%40264662E1739B1F60_0066SID When you click eMolecules you get this: 0 hits http://www.emolecules.com/cgi-bin/search?t=ex&q=%5BNH3%2B%5DCCC1%3DCNC2%3DC1C%28OP%28%5BO-%5D%29%28O%29%3DO%29%3DCC%3DC2 The connections should be real to a 1:1 record. Same here: http://en.wikipedia.org/wiki/O-Acetylpsilocin Comments Pectic_acid No structure on Wikipedia/ The structure is here]. Comments Phosphopantetheine Structure needs stereochemistry and a IUPAC Name. ChemSpider says the structure is this. (3R)-3-hydroxy-4-({3-[(2-mercaptoethyl)amino]-3-oxopropyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen phosphate Comments Plicatic_acid I believe the structure might be wrong. The structure shown here should be validated. (1S,2S,3R)-1-(3,4-dihydroxy-5-methoxyphenyl)-2,3,7-trihydroxy-3-(hydroxymethyl)-6-methoxy-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid The ChemSpider record is here. Comments Pyrrolizidine Is Pyrrolizidine itself a naturally occurring alkaloid? It appears to be a fragment of the alkaloid. [73] Comments Pyrrolysine Should the carboxylic acid and amine be charged or neutral. The name suggests neutral N6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine Comments QS21 No structure on the record. Confirm this as the structure and add: (structure) Also see this. Comments Quaternium-15 Drawn as a cis-compound. Should it be a trans compound: [74] Comments Quercitron The label on the structure image suggests the structure is wrong…shouldn’t it be replaced.? Comments Quinoline_Yellow SS version is: [75] WS version is: Comments Ristocetin No structure on Wikipedia. Suggested structure is on ChemSpider [here]. Comments Roseophilin No structure on Wikipedia. Suggested structure on ChemSpider here. Comments S-Adenosyl_methionine Structure is not charge balanced because of the NH3 plus charge. Is there a counterion? Comments S-Allyl_cysteine The IUPAC name is not consistent with the structure. Actual IUPAC name should be: (2R)-3-(allylthio)-2-aminopropane-1,1-diol Comments No! No way is this a 1,1-diol! I think perhaps the current name is a little wrong, I suspect the person meant S-{2-propenyl}-L-cysteine - is this IUPAC though? Walkerma (talk) 05:03, 7 February 2008 (UTC) Comments back..no, clearly it is NOT a diol. I don't where this association came from. I checked back in my files and could not see why I said this. This is why we need eyes checking my comments. After 4800 structures they are tired eyes.--ChemSpiderMan (talk) 23:25, 7 February 2008 (UTC) Spirotryprostatin_A WP says mass is 365.43. Actual mass is 395.43. Comments The Chembox originally went with a different image, Image:Spirotryprostatin A.JPG, which is missing the methoxy group (Note, the Edmondson/Danishefsky paper draws this demethoxy compound too, as an analogue). Someone fixed the structure but not the formula or the mass. The formula should be C22H25N3O4 (mass 395), not C21H23N3O3 (mass 365), which was "correct" for the original structure. Now fixed. Sulforhodamine_B No structure for this article Structure is here]/ Comments Now done (More to follow) Status of Wikipedia Curation Project I am taking some downtime from the curation project for a few days to finish some other projects (publications, book chapter etc.) I will provide Walkerma with the latest report for him to post into this Sandbox for discussion. I am up to the letter "P", have already knocked out "X,Y,Z". I think it will be another couple of weeks before I return to the project. --ChemSpiderMan (talk) 14:22, 18 January 2008 (UTC) That's fine! I'm running around trying to get ready for the new semester (Monday), so I'm behind in transferring things over to here. We really appreciate the immense amount of work done so far! Look at the no. of daily hits on a typical page and you can see the importance of the work. Hope you can get caught up - though don't forget about us! Walkerma (talk) 14:58, 18 January 2008 (UTC) The link to the updated copy of the report issued on 011808 is here--ChemSpiderMan (talk) 13:37, 19 January 2008 (UTC) Another update to the curation report is here--ChemSpiderMan (talk) 05:21, 4 February 2008 (UTC) The link above has been updated to allow login without a password.--ChemSpiderMan (talk) 01:39, 6 February 2008 (UTC)
These are article drugboxes and chemboxes checked by User:ChemSpiderMan, using PubChem, CAS no. checks, ChemSpider, ACD/Name. See this paper for a recent paper on errors in IUPAC name generators; ACD/Name is clearly the best. The original PDF includes the actual structures, and also lists a few that have been fixed. You can leave comments below. Thanks for helping! Note: entries that have been fixed for more than two weeks have been removed from this list, assuming they have no residual problem associated with them. Xylulose_5-phosphate As drawn this is not a phosphate. This is a dihydrogen phosphate. EDIT: Redraw the structure. Comments Done. Most databases show it as the dihydrogen phosphate, though. Fvasconcellos (t·c) 14:02, 9 January 2008 (UTC) We should probably discuss this in our IRC on Tuesday. Yellow_2G ChemSpider suggests the CAS NUMBER is for the free acid but I am not sure. Can anyone confirm? Beta-hydroxybutyryl-CoA I believe that coenzyme A should be fully protonated yet the majority of sites are charged. A WP-CHEM needs to be made about all CoEnZA compounds for consistency EDIT: WP-CHEM decision required Comments Betanin The structure on ChemSpider is [76] EDIT: Decision to be made about what the structure is , WP-CHEM decision Comments As a betalain, I'm pretty sure betanin exists as a zwitterion. Fvasconcellos (t·c) 14:10, 9 January 2008 (UTC) Bis(2,4,5-trichlorophenyl-6-carbopentoxyphenyl)oxalate The CAS number is listed below as 1165-91-9 ChemSpider lists the structure below for that number: [77] Also…ChemExper says [78] I DON’T know which structure is associated with that CAS Number. Can it be confirmed? The structure as drawn is: EDIT: Someone confirm the CAS Number. Also, the molecular formula is INCORRECT Comments CAS 1165-91-9 is bis(2,4,6-trichlorophenyl)oxalate (TCPO). This compound (CPPO) is, according to eMolecules, 30431-54-0 and 102579-84-0 ... Molecular formula fixed. Fvasconcellos (t·c) 00:10, 9 January 2008 (UTC) Bis(triphenylphosphine)iminium_chloride Ugly structure . I prefer… EDIT: WP-CHEM choose to replace structure Comments I disagree, I like the fact that the structure shows how the P is tetrahedral. Walkerma (talk) 05:42, 8 January 2008 (UTC) I agree that it communicates the Tetrahedral nature better but the overlap, for me, looks confusing. The question is whether to reduce confusion or communicate tetrahedral nature. I'll leave the decision to WP:Chem of course.--ChemSpiderMan (talk) 05:56, 8 January 2008 (UTC) Why not replace the phenyl rings with C6H5 or Ph? And note Ph = (benzene ring) in the image? --Rifleman 82 (talk) 17:51, 14 February 2008 (UTC) Bismarck_brown_Y Insert Chembox Insert IUPAC Name = 4,4'-[1,3-phenylenedi(E)diazene-2,1-diyl]dibenzene-1,3-diamine CONFIRM E/Z Comments For CAS#10114-58-6, Chemical Abstracts gives the 2HCl salt and has undefined double-bond geometry. For the neutral structure in the image Chemical Abstracts has CAS#1052-38-6, again with undefined double-bond geometry, but lists Basic brown G as a synonym, but not Bismark brown Y. -- Ed (Edgar181) 17:07, 10 January 2008 (UTC) Bistriflimide I disagree with the systematic name EDIT: Replace name if agreed. Comments This is being debated by IUPAC, see [79]. Walkerma (talk) 05:42, 8 January 2008 (UTC) Now...you are a wealth of information Walkerma! --ChemSpiderMan (talk) 05:51, 8 January 2008 (UTC) Bromocresol_purple The InChI String has been generated with the wrong settings and therefore generates the WRONG structure. The correct InChI is: InChI=1/C21H17BrO5S/c1-12-9-14(7-8-18(12)23)21(15-10-13(2)20(24)17(22)11-15)16-5-3-4-6-19(16)28(25,26)27-21/h3-11,23-24H,1-2H3 Comments FIXED: SORT OF. I replaced the InChI from the ChemBox with Physchim62's {{InChI}}, but now the InChI intrudes slightly into the Chembox. I've requested a modification which (if doable) should fix this. Walkerma (talk) 07:09, 9 January 2008 (UTC) The WP:CHEM team should be interested in this email send out today for comments. This is from the InChI team and is encouraging the adoption of standard settings. This was the issue with Bromocresol Purple...settings were chosen. If and when these standards were adopted then these problems should go away. We will be making these settings on our [ http://www.chemspider.com/InChI.asmx InChI Web service] for everyone to use. --ChemSpiderMan (talk) 22:02, 10 January 2008 (UTC) Calcium_carbimide The name says it’s a TRIcarboxylate but it is only doubly charged. Assuming it is then you need a 2:3 stoichiometry with Calcium Pubchem shows the neutral compound http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6335910 ChemSpider suggests it’s a 1:1 ratio. So, I think just the name is wrong? calcium 2-(carboxymethyl)-2-hydroxysuccinate - methylcyanamide (1:1) EDIT: Change the name? Comments Carthamin ChemSpider says: [80] The masses and the formulae are different. Which one is correct??? The name is: 3-[(Z)-{5-(β-L-Glucopyranosyloxy)-4,5-dihydroxy-3-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-2,6-dioxo-3-cyclohexen-1-ylidene}methyl]-1,2,6-trihydroxy-5-[(2E)-3-(4-hydroxyphenyl)-2-propenoyl]-4-oxo-2,5-cyclohexadien-1-yl β-D-glucopyranoside Comments The mass and formula in the Wikipedia article are consistent with those reported in Chemical Abstracts, PubChem, EINECS and the Merck Index. ChemSpider appears to be the outlier.-- Ed (Edgar181) 16:07, 9 January 2008 (UTC) I click on the emolecules link and find three compounds...two of mass of 910.78 but with different logP values (so they should be different molecules since they were calculated by the same algorithm) and one with a mass of 450. Then I click on the PubChem link and got a structure of mass 562 and a TOTALLY different structure..so, at least the PubChem link needs changing. The PubChem link is http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=11968069. I checked for the PubChem based InChi and found the structure on ChemSpider here but under the name Carthamine not Carthamin. Thanks to this work I have now curated out the INCORRECT names associated with the structure on ChemSpider.. All carmathine related names are removed from [here http://www.chemspider.com/Chemical-Structure.16736410.html]. I'll take CAS as the definitive call on this one. Ed..thanks for the help on this one.--ChemSpiderMan (talk) 05:24, 10 January 2008 (UTC) One more comment on this. Ed commented on the Carmathin record "I don't understand why emolecules has inconsistent data." This is in regards to linking the CAS number from Carmathin to eMolecules and seeing three different structures. This is not a comment against eMolecules as the same issue WILL exist on PubChem and CHemSPider in theory. NONE of these databases should be the primary reprepsentatives for CAS Numbers. I don't think the CAS Number should be linked to ANY external database in the way implemented now...that is doing a CAS number search. Why? The record on Wikipedia has the structures already. What is the value of linking the CAS Number. It's fine to link the PubChem ID, the eMolecules ID or even the ChemSpider ID but this will go directly to a record. However, a CAS Number search can take you to many structures with the same CAS number and create confusion.--ChemSpiderMan (talk) 05:08, 11 January 2008 (UTC) Coenzyme_F420 Add the structure : http://www.chemspider.com/Search.aspx?q=coenzyme+F420 13,16,17,18-tetrahydroxy-11-methyl-5,10-dioxo-19-(2,4,8-trioxo-1,3,4,8-tetrahydropyrimido[4,5-b]quinolin-10(2H)-yl)-12,14-dioxa-4,9-diaza-13-phosphanonadecane-1,3,8-tricarboxylic acid 13-oxide Comments Ethocybin Should the molecule in Wikipedia be drawn as charged or as above with the name 3-[2-(diethylamino)ethyl]-1H-indol-4-yl dihydrogen phosphate Comments F430 Please confirm my representation below. The SMILES string is: [Ni].O=C(O)CC[C@@H]1C\6=N/[C@]2(NC(=O)C[C@@]12C)C[C@@H]3/N=C (\[C@](CC(=O)N)(C)[C@@H]3CCC(=O)O)C[C@H]5/N=C4/C(C(=O)CC[C@H ]4[C@@H]5CC(=O)O)=C7\[N-]/C(=C/6)[C@@H](CC(=O)O)[C@@H]7CCC(=O)O From http://www.chemspider.com/Chemical-Structure.4573710.html I find: 73145-13-8 (can someone check the CAS number) Coenzyme F430 factor 430 Factor F430 Comments FADH2 Confirm the structure I have drawn and add the name. [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate Comments Fructose-1-phosphate Problems with this one…. The name does not have stereochemistry The name converts to the cyclic form: The PubCHem link is to the cyclic form [81] Is there a WP:CHEM policy about sugars in linear, cyclized form? The CAS number links to both linear and cyclic forms. Compare it to: Fructose_1,6-bisphosphate which is cyclic Comments (Also see below) Fructose_1,6-bisphosphate I think there needs to be a WP:CHEM statement on sugar representations. Also, protonation states ESPECIALLY if InChIKeys are going to be generated… [(2S,3S,4S,5R)-2,3,4-trihydroxytetrahydrofuran-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)] RNBGYGVWRKECFJ-CERMHHMHBJ is for the structure above RNBGYGVWRKECFJ-GSMOWLIGBO is for the structure in the ChemBox Consistency Issues Record to Record There needs to be consistency around linear vs cyclic, charged versus uncharged, named with stereo or not. Comments Fructose_6-phosphate The structure as drawn is not consistent with the name…which is right? [(2R,3S,4S,5S)-3,4,5-trihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate Comments Fumonisin_B2 Formatting issues: From ChemSpider: [82] I have not proven the structure to be correct though. But it is consistent with PubChem. Comments Gamma-amanitin No structure. This structure is in ChemSpider… [83] It has no stereochemistry Comments Geranyl_pyrophosphate A decision needs to be made about charged state/protonation state. The structure does not coincide with the SMILES or the PubChem link. (2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate Comments Geranylgeranyl_pyrophosphate Same issue with protonated/charged states – the MF and Mass do not match the structure Comments Glycerate_3-phosphate Name does not match the structure. Glycerate phosphate, (2R)-2-hydroxy-3-phosphonooxy-propanoate, (2R)-2-hydroxy-3-(phosphonooxy)propanoic acid. EDIT: Decide what the structure should be and name appropriately Comments Guanosine_diphosphate_mannose I think a better image is at: [[84]] IUPAC NAME [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate Comments I added the IUPAC name, but a suitable structure needs to be drawn (with clear copyright) Redrawn from Chemspider's SMILES. Please let me know if I made a mistake! --Rifleman 82 (talk) 17:59, 14 February 2008 (UTC) HMG-CoA Add IUPAC Name and add stereochemistry to the structure. (9R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8,21-trimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide Comments I added the IUPAC name, structure still needs to be done. Comments Heme_b Compare the Wikipedia structure with the PubChem structure and notice the difference in MF. Also, what is the best representation for the structure? WP or PubChem? I'd like to know the consensus to reproduce it in ChemSpider since there are THREE representations in CS [85] Comments Heme c The link in PubChem goes to the identifiers HEC or Hem. PubChem has heme c as [86] What is the correct structure? Hippuristanol No structure. I suggest validating the full stereochemistry here: but the structure is available on ChemSpider here Comments I've uploaded a structure based on that found at the discoverer's website; does it match the one currently at CS? It also needs an IUPAC name; I use the free version of ChemSketch (only names compounds up to 50 atoms or 3 cycles), and my skills aren't up to that :) Fvasconcellos (t·c) 00:33, 21 January 2008 (UTC) ChemDraw 11 cannot generate a name either. A minor remark: IUPAC recommends not to attach wedged bonds to each other like in this structure but to use a wedged H. Сасусlе 00:53, 21 January 2008 (UTC) ACD/Name CAN generate a name "(2R,2'R,4S,4a'S,4b'S,5'S,6a'S,6b'R,7'R,9a'S,10a'S,10b'S,12a'S)-4,4a',5,5,6a',7'-Hexamethylicosahydro-3H-spiro[furan-2,8'-naphtho[2',1':4,5]indeno[2,1-b]furan]-2',5',7'-triol" The structure as drawn is incorrect I believe since a number of stereocenters are not defined. I will submit the actual structure with full stereo onto ChemSpider and send you the link.--ChemSpiderMan (talk) 02:56, 22 January 2008 (UTC) Chemical Abstracts gives a structure for hippuristanol with all the stereocenters defined. CAS#80442-78-0. I've added a corresponding image and SMILES to the article. I'm unable to generate and IUPAC name. -- Ed (Edgar181) 14:10, 22 January 2008 (UTC) The structure is consistent with the one on ChemSpider now http://www.chemspider.com/Chemical-Structure.21105577.html. The IUPAC Name is above in the text...--ChemSpiderMan (talk) 17:02, 22 January 2008 (UTC) Thanks, and sorry about that; I've updated the SVG. Is there any way to break the SMILES string? Fvasconcellos (t·c) 19:21, 22 January 2008 (UTC) Hydrastine Hydrastine is lacking stereochemistry. Suggested structure is here. Suggested name is (3S)-6,7-dimethoxy-3-[(5R)-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-2-benzofuran-1(3H)-one Comments Should it be (+)-hydrastine or (−)-hydrastine? (+)-Hydrastine is (3R, 5S), not the other way round; (−)-hydrastine is all-R.[87] Fvasconcellos (t·c) 12:29, 20 January 2008 (UTC) Inositol_pentakisphosphate No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE As host of ChemSpider I grant Copyright to you...However, I don't think the images are of sufficient quality for you. I had started a conversation on Wikipedia previously about the possibility to generate PNG images off of ChemSpider but I don't think I received any feedback and we cannot do this right now because of the list of other things to do. It would be many weeks now before we could do it. i would suggest downloading the structure from ChemSPider into an appropriate package at the desktop and generate the PNG or SVG image from that package. I am opening the discussion here again about whether or not there is interest in us generating PNG/SVG images of the structures from ChemSpider for use on Wikipedia?--ChemSpiderMan (talk) 16:33, 20 January 2008 (UTC) Kallidin No structure available on Wikipedia Download the structure from ChemSpider. Comments CHECK COPYRIGHT STATUS IF USING CHEMSPIDER IMAGE Laminarin No structure. One is listed on ChemSpider that needs validating here. Comments MTSL The structure shown is: (an N-oxide) It says the name is: S-(2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate This converts to: (different structure, the corresponding amine) Comments Neocarzinostatin There is no structure on the record. This record is on ChemSpider for validation and inclusion here. Comments Looks like it's lacking a stereo descriptor? See reference 5 here and this, which also appear to show the most common orientation. Interestingly, PDB has plenty of crystal structures deposited for it, such as PDB: 1NCO​. Fvasconcellos (t·c) 12:49, 22 January 2008 (UTC) The structure at ChemSpider and the structure at "reference 5" linked above seem to be missing a double bond (exocyclic from the cyclopentane ring). Although Chemical Abstracts lists the structure as "No structure diagram available", I found a J. Org. Chem. reference from someone who actually made the compound and filled the chembox with the structure and data they report. That structure is the same as the one shown in 3 or 4 other recent journal articles I looked at. Our article refers to it as a "dienediyne" which is consistent with the structure I've added, but not the ChemSpider one. If anyone can double check me with other references, that would be nice. -- Ed (Edgar181) 12:29, 25 January 2008 (UTC) I have done some additional literature research but remain confused. An examination of PubChem shows the structure Edgar181 has drawn as the Neocarzinostatin chromophore rather than Neocarzinostatin itself. The difference is the one exocyclic bond. Since it has a MeSH annotation I am going to contact MeSH directly and get their comments. I DO agree that there are publications out there with the exocyclic double bond and labeled as Neocarzinostatin. For example 1. So, I'm not sure we're there yet.--ChemSpiderMan (talk) 15:15, 25 January 2008 (UTC) I've done a bit more reading too, and here's what I can tell. Neocarzinostatin is a complex of a small molecule (properly referred to as neocarzinostatin chromophore) bound to an amino acid, but the term neocarzinostatin sometimes gets used to refer to just the chromophore part. I think Wikipedia just needs a single article for neocarzinostatin and neocarzinostatin chromophore so I've tried to reword the article a bit to reflect this. The chembox is titled "neocarzinostatin chromophore" and the data in the box is for just this part (except that it now has two CAS numbers, each denoting what it corresponds to). The structure associated with CAS#79633-18-4, which I just added to the article, does indeed have the exocyclic double bond. Hopefully, this helps reduce the confusion instead of creating more. 15:37, 25 January 2008 (UTC) Yes, neocarzinostatin (properly holo-neocarzinostatin) is a protein-chromophore complex; see the PDB link I provided above. The protein alone would be "apo-neocarzinostatin", and the small molecule (prosthetic group) is the "neocarzinostatin chromophore", as Ed mentioned in the chembox. Fvasconcellos (t·c) 15:40, 25 January 2008 (UTC) Then it looks like we are dealing with an error of the absence of the double bond in other multiple databases? This includes KEGG and PubChem. I couldn't find it in eMolecules. ChemSpider is now corrected. The IUPAC Name (software generated) is: (1aS,5R,6R,6aE)-6-{[(2R,3R,4R,5R,6R)-4,5-Dihydroxy-6-methyl-3-(methylamino)tetrahydro-2H-pyran-2-yl]oxy}-1a-(2-oxo-1,3-dioxolan-4-yl)-2,3,8,9-tetradehydro-1a,5,6,9a-tetrahydrocyclopenta[5,6]cyclonona[1,2-b]oxiren-5-yl 2-hydroxy-7-methoxy-5-methyl-1-naphthoate. If you accept it either insert or let me know and I will.--ChemSpiderMan (talk) 16:01, 25 January 2008 (UTC) OK, I added it. -- Ed (Edgar181) 16:12, 25 January 2008 (UTC) Apparently, holo-neocarzinostatin has the proposed INN "zinostatin". Proposed INN list 74 has the structure as Ed drew it, with the double bond—so yes, it appears other databases are in error :) Fvasconcellos (t·c) 16:19, 25 January 2008 (UTC) Nile_blue The formula and the SMILES include chlorine. Should the image be a chloride salt ? EDIT: Decide on salt or not and make modifications Comments Norbaeocystin I think it’s a bad idea to hook a ChemBox to a PubChem or eMolecules search. When you click PubChem you get this: 45 HITS! http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=HistorySearch&WebEnvRq=1&db=pccompound&query_key=4&WebEnv=0WZ72yTPcueOePRfvFnsns4pyG6_yXI3zQjko-Hmmo0niFnKvuq0kSzEag9oycHVtGsi4aAsh5IvYR%40264662E1739B1F60_0066SID When you click eMolecules you get this: 0 hits http://www.emolecules.com/cgi-bin/search?t=ex&q=%5BNH3%2B%5DCCC1%3DCNC2%3DC1C%28OP%28%5BO-%5D%29%28O%29%3DO%29%3DCC%3DC2 The connections should be real to a 1:1 record. Same here: http://en.wikipedia.org/wiki/O-Acetylpsilocin Comments Pectic_acid No structure on Wikipedia/ The structure is here]. Comments Phosphopantetheine Structure needs stereochemistry and a IUPAC Name. ChemSpider says the structure is this. (3R)-3-hydroxy-4-({3-[(2-mercaptoethyl)amino]-3-oxopropyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen phosphate Comments Plicatic_acid I believe the structure might be wrong. The structure shown here should be validated. (1S,2S,3R)-1-(3,4-dihydroxy-5-methoxyphenyl)-2,3,7-trihydroxy-3-(hydroxymethyl)-6-methoxy-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid The ChemSpider record is here. Comments Pyrrolizidine Is Pyrrolizidine itself a naturally occurring alkaloid? It appears to be a fragment of the alkaloid. [88] Comments Pyrrolysine Should the carboxylic acid and amine be charged or neutral. The name suggests neutral N6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine Comments QS21 No structure on the record. Confirm this as the structure and add: (structure) Also see this. Comments Quaternium-15 Drawn as a cis-compound. Should it be a trans compound: [89] Comments Quercitron The label on the structure image suggests the structure is wrong…shouldn’t it be replaced.? Comments Quinoline_Yellow SS version is: [90] WS version is: Comments Ristocetin No structure on Wikipedia. Suggested structure is on ChemSpider [here]. Comments Roseophilin No structure on Wikipedia. Suggested structure on ChemSpider here. Comments S-Adenosyl_methionine Structure is not charge balanced because of the NH3 plus charge. Is there a counterion? Comments S-Allyl_cysteine The IUPAC name is not consistent with the structure. Actual IUPAC name should be: (2R)-3-(allylthio)-2-aminopropane-1,1-diol Comments No! No way is this a 1,1-diol! I think perhaps the current name is a little wrong, I suspect the person meant S-{2-propenyl}-L-cysteine - is this IUPAC though? Walkerma (talk) 05:03, 7 February 2008 (UTC) Comments back..no, clearly it is NOT a diol. I don't where this association came from. I checked back in my files and could not see why I said this. This is why we need eyes checking my comments. After 4800 structures they are tired eyes.--ChemSpiderMan (talk) 23:25, 7 February 2008 (UTC) Spirotryprostatin_A WP says mass is 365.43. Actual mass is 395.43. Comments The Chembox originally went with a different image, Image:Spirotryprostatin A.JPG, which is missing the methoxy group (Note, the Edmondson/Danishefsky paper draws this demethoxy compound too, as an analogue). Someone fixed the structure but not the formula or the mass. The formula should be C22H25N3O4 (mass 395), not C21H23N3O3 (mass 365), which was "correct" for the original structure. Now fixed. Sulforhodamine_B No structure for this article Structure is here]/ Comments Now done (More to follow) Status of Wikipedia Curation Project I am taking some downtime from the curation project for a few days to finish some other projects (publications, book chapter etc.) I will provide Walkerma with the latest report for him to post into this Sandbox for discussion. I am up to the letter "P", have already knocked out "X,Y,Z". I think it will be another couple of weeks before I return to the project. --ChemSpiderMan (talk) 14:22, 18 January 2008 (UTC) That's fine! I'm running around trying to get ready for the new semester (Monday), so I'm behind in transferring things over to here. We really appreciate the immense amount of work done so far! Look at the no. of daily hits on a typical page and you can see the importance of the work. Hope you can get caught up - though don't forget about us! Walkerma (talk) 14:58, 18 January 2008 (UTC) The link to the updated copy of the report issued on 011808 is here--ChemSpiderMan (talk) 13:37, 19 January 2008 (UTC) Another update to the curation report is here--ChemSpiderMan (talk) 05:21, 4 February 2008 (UTC) The link above has been updated to allow login without a password.--ChemSpiderMan (talk) 01:39, 6 February 2008 (UTC)
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