User talk:Benjah-bmm27

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Trigonal prismatic image request[edit]

Ben, thanks for all your very nice graphics! Would you be able to make an image of trigonal prismatic geometry in the same style/colors as your other ones (e.g. octahedral)? 129.105.92.25 (talk) 16:49, 8 June 2017 (UTC)

Some baklava for you![edit]

Baklava - Turkish special, 80-ply.JPEG Баклавата е появена през XІX век. Human anatomy (talk) 14:29, 2 January 2012 (UTC)

request structure diagram[edit]

Hi Ben:

Hope I am not bothering you!

Wondered if you could please make a structure drawing of Trifluralin. Would like it in the same format (colors and such) as done for the other molecules in the organofluorine strip.TCO (Reviews needed) 23:33, 22 January 2012 (UTC)

(as long as I am pushing my luck) Any chance of getting this one also? Fludrocortisone Also in the same format as the organofluorine strip molecules. (and if you can make the fluorine visible/prominent in the view, that would help.) Trifluralin is higher priority though.  :) TCO (Reviews needed) 00:57, 23 January 2012 (UTC)

Hi TCO,

I'd be delighted to draw these two for you. I just need to put my PC back together to do it. I'll let you know when it's done. --Ben (talk) 13:21, 23 January 2012 (UTC)

Thanks man. 'preciate! It is for a good article!TCO (Reviews needed) 17:58, 23 January 2012 (UTC)

OK, here you go: File:Fludrocortisone-from-xtal-1972-matt-3D-sf.png, File:Trifluralin-3D-matt-sf.png. Hope this is what you need. If not, let me know. --Ben (talk) 22:12, 23 January 2012 (UTC)

Thanks Ben. I know you are busy. Is for a good cause, important article! I will get a new ministrip made (just the biologically significant molecules). need to play with which ones I use and the order and all (I like making the order match the text order [and I am rewriting test for other reasons], so the article and text work together). These look exact same style, so should be no issues, but if anything comes up will bother you (I doubt it!)TCO (Reviews needed) 23:01, 23 January 2012 (UTC)

Lipitor[edit]

I think I want Lipitor also. You already have a drawing of that. I can't tell the matte/gloss stuff. Will just go with what is there and maybe come back to you if some look different from others. Compiling new strip now (request in at graphics lab). Thanks as always. Incredible what talent we have here at the Wiki and how many places I find your name on structures!!!

TCO (talk) 20:58, 2 February 2012 (UTC)

Do you want a new image of atorvastatin (Lipitor)? --Ben (talk) 22:38, 5 February 2012 (UTC)
No. I am good, thanks!TCO (talk) 22:48, 5 February 2012 (UTC)

Greek loanwords[edit]

Hello. Your username is in Category:Greek loanwords. I want to clean-up this category a bit from invalid entries so I want to remove your name from it, but I can't since it's archived in an old talk page of yours. Will you please do it for me? Macedonian (talk) 13:14, 27 January 2012 (UTC)

Done. Thanks. --Ben (talk) 13:20, 27 January 2012 (UTC)
Thank you. Macedonian (talk) 06:37, 28 January 2012 (UTC)

File:MPV-reduction.png[edit]

Image used in the aluminium isopropoxide article

Hi Ben,
I want to ask you about the image at right (File:MPV-reduction.png) which you uploaded some years ago. It seems to me that the alcohol in the product should be R1–CH(OH)–R2 rather than R3–CH(OH)–R4 (a starting material). Also the mechanistic arrows appear to me to produce R3–C(O)–R4 as the ketone product of both the MPV and OPP processes, yet that ketone is consumed in the OPP process and the ketone R1–C(O)–R2 produced instead. Perhaps you might be able to provide a corrected image, assuming you agree that corrections are needed? Thanks.
EdChem (talk) 10:39, 30 January 2012 (UTC)

Hi EdChem, yes, you're right. I'll fix it an re-upload. Thanks very much for spotting this and letting me know. --Ben (talk) 11:34, 30 January 2012 (UTC)
Done. Thanks for your help. --Ben (talk) 00:49, 3 February 2012 (UTC)
Thank you, your new version is excellent. :) EdChem (talk) 06:14, 3 February 2012 (UTC)

I hope I'm not really bothering you[edit]

Hello. I am working on (for purposes listed below) on astatine. I want a molecule for it. I honestly tried to make one. Downloaded a molecule structurer. Really tried to do it myself. I failed :( Seems I'm not so good at designing.

If this does not bother you, would you mind helping me by drawing a molecule? (I'm inclined to ball and stick C6H5—AtO2, but it does not matter.) If you are so kind to help, I'll gladly take any (just not HAt, please). This would be really appreciated!--R8R Gtrs (talk) 15:59, 3 February 2012 (UTC)

P.S. I understand if you just can't, for any reason.

I'm sure I can draw you something, but I'd prefer to draw a molecule which has actually been structurally characterised. I assume no astatine compounds have known structures, but maybe you could find out for me. I think a computed structure would be OK, but I don't want to compute one myself because it'd be original research and I might get it wrong. --Ben (talk) 16:13, 3 February 2012 (UTC)
I'm happy to know you're so easy to interact with :)
If you want bong lengths stuff, then it's probably very hard to find. But if it is what you want, I'll search as I can. And I believe it may be a failure anyway. Pretty possibly none calculated it. But I originally thought of something more "down-to-earth." I mean, to go without bond lengths. We can point out that the image is just not to scale, which is obvious, to avoid this. Structure of C6H5—AtO2... I haven't seen it anywhere discussed, maybe because actual readers find it obvious anyway. Especially given the route to the chemical (C6H6 (+At2)→ C6H5—At (+Cl2) → C6H5—AtCl2 (+NaOCl) → C6H5—AtO2). The benzene ring, with one hydrogen replaced by —AtO2 group (double bonds between At and O)
--R8R Gtrs (talk) 16:35, 3 February 2012 (UTC)
Ben, I looked hard for the bond lengths. Of course, I found nothing. But I checked the literature. It says that C6H5AtO2 can be synthesized in the absolutely same manner as C6H5IO2. This, given analogous empirical formulas, brings me to the logical conclusion they have the same structure. And here lies the structure for C6H5IO2. If you need some other info, please tell me.--R8R Gtrs (talk) 12:30, 5 February 2012 (UTC)

Thank you very much for looking, I've been too busy to do it myself. Can you provide a link to the literature describing PhAtO2, please? It is very dangerous to "logically" conclude structures from empirical formulas – see Talk:Dibutyltin oxide#Structure for an example of such logic leading to inaccurate information in a Wikipedia article. Such "logic" is basically banned on Wikipedia. The section Synthesis of published material that advances a position at Wikipedia's "no original research" policy describes the rules. --Ben (talk) 22:49, 5 February 2012 (UTC)

I've checked the literature and databases, and PhIO2 is polymeric (N. W. Alcock, J. F. Sawyer (1980) Dalton Trans., 115). A polymer would be highly improbable for astatine (random and rapid radioactive decay would mean one of two neighbouring At atoms in a polymer would very likely decay after a very short time). I don't know what effect a lone pair on At would have on the structure of an isolated PhAtO2 molecule. I need to find either (i) a calculated structure for PhAtO2 or (ii) a calculated or experimental structure for an isolated (e.g. gas phase) PhIO2 molecule and a reference stating the At analogue is likely to be isostructural. Else we risk speculation. --Ben (talk) 00:39, 6 February 2012 (UTC)

Thanks. Got your point, it seems reasonable. Gimme a few days, OK? I'll try to find something. (I don't believe to succeed, but who knows?) Also, will check the less complicated molecules. If I fail, can I at least get the space-filling HAt? I can give you a ref telling it's molecular. There is some molecule in the main article, but I want one of your beautiful 3D molecules (I really like them; no wheedling).--R8R Gtrs (talk) 16:58, 6 February 2012 (UTC)

Fair enough. So, for the meantime, do you want a shinier version of File:Hydrogen-astatide-3D.png? J. Styszyński, J. Kobus, Chem. Phys. Lett (2003) 369, 441–448 gives the H–At bond length as about 1.72 Å, depending on computational method employed. I'm making an image of it now. --Ben (talk) 22:36, 6 February 2012 (UTC)

Found nothing. So yes, I want a shinier version of File:Hydrogen-astatide-3D.png, please.--R8R Gtrs (talk) 16:28, 8 February 2012 (UTC)

(talk page stalker) The following ref might be useful: "Temperature dependence of the ion–ion distance of crystalline francium halides and alkali metal astatides". Radiokhimiya (in Russian). 11 (6): 698–706. 1969.  I can't find the journal at any local library and I can't read Russian, but could request it by interlibrary loan and hope that at least some data-tables would be understandable if you want it. DMacks (talk) 16:57, 8 February 2012 (UTC)
Would generally love to :) Just in case: if nothing understandable for you is present, you may note that I can read Russian (so if you photographed it, it would be easy to me to read ;))--R8R Gtrs (talk) 17:42, 8 February 2012 (UTC)n.
Requested it and another more recent article that may have additional information...will probably take a few days to arrive. DMacks (talk) 19:51, 8 February 2012 (UTC)
Ok. Thank you!--R8R Gtrs (talk) 11:48, 9 February 2012 (UTC)

Here you go: File:Hydrogen-astatide-calculated-3D-sf.png. --Ben (talk) 13:19, 9 February 2012 (UTC)

Thank you very much! Mind if I ask you for anything ever again? :) --R8R Gtrs (talk) 12:03, 10 February 2012 (UTC)

Molybdocene dichloride[edit]

Hi Ben, I have started a page on the organometallic compound molybdocene dichloride, Cp2MoCl2, which is structurally similar to titanocene dichloride. That is, two η5 cyclopentadienyl ligands and two chloro ligands around the MoIV centre in a distorted tetrahedral arrangement. Would you be willing to prepare an image suitable for illustrating its geometry? Thanks, EdChem (talk) 15:37, 4 February 2012 (UTC)

Sure. Skeletal formula or ball-and-stick model or both? --Ben (talk) 18:38, 4 February 2012 (UTC)
Thanks. Both would be excellent, to go in the infobox much like in the Cp2TiCl2 article. EdChem (talk) 17:17, 5 February 2012 (UTC)

Done - enjoy. --Ben (talk) 00:18, 6 February 2012 (UTC)

Side by side CaF2 and BeF2[edit]

I want to create a little side by side comparison of CaF2 and BeF2 for Fluorine#Low oxidation state metal fluorides.

http://en.wikipedia.org/wiki/Wikipedia:Graphic_Lab/Illustration_workshop#Make_BeF2_glass_diagram.2C_possible_crop.2Fpad_of_other_image

Any help appreciated. Mostly, just need the BeF2 image. I can handle the putting it into a table and all. Even get aspect ratio tweaking if that is not your bag. (will be centered, which is why I prefer wide and short aspect). I realize drawings won't be same scale and one is ball and stick versus the other being space filling. THat said, I still think it will work to show the basic point (super rigid CaF2 versus deviant loosey-goosey BeF2) and they are so clearly different scale that reader will not be confused. Also, I'll use caption to explain that glass is a 2-d slice)TCO (talk) 19:11, 4 February 2012 (UTC)

I can re-draw these things in the same style – do you want them both ball-and-stick or both space-filling?
Another important point is that BeF2 can adopt more than one structure. Which structure do you want drawn?
According to Greenwood & Earnshaw, beryllium fluoride is "a glassy material that is different to crystallize; it consists of a random network of 4-coordinate F-bridged Be atoms similar to the structure of vitreous silica, SiO2." They mention two crystalline quartz structures (a low temperature α modification and a higher temperature β one), plus cristobalite and tridymite analogues.
J. Am. Chem. Soc. (2008) 130, 11082–11087 investigates polymorphism in BeF2 computationally. They mention a coesite analogue, as well as the structures noted by Greenwood & Earnshaw.
Ben (talk) 22:26, 5 February 2012 (UTC)
Yeah, I got the same info for BeF2 polymorphs. I think showing the glass versus fluorite is most helpful in terms of storyline. They are obviously not the same sort of drawings (or to scale), but presumably different enough so that is obvious to the reader anyway, and I can clarify with caption. If we did a BeF2 xtal structure, than alpha quartz would make most sense. And I assume ball and stick is needed to see what is going on. But I really prefer the glass as it is more common and makes more sense as extreme of "abnormalness" of BeF2. I actually think I have what I need from the Graphics Lab, now, except I will get the aspect ratio worked on (is a reason why I prefer short and wide, has to do with layout issues and text wrap).TCO (talk) 22:43, 5 February 2012 (UTC)

OK, cool. That glass structure might be nonsense, though. None of the images cites a reference. --Ben (talk) 22:52, 5 February 2012 (UTC)

I'll clarify that it is a sketch. I think even for silicate glass, it would be a cartoon, not "the structure".TCO (talk) 01:14, 6 February 2012 (UTC)

Three of your molecules as sphere-representation[edit]

Hi Ben,

Thanks for publishing chemical structures. You published 3 of them as balls and sticks, but I need them as a spherical representation. The files are the following:

Could you please change these structures to the sphere-representation?

Thanks in advance and best regards from Germany JF Jotef (talk) 13:09, 9 February 2012 (UTC)

When you say "spherical represenation", do you mean space-filling models? If so, yes I can do this for you. --Ben (talk) 13:16, 9 February 2012 (UTC)

Done:

--Ben (talk) 23:36, 9 February 2012 (UTC)

Wow, thanks a lot!!!! Jotef (talk) 06:12, 10 February 2012 (UTC)

Hiatus[edit]

Hey Ben,


You may have noticed that I have not created structures for Wikipedia in a while; over time I notice more and more how little I know about Chemistry. However, I miss doing it.

I am still an undergraduate, but I am going to be participating in research with my professor soon. I feel that my understanding of chemistry just keeps increasing! I would like to resume contributing to Wikipedia some time soon. I now have tons of access to crystallographic data, and my professor would probably be more than willing to help me. I understand that interpreting crystallographic data is a graduate level course, but I hope you don't think that I am pompous for asking this: granted a basic understanding of multivariate calculus and ordinary differential equations, would one be able to learn how to recreate structures after reading a decent amount? For example, I found a great slide show that I think may supply all of the information that I need to tackle this task, tell me what you think: http://www.cryst.chem.uu.nl/huub/notesweb.pdf


Thank you,

SubDural12 (talk) —Preceding undated comment added 08:48, 16 February 2012 (UTC).

Hi SubDural,
Yes, I wondered where you had gone - glad to see you back.
I'm still an undergraduate too, so don't worry about that. I really don't think you need to worry about multivariate calculus and ordinary differential equations in order to use published crystallographic data to make images for Wikipedia. It's much simpler than that.
You can either type the Cartesian coordinates into Accelrys DSV (I'll tell you how if you want to do it that way) or open a CIF file in a crystal structure viewer like Mercury (which is free). You can get many CIFs free at http://journals.iucr.org/, or you may have access to a database of CIFs like the Cambridge Structural Database or the Inorganic Crystal Structure Database (ICSD).
That PDF you link to is excellent, but it contains fair more information than you need. Use it if you want to learn how to solve crystal structures yourself. Are you doing any crystallography yourself at university? --Ben (talk) 10:23, 16 February 2012 (UTC)

Ben,

I like the idea of the CIF, because the work is basically done for me. However, there are some structures that only allow me to view the coordinates, so I think that it would be important for me to understand how to do it that way as well. I was wondering where you obtain the coordinates - generally in the image section? For example, I would never have known that there was partial bonding between the nitrogen and the alcohol group in your rendition of monoethanolamide if it were not for the crystallographic data. I found on table VI of doi:10.1063/1.1612919 that there was a list of "principle-axis-system coordinates." Is this where I should be looking? How do I utilize this information? Also, I see that you have calculated some structures using Spartan Student. What is this program, and do you recommend getting it?

Also, I am not doing any crystallography yet. University here in the states is not as complicated as it is over there. However, I will be synthesizing novel metal complexes that may have practical uses. This will be fun :). I appreciate the help.

SubDural12 (talk) 21:17, 16 February 2012 (UTC)

Hi SubDural. I just noticed I never replied to this message. You don't need to know about multivariate calculus and ordinary differential equations to use coordinates from an article to make a molecular model. You can just type them into DSV (there's a way of creating a unit cell and then adding atoms, I can't remember how off the top of my head but the help files should guide you).
The paper you link to, J. Chem. Phys. (2003) 119, 8397–8403, uses microwave spectroscopy to study the gas-phase structure of ethanolamine. It's a completely different technique to crystallography. I sometime use microwave papers, but only if the bond lengths and angles are explicitly stated.
Spartan Student is an easy-to-use computational chemistry application. You can get it to calculate the minimum energy structure of a molecule for you. It's fun and teaches you a few things about chemistry and molecular modelling. I used to use it when I couldn't find a molecular structure in the literature, or to draw diagrams of molecular orbitals. I wouldn't recommend this, though. It's verging on original research, which is forbidden on Wikipedia. You can think you've calculated the correct structure of a molecule, but you haven't really got it right and you'll have no way of knowing. Computational chemistry should really be done by experts and carefully checked against experimental structures. As an encyclopaedia, Wikipedia should just cite textbooks and other scientific literature. We shouldn't really be doing our own experiments (even computer experiments) and reporting the results here.
So I recommend Spartan for learning chemistry but not for Wikipedia, not unless you're refining a literature structure or something similarly uncontroversial.
Good luck with your synthetic project. I'll be interested to see what you make.
Ben (talk) 12:00, 4 April 2012 (UTC)

2 last local space-filling models[edit]

Hi Ben. The space-filling models in CLD chromophore and Octadecyltrichlorosilane are the two last local ones that are in the inappropriate JPG type and in use. It would be great if you could redraw them in your high quality way. --Leyo 09:51, 26 March 2012 (UTC)

Hi Leyo, thanks for the request. I'll do them ASAP. Cheers. --Ben (talk) 11:06, 26 March 2012 (UTC)
All done. --Ben (talk) 11:29, 1 April 2012 (UTC)
Great, thanks a lot. I nominated the two replaced JPG images for deletion. --Leyo 10:55, 2 April 2012 (UTC)

Levonorgestrel[edit]

Hi Ben, I've been doing tons of molecules thanks to your guide. So, I wanted to thank you for that.

Now, back to business, could you check the 3D model I made for Levonorgestrel? The far right C-C---C-O (--- triple bond) apparently goes down in the 2D model yet it doesn't in the 3D model, I've tried all the SMILES and InChI keys and once I copy paste the 2D model from ChemSketch to the 3D model in Discovery and then apply clean geometry, the C-C---C-O "tail" (electrical, not chemical, engineer here, bear with me) never goes down. Oddly enough, this "tail" DOES go down here Gestodene (also made by me). So, what gives? Thanks for your time. MindZiper (talk) 04:44, 4 April 2012 (UTC)

Hi MindZiper, thanks for your message. Beautiful images, well done.
I think it's the presence of the C=C double bond next to your atoms of interest in gestodene that keeps the CCH group down (chemists would say CCH is in the axial position and OH the equatorial). The C=C makes the five-membered ring more rigid, reducing the number of different possible conformations. This makes it easier for DS Visualizer to get it right.
I was surprised at the conformation DSV calculated for levonorgestrel, so I checked the crystal structure. The true conformation is different, it's like gestodene. I can send you a PDB file of the structure if you want to update your image.
The reason DSV didn't calculate the correct conformation is probably that it got stuck in a local energy minimum and wasn't brave enough to jiggle the atoms around sufficiently to find the global minimum. But I'm not a computational chemistry specialist, so I don't really understand much about how the software operates.
It's verging on original research (which is banned) to calculate your own 3D molecular models and put them in articles. It's much better to use the scientific literature (journal articles, reviews, textbooks) to confirm the structure. Almost all of my images are based on crystallographic (or occasionally spectroscopic) reports. I include references to the original publication on the image description page. If you're able to do this too, your images will be more trustworthy and are likely to remain in articles for longer.
I know it's difficult to search the literature systematically and obtain models or structural data without the tools available to professional and academic chemists. Some crystallography journals are open-access or partially open-access. Some articles in IUCr journals are open-access, as is all of Acta Crystallographica Section E: Structure Reports Online. For example, the article Acta Cryst. (2012) E68, o1279 gives you free access to a CIF file, which you can open in DSV and make an image of the molecule. You can use the search bars on those websites to see if the molecule you want has been reported and is free to download.
I'll be happy to help if you get stuck. --Ben (talk) 09:26, 4 April 2012 (UTC)
There, I think I fixed it, and now it looks exactly like the 3D model from ChemSpider. I verify the models using the 3D models from PubChem or ChemSpider (I suppose they have their stuff done right), and I always got that little meddling "tail" wrong UNTIL gestodene, which is why I asked you about it before I kept making the same mistake. So apparently all the molecules that I've drawn that have this "tail" in them are slightly wrong (very wrong actually, mifepristone depends on its propynyl that goes down. I need to fix that as well). Thanks for the journals, they'll come in handy next time I try to model anything. Thanks again for your time. MindZiper (talk) 02:07, 7 April 2012 (UTC)

No problem. I wouldn't trust PubChem or ChemSpider for 3D models unless they specifically state they're experimentally determined by X-ray diffraction or similar. You've done well to consider whether your models are realistic, unlike many of the others who upload 3D molecule diagrams here. If you need any more advice, feel free to ask again. Good luck! --Ben (talk) 09:33, 7 April 2012 (UTC)

Bond length and angle in ammonia[edit]

Hi Ben, I wanted to verify the data for the bond length and angle in ammonia. What I found in the CRC handbook and in other published sources was 101.2 pm and 106.7°, rather than 101.7 and 107.8°. Do you have a reference for your data? Chrom69 (talk) 14:43, 10 May 2012 (UTC)

Hi Chrom, I got it from Greenwood & Earnshaw, p.423. These dimensions are often a bit tricky - the value you obtain depends on the analytical technique you use. There are all sorts of issues with excited states and what not. Perhaps CRC is the way to go. --Ben (talk) 21:06, 10 May 2012 (UTC)

Drawing needed for ReH9(2-)[edit]

Hello

I would like to ask you to create a ball-and-stick drawing of the correct trigonal capped triprismatic (D3h) structure of ReH92-, in the same style as the other drawings in the VSEPR article. As you noted recently on the VSEPR talk page, this is not the same structure as the monocapped square antiprism (C4v) currently in the table in the VSEPR article. I did find an image of the D3h structure in another (less attractive) style and placed it on the page for ReH92-. However when I tried to place that image in the VSEPR article, another editor substituted the C4v image; apparently s/he still thinks the two are equivalent despite your explanation. So perhaps it would help to have a good D3h image which can be used in both articles. I don't have software to draw it so I am asking for your help.

As for the C4v image, I note that it was drawn by you in 2008 and labeled as ReH92-. Perhaps you did not realize in 2008 that it does not correspond to the experimental structure of this ion. That image could be relabelled as Monocapped square antiprismatic geometry, although I do not know if there are any real molecules with that structure. Dirac66 (talk) 12:45, 18 May 2012 (UTC)

Hi Dirac66, thanks for updating me. I actually made images based on the crystal structure of potassium nonahydridorhenate in 2009, but had forgotten about them until you reminded me: Commons:Category:Potassium nonahydridorhenate. I can't remember what I thought when I made the 2008 image! I probably just got the software to guess some hydrogens in sensible places. This guy Whoop, what is his obsession with the two structures being equivalent? --Ben (talk) 17:54, 18 May 2012 (UTC)

I just read the 1999 redetermination of the crystal structure again. From what I could gather with my limited knowledge of German, the structure of ReH92- is a monocapped square antiprism (i.e. C4v). The authors note that the tricapped trigonal prismatic structure (D3h) is closely related.

Here's the original German quote: "Als Koordinationspolyeder ergibt sich ein einfach überdachtes vierseitiges Antiprisma, das dem dreifach überdachten trigonalen Prisma eng verwandt ist." And my (rough) English translation: "The coordination polyhedron is a singly-capped four-sided antiprism, to which the tricapped trigonal prism is closely related." --Ben (talk) 18:18, 18 May 2012 (UTC)

In fact, I made Jmol models of the crystal structure and the anion a while ago, too: http://www.benjamin-mills.com/chemistry/structures/K2ReH9/. Enjoy! --Ben (talk) 18:32, 18 May 2012 (UTC)
Thanks for your replies and for the German translation. (It has been many years since I passed a German-to-English translation exam, and I can no longer translate that whole sentence by myself.) Also I didn't know the structure had been re-determined, and now I think we should decide what the facts are before modifying the article. Perhaps you could start a discussion on the ReH92- page by citing the 1999 reference (which is not now cited in the article) and describing its conclusions there. Since this paper contradicts the two textbooks cited which say D3h, do you think it is definitive? Should the Wiki article say that it has been recently corrected or that it is now in doubt?
Also can you figure out from the article what is meant by closely related (eng verwandt) in this context? Does it mean (1) that the displacement of H atoms required to transform one structure to the other is small, or (2) that the interconversion is facile (with a low energy barrier), or (3) something else?
Finally I looked at your Jmol models and I am confused. The most relevant model would be the ball-and-stick model of the anion, but it seems to have only six hydrogens instead of nine. What have I not understood? Dirac66 (talk) 19:34, 19 May 2012 (UTC)
OK, I understand this model now. We are looking down the C3 axis so the other 3 H are behind the 3 H connected by the shorter Re-H bonds. Dirac66 (talk) 20:36, 19 May 2012 (UTC)
Thanks for your thoughts, they've made me double check. This 1999 redetermination is apparently no different to the previous crystal structures (X-ray and neutron from 1964). 'Eng' means 'narrow' or 'tight' - I took this to mean 'closely'. 'Verwandt' means related. The article doesn't elaborate further. I think I misinterpreted the section about the anion geometry. It says early in the article that it's tricapped trigonal prismatic (D3h). At the end, they mention monocapped square antiprismatic [ReH9]2− in a different compound, Rb3ReH10 (weird stoichiometry - apparently Rb3H[ReH9]). So there's no controversy, the structure of [ReH9]2− is D3h, as you and the textbooks state. The Jmol model should now be rotatable - click and drag to manipulate it. You can see the threefold symmetry for yourself, as you say. --Ben (talk) 22:05, 19 May 2012 (UTC)
OK thanks. I'm glad to know that the scientific literature is in agreement on the D3h structure. Perhaps you could add the 1999 German reference to the article on [ReH9]2−. Also the click and drag does indeed help the visualisation.
As for the VSEPR article, we still need an image of the tricapped trigonal prismatic structure in the same format as the others in the table, drawn with all nine H visible (at least in part). This can replace the incorrect C4v image which is there now. Dirac66 (talk) 00:44, 20 May 2012 (UTC)

I've added the references (1999 and original 1964). I'll make a new image for VSEPR theory as soon as I can. Thanks for the discussion! --Ben (talk) 10:49, 20 May 2012 (UTC)

Very good. Dirac66 (talk) 16:28, 20 May 2012 (UTC)
Thank you, the drawings you have added today look very good. I see that you even drew the AX8 square antiprism from two different perspectives. I have now copied the AX9 drawing into the potassium nonahydridorhenate article to replace the one I copied previously. (And I'm glad to see you are in Bristol - I spent two years there, long ago before you were born.) Dirac66 (talk) 20:05, 30 May 2012 (UTC)

A useless (theoretically interesting) molecule[edit]

Hello, Ben. Could I ask you to re-draw this into a ball-and-stick picture, one of those cool ones you draw? I think it's (I mean the image) more interesting than simply HgF4 we've got in (fluorine) now. Also, don't want to use the existing image (seems too boring mb, dunno, no excitement about it). Do you think you could help?--R8R Gtrs (talk) 11:50, 24 May 2012 (UTC)

Yep, no problem, give me a few days as I have exams at the moment. --Ben (talk) 11:53, 24 May 2012 (UTC)
Calculated structure (p. 618). Double sharp (talk) 09:19, 29 November 2012 (UTC)

lysine[edit]

Some while ago an editor queried the diagrams on the page about lysine, to which you replied. I happened to look at the page and was staring at the diagrams there now, because it looked wrong. So I hopped over to talk and found the existing conversation about it. I think you posted a 3-D diagram of a lysine cation which is now on the lysine page purporting to be lysine. Surely this is wrong, because it isn't what it is claiming to be? Sandpiper (talk) 06:06, 20 July 2012 (UTC)

Hi Sandpiper,
When I wrote at Talk:Lysine#Wrong diagram on page that File:L-lysine-monocation-from-hydrochloride-dihydrate-xtal-3D-balls.png isn't a mistake, I meant it was not an oversight. I deliberately uploaded the cation because the crystal structure of the neutral lysine molecule has not been reported. This is the closest we have to the true structure. I just searched again, still no neutral lysine crystal structure. Finally, lysine is protonated at physiological pH so the monocation is a realistic model. --Ben (talk) 09:06, 20 July 2012 (UTC)
Well thats interesting, but arguably makes matters worse. On the page there is a line diagram corresponding to C6H14N2O2 sitting next to a 3d diagram with 15 Hydrogens. They cannot both be the same thing, and as there is no explanation to the contrary why the 3D is different, its rather misleading and confusing for anyone who might be looking (me, for example, having stared at it and come to the correct conclusion that it is wrong). I dont know how this is usually handled, but you cant really put up representations of two different things under captions which imply they are the same. Something needs to be changed. But also, if I walk into a chemist and get a bottle labelled lysine containing solid material, what form would the lysine be in? Are you saying lysine does not actually exist? You give quite a detailed name for the molecule you drew, but my very rusty chemistry suggests that perhaps it could be more helpfully described as Lysine hydride? Sandpiper (talk) 20:31, 21 July 2012 (UTC)

I agree the chemistry merits discussion. The problem is, a satisfactory representation of the neutral molecule is not available. You wouldn't buy pure lysine from a pharmacy, it would be a tablet containing lysine hydrochloride (i.e. what the image depicts, plus a chloride counterion) plus inert white powdery substances to bulk out the tablet. See, for example, http://www.hollandandbarrett.com/pages/product_detail.asp?pid=117&prodid=29. A shorter name for the cation I drew might be lysinium. Hydride refers to the anion H (hydrogen with two electrons rather than one), whereas the extra hydrogen here is H+ (hydrogen without any electrons). I will update the article to clarify the situation. --Ben (talk) 21:21, 21 July 2012 (UTC)

Sorry, havnt had time to follow this up, and I guess nor have you. I see wiki says about hydrides, "Covalent hydrides According to the antiquated definition of hydride covalent hydrides cover all other compounds containing hydrogen. The more contemporary definition limits hydrides to hydrogen atoms that formally react as hydrides and hydrogen atoms bound to metal centers. " Which seems to be a rather perverse self-referential definition of a hydride as something which is a hydride, but that is a different problem. My rusty chemistry suggests we are not talking about hydrogen ions as such at all, more a charge redistribution within the molecule. In the sense you argue lysine never exists as such, nor do these hydrogen ions. That would be lysinium as in zirconium, magnesium, caesium? Sandpiper (talk) 08:01, 7 August 2012 (UTC)

Hi again Sandpiper. Really sorry for taking so long to reply. I've been pretty busy travelling and then starting a PhD these past few months. I'm not saying neutral lysine doesn't exist, because it almost certainly does. I'm just saying we don't have a crystal structure of it. I will look again to find something closer to what we want. Neutral lysine C6H14N2O2 would react with a bare H+ ion (i.e. a proton) to form the cation C6H15N2O2+. Lysinium would be the obvious name for this cation. It's not quite the same as zirconium etc, as these are the names of the elements involved. It's analogous to ammonia NH3 vs. ammonium NH4+. You see the same convention with many basic species and their conjugate bases, e.g. pyridine and pyridinium. --Ben (talk) 10:37, 23 December 2012 (UTC)

structure of MnF4[edit]

Article(s): Fluorine, Manganese(IV) fluoride

Request: Create an illustration for the MnF4 structure. See para in "Fluorine" for context. I would like it for two reasons: (1) the discussion is complex and a graphic will help people (especially non-technical ones) feel more comfortable and (2) it is sort of different than the chains and lattices shown.

In terms of the appearance, I would like something showing "octahedra" (since they are referred to in the text) and showing a ring of 4 of them. Perhaps use a dashed "circle" to emphasize the ring-ness. I am really more concerned with something a little cartoonish that illustrates the text than making sure we have a complete unit cell or the like.

Here is only non-free illo I could find [1]. It's quite nice in that it shows the octahedra, but also the little knobs of atoms at the vertices (think about the non chemical reader). But in addition, I would like the dashed circle added for the reader to see ring-ness emphasized.

I don't have crystal structure date, but perhaps you can research it (I am really not a purist on that sort of thing, but feel free if you are). Here is a reference: [2].

TCO (talk) 18:06, 15 July 2012 (UTC)

P.s. I prefer aspect ratio that is "wide and short" if it does not otherwise hurt the image (fits better in text wrap).

Graphist opinion(s):  Done - see Commons:Category:Manganese(IV) fluoride. Let me know which one you want to use and I will add the dashed circle. --Ben (talk) 23:21, 21 July 2012 (UTC)

thank you.TCO (talk) 01:26, 22 July 2012 (UTC)

explanatory sketch of F2 research piping station[edit]

For Fluorine, please draw a diagram that shows F2 research handling station. Not really sure what I want, but show the valves and cold trap and just the linear manifold and all.

See the para within Fluorine. Also this photo. And explanation. The enclosure with remote valve shuttof is quite interesting as is the placing it in a hood. Of course it is just one uni's method, but it seems state of the art (and I'll add a citation to their web page).

Maybe letters indicating materials (with legend). or just labels in drawing? Donno. Could probably strip out some of the scaffolding and other stray stuff for simplicity.

Also there is this classic diagram in Shriver Inorganic Chem page 427.

TCO (talk) 18:53, 15 July 2012 (UTC)

Straight to the point, there TCO! I don't have any experience with fluorine rigs, so I'm no better for this task than someone at Wikipedia:Graphic Lab/Illustration workshop. Might be best to ask there. --Ben (talk) 23:01, 21 July 2012 (UTC)
How about the MnF4 then? TCO (talk) 23:08, 21 July 2012 (UTC)

See new chem project proposal[edit]

See new chem project proposal

http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/Participants#Proposal_for_project. — Preceding unsigned comment added by Meduban (talkcontribs) 22:02, 22 July 2012 (UTC)

Congrats on the sheepskin, man[edit]

Major congrats on getting the degree. You have always been super kind and helpful around here and I hope you have lots of great things coming your way with that new credential.TCO (talk) 01:14, 23 July 2012 (UTC)

Good job[edit]

Academic procession.jpg The real life accomplishment award
Good job getting it over the goal line! TCO (talk) 01:18, 23 July 2012 (UTC)
Haha, thanks very much, TCO. --Ben (talk) 07:13, 23 July 2012 (UTC)

Technical help, please[edit]

Hi Ben! I recently figured how you make molecules, all thanks to your guide. However, I've got a problem I hope you can help me with. Your molecules are so smooth, and what I can make reflects shine like polished (they are in majority over Wiki, so don't want to introduce another minorish style). I have tried to change Preferences, but even after agreeing with the changes, the light problem doesn't change. What is the way out to make them smooth?

P.S. Many congrats about your recent success!--R8R Gtrs (talk) 10:25, 26 July 2012 (UTC)

In reverse order: (i) thanks very much! (ii) Newer versions of DSV have different surfaces to choose from (glass, plastic, wood etc). Play around with those to get as close a match as you can. It's not essential to make identical images. For me, a consistent colour scheme is the most important feature. --Ben (talk) 22:02, 26 July 2012 (UTC)
Not that I can't match your lighting. No preferences change actually changes the looks of the models! Regardless of what settings I choose, the result is always the standard lights -- as you can see here. Not even a slightest change. There must be a problem somewhere... But I don't know where and thus how to fix it. (I brightened the image in Photoshop, thankfully I have a copy, but it still looks too dark. Brightening any further makes the green look ugly... Really hope there's a way out!)--R8R Gtrs (talk) 22:28, 26 July 2012 (UTC)

Discovert Studio 3.5 Visualizer help - colour schemes[edit]

Hey, I followed your guide about using Visualizer for molecules, and everything works, but I can't figure out how to use the colour scheme you have. Is there a quick way to load the colour scheme, or do I have to change each individual atom by hand? Thanks. Elite6809 (talk) 11:54, 27 July 2012 (UTC)

Hi Elite. As far as I know, it has to be done by hand. You may be able to drag the colour scheme image into your colour picker. --Ben (talk) 12:11, 27 July 2012 (UTC)

WP Chemicals in the Signpost[edit]

The WikiProject Report would like to focus on WikiProject Chemicals for a Signpost article. This is an excellent opportunity to draw attention to your efforts and attract new members to the project. Would you be willing to participate in an interview? If so, here are the questions for the interview. Just add your response below each question and feel free to skip any questions that you don't feel comfortable answering. Multiple editors will have an opportunity to respond to the interview questions, so be sure to sign your answers. If you know anyone else who would like to participate in the interview, please share this with them. Have a great day. -Mabeenot (talk) 05:50, 22 September 2012 (UTC)

What software do you use for these models?[edit]

Hey, nice work! What software do you use to make these gorgeous ball and stick models (like the one in the link below)? I need to make a letter sized diagram, and these ball and stick models easily show relative bond lengths and 3D geometry. I also happen to be in love with the awesome lighting and gradient colour fills. I've looked around everywhere, but no one mentions what software is used for these gorgeous models. :(

http://en.wikipedia.org/wiki/File:Glycerol-3D-balls.png

--Amomchilov (talk) 16:41, 14 October 2012 (UTC)

I only just noticed this message, Amomchilov. Some details are given at User:Benjah-bmm27/MakingMolecules, and each image I upload now has information about the software used. If you have any further queries, just let me know. --Ben (talk) 14:31, 21 December 2012 (UTC)

3D model request[edit]

I see that you do a lot of chemistry modeling and imaging here. For a class, I created the article Brookhart's Acid. I have an x-ray crystal structure, which I took from an article and claimed fair use. Would it be possible for you to create a free image from the crystallography data? The article is Template:Cite doi/10.1021.2Fom990612w. Or else could you suggest who I should talk to for help with this? Thanks. JDS Chem 444 Sp2012 (talk) 05:06, 15 November 2012 (UTC)

I've made two free images for you, see Commons:Category:Tetrakis(pentafluorophenyl)borates. Best wishes, --Ben (talk) 14:07, 15 November 2012 (UTC)
Thanks a lot, those look great. JDS Chem 444 Sp2012 (talk) 16:24, 15 November 2012 (UTC)

I guess I didn't see this conversation. I made one too File:BArF acid crystal structure.png. Ben, I'm not sure how well the H+ is located. The article itself talks about how there's some uncertainty in that. I wonder if it might be better not to depict it? --Rifleman 82 (talk) 19:39, 15 November 2012 (UTC)

Good point. I just took the CSD data at face value. It's quite a niche compound, so the article's main audience is probably pretty chemically literate people. In general I tend to think it's better to make more easily understood images with all the hydrogens present and then discuss the limitations of the oversimplified model in the text. It's up to you guys, though. We now have both kinds of image. --Ben (talk) 21:14, 15 November 2012 (UTC)

Captopril 3D structure[edit]

Hi Benjah-bmm27,

Could you check your 3D structure of Captopril (File:Captopril-3D-vdW.png)? I believe that it is incorrect. It's close but Captopril should not have an N-H.

Thought you might like to know.

Methano (talk) 18:26, 20 November 2012 (UTC)

Thanks Methano, I've made new images based on experimental data now: File:Captopril-from-xtal-1980-3D-balls.png and File:Captopril-from-xtal-1980-3D-sf.png. --Ben (talk) 10:24, 23 December 2012 (UTC)

Could you please upload an image[edit]

I'd like you to please create an space-filling model of 1-fluorohexane in your fancy software that you have. IT would be a great help to add it to the article titled "1-Fluorohexane". Save as 1-Fluorohexane-3D-vdW.png

76.226.115.236 (talk) 00:17, 25 November 2012 (UTC)

Done: File:1-fluorohexane-3D-sf.png. Apologies for the long wait. --Ben (talk) 10:02, 23 December 2012 (UTC)

When you said to make a structure in ChemDraw (or related), what other software can you use? — Preceding unsigned comment added by 76.226.112.149 (talk) 03:42, 2 December 2012 (UTC)

M-CO-M things[edit]

Your fellow countrymen have made more work for you. There are no M-M bonds in the species with two (not sure about one) bridging CO's. There is no rush but Fe2(CO)9, Fp2, and Co2(CO)8 eventually could use refreshing. Thanks and hope you are well.--Smokefoot (talk) 23:35, 9 December 2012 (UTC)

Thanks Smokefoot. I made these images before I'd had any lectures on organotransition metal compounds, so I didn't know of the 18e rule or anything. I understood them in terms of the electrostatic 'metal ion + as many ligands as will fit' model I learned at A-level. Definitely time for an upgrade with X-ray structures. It's on the list. Cheers, --Ben (talk) 08:36, 10 December 2012 (UTC)
Thanks. The M-M bonds would be consistent with 18e rule, but the theorists are adamant that nothing is going on between the metals when there are bridging CO's. Now this message is migrating into the mainstream, per the Green-Green-Parkin review in ChemComm. An inconvenient truth for those who teach organometallics.
By the way, best wishes for a nice Christmas holiday. --Smokefoot (talk) 14:25, 23 December 2012 (UTC)
Thank you very much for bringing it to my attention. It's always tempting to ignore those inconvenient facts until they're so blindingly obvious you can't get away with it any more. Indeed, a very merry Christmas to you too, Smoke. --Ben (talk) 15:35, 23 December 2012 (UTC)

please add a molecule[edit]

Not to annoy you, but please create ball-and-stick and space-filling molecule models for the following articles:

Trioctylphosphine, n-Butylamine, sec-Butylamine, Isobutylamine, Thiophosphoryl fluoride — Preceding unsigned comment added by 69.212.172.168 (talk) 01:10, 31 December 2012 (UTC) Hexylamine.

Also a space-filling model of trimethylsilyl isothiocyanate would be nice.

69.212.172.168 (talk) 00:37, 31 December 2012 (UTC)

Done. See Commons:Category:Trioctylphosphine, Commons:Category:Butylamines, Commons:Category:Hexylamine. --Ben (talk) 01:56, 2 January 2013 (UTC)

Peter Proctor[edit]

There is yet another attempt to discuss Peter Proctor. I got a notice on my talk page. You are not expected to do anything, but you are welcome to comment at the dispute page about your experience/views on this theme. There are issues with WP:UNDUE and WP:COI and WP:OWN in my view.

By the way, thanks again for the work on the revised metal carbonyl structures. There are probably other M2(mu-X) images where the M-M bond should be removed.--Smokefoot (talk) 17:36, 5 January 2013 (UTC)

Thanks for the heads up. I'll have a look at both issues. --Ben (talk) 20:45, 6 January 2013 (UTC)

Formal mediation has been requested[edit]

The Mediation Committee has received a request for formal mediation of the dispute relating to "Peter Proctor". As an editor concerned in this dispute, you are invited to participate in the mediation. Mediation is a voluntary process which resolves a dispute over article content by facilitation, consensus-building, and compromise among the involved editors. After reviewing the request page, the formal mediation policy, and the guide to formal mediation, please indicate in the "party agreement" section whether you agree to participate. Because requests must be responded to by the Mediation Committee within seven days, please respond to the request by 25 January 2013.

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Nobel prize controversy[edit]

Hi. I'm a volunteer at WP:DRN, and the Peter Proctor article was mentioned in that venue. There are several editors that are adding unsourced material to the article. One of the topics is the suggestion that Proctor discovered something before the 2000 Nobel prize winner, and that there is a "Nobel prize controversy" about this discovery. I looked in the article Nobel prize controversies and Proctor is not mentioned, but there is a section on this 2000 Chemistry prize. The Talk page contains some history of that section. The section seems to based nearly entirely on primary sources, so it raises red flags about original research. The only source that appears to be at all secondary is the following:

Inzelt, György (2008). "Chapter 1: Introduction". In Scholz, F.. Conducting Polymers: A New Era in Electrochemistry. Monographs in Electrochemistry. Springer. pp. 1–6. ISBN 978-3-540-75929-4.

In looking at the Talk page, I don't see a quote from this source that says "there is a controversy" or something similar. So, I see two issues here:

1) Is there a source that explicitly says "there is a controversy"? What is the exact quote from Inzelt which demonstrates the existence of a controversy?
2) Why are there so many primary sources in that section? E.g. the sentence "Moreover, three years before, John McGinness and coworkers reported an active organic polymer electronic device in the journal Science.[34][35] " is based on primary sources, and thus is a violation of OR and SYNTH policies.

Can you shed some light on this? Cheers. --Noleander (talk) 02:00, 5 February 2013 (UTC)

Through innuendo and intimidation, many articles highlight the so-called achievements of Peter Proctor and his collaborator John McGinness while simultaneously "enlightening" readers on a variety of so-called controversies that diminish the achievements of others. The campaign was led by User:Pproctor who managed to get a biography of John McGinness, once of disputed notability, and then one glorifying himself (Peter Proctor). Following are some of a handful of articles that have been affected: Molecular electronics, Melanin, Conductive polymer, Organic semiconductor. And then there is a slew of articles that touch on other aspects of Proctor's world. Several of us have tried to tone down or eliminate some of the hype, only to be run off by a crew of loyalists that watch and guard all things Proctor. The loyalist crew, consisting of 2-4 users (more seem to materialize at times of stress), are clever, litigious, and unwavering. The entire affair is an embarrassment for Wikipedia, but it does have the salutary effect of reminding us that "it's only Wikipedia."--Smokefoot (talk) 02:29, 5 February 2013 (UTC)
To respond specifically to your request, I had never heard of a controversy over the 2000 Nobel for organic conductors, at least until I ran into the articles about Proctor. Proctor and his loyal coeditors have identified a series of papers that discussed work on the electrical properties of organic compounds as the basis of their diminishing the recognition to Shirakawa et al. Proctor. The tactic is of appearing to be open-minded ("I just happened to notice that other researchers did similar (to the Nobelists) work decades before"). It is all OR. Of course scientists have studied electrical properties of stuff for a long time and some of that stuff was organic. I in fact teach about conductive materials at a university level and have never ever encountered any reference to any controversy on this matter nor heard of Proctor and McGinness. The other aspect that these authors rely on is identifying a connection, which is tenuous at best, between melanin (which Proctor worked on) and polyacetylene and polypyrrole (which the Nobelists worked on). God only knows what these editors have done with other articles that relate to Proctors product line - hair loss, reactive oxygen species, etc. It is the absence of secondary sources (including any accolades) about Proctor's stature that suggests that he might not be notable.--Smokefoot (talk) 14:01, 5 February 2013 (UTC)
Okay, thanks for the info. Do you know which quote from the Inzelt source served as the basis of the inclusion of the material in the Nobel Controversies article (I don't have access to the Inzelt text)? I'll wait for user Ben to provide some input .... but an RfC on this section may be useful. --Noleander (talk) 14:44, 5 February 2013 (UTC)

Smokefoot has described the situation more eloquently than I could. You can read my discussions with pro-Proctor editors on the Inzelt text at Talk:Nobel Prize controversies#Inzelt reference 2000 Chemistry Prize.. I believe the pro-Proctor editors' approach is as follows:

  1. find reasonably reliable sources like Inzelt that describe a few discoveries in molecular electronics and conducting polymers prior to the Nobel Prize work
  2. add text to Wikipedia that exaggerates the importance of the prior work and diminishes the importance of the Nobel Prize work, citing Inzelt
  3. add further text citing Proctor's papers as examples of important prior work
  4. leave the reader with the impression that Proctor's work is as important as the Nobel Prize work, and was conducted some years earlier

It's deeply frustrating trying to engage with these editors because they argue every point, they turn your own words against you and use faulty logic in an aggressive manner. You'll post a quote that says "some work was done on conducting organic materials before the Nobel Prize work" and they'll come back to you and say "don't you agree that your quote implies Proctor revolutionised the field?" or something equally illogical. The large number of primary references are there because they're the only way to link Proctor's work to good secondary sources, which don't mention Proctor.

The relevant quotes from Inzelt are from Chapter 1 and Chapter 8. The Chapter 1 quote is as follows:

This story began in the 1970s, when, somewhat surprisingly, a new class of polymers possessing high electronic conductivity (electronically conducting polymers) in the partially oxidised (or, less frequently, in the reduced) state was discovered. Three collaborating scientists, Alan J. Heeger, Alan G. MacDiarmid and Hideki Shirakawa, played a major role in this breakthrough, and they received the Nobel Prize in Chemistry in 2000 "for the discovery and development of electronically conductive polymers.

As in many other cases in the history of science, there were several precursors to this discovery, including theoretical predictions made by physicists and quantum chemists, and different conducting polymers that had already been prepared. For instance, as early as 1862, Henry Letheby prepared polyaniline by the anodic oxidation of aniline, which was conductive and showed electrochromic behaviour.

Nevertheless, the preparation of this polyacetylene by Shirakawa and coworkers and the discovery of the large increase in its conductivity after "doping" by the group led by MacDiarmid and Heeger actually launched this new field of research.

The whole of Chapter 8 is relevant, but it's two pages long so I won't quote the whole thing. You can read the Google Books version of it at http://books.google.co.uk/books?id=4rFDAzo5lPQC&printsec=frontcover&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false, pages 265-267.

Ben (talk) 15:14, 5 February 2013 (UTC)

p.s. There is one review that directly mentions Proctor's work and says it's important: Hush, NS (2003). "An overview of the first half-century of molecular electronics". Annals of the New York Academy of Sciences. 1006: 1–20. Bibcode:2003NYASA1006....1H. doi:10.1196/annals.1292.016. PMID 14976006.  Hush says

Also in 1974 came the first experimental demonstration of an operating molecular electronic device that functions along the lines of the biopolymer conduction ideas of Szent-Gyorgi. This advance was made by McGinness, Cony, and Proctor[ref 57, Proctor's Science paper] who examined conduction through artificial and biological melanin oligomers. They observed semiconductor properties of the organic material and demonstrated strong negative differential resistance, a hallmark of modern advances in molecular electronics.[ref 58] Like many early advances, the significance of the results obtained was not fully appreciated until decades later.

The problem is, this is the only one. A few reviews specifically covering melanin (one from 2006, one from 2009 and one from 2010) cite Proctor, but only briefly (e.g. "In the 1970s, McGinness and his associates showed that natural and synthetic eumelanin behave like amorphous semiconductors", "The prevailing paradigm in the field is that melanins are indeed disordered organic semiconductors", and "In fact, some of the initial discoveries of semiconducting organic solids were made using melanin as a model material."). Nowhere in any of these secondary sources does it say there is a Nobel Prize controversy. It's all WP:SYN. Ben (talk) 15:28, 5 February 2013 (UTC)
I read all of chapter 8 from Inzelt, still don't see there - or anywhere - a source that states there is a controversy surrounding the 2000 Ch prize. The article states "Likewise, Inzelt states that Nobel citation's "The Discovery of Conductive Polymers" is an "exaggeration"." I cannot find the word "exaggeration" in the Inzelt book. The Talk page says

The relevant chapter from Inzelt's new book is at Conductive Polymers, 2012. Page 295. He now cites the Australian researchers early work with conductive iodine-doped polypyrolle ("which showed rather good conductivity"), as well as (interestingly) that of Szent-Gyorgyi and Isenberg. Among other things, also states that Nobel citation's "The Discovery of Conductive Polymers" is an "exaggeration". Nucleophilic (talk) 23:52, 24 May 2012 (UTC)

But there is no page 295 in that book (the chapter starts on page 265, so perhaps that is a typographical error). Can anyone identify where the source of the word "exaggeration" is? Even if the word "exaggeration" is found in a source, that is still not sufficient to make it a "controversy", and I'm inclined to create an RfC to remove the entire section. --Noleander (talk) 16:23, 5 February 2013 (UTC)

I gave you a link to the first edition, published in 2008. Chapter 8 is pp. 265-267 in that edition. The second edition of the book, published in 2012, states on p. 296 "It should be mentioned that the "discovery of conducting polymers" in connection with polyacetylene is an exaggeration not only because of the example of polyaniline...". I can't access p. 297 so I can't see what else it says on the matter.

You're absolutely right that the word controversy is not mentioned. --Ben (talk) 18:20, 5 February 2013 (UTC)

Update: we can access the 2012 second edition via Google Books: http://books.google.co.uk/books?id=X5TUXdUuCq0C&printsec=frontcover&dq=Conducting+Polymers:+A+New+Era+in+Electrochemistry&hl=en&sa=X&ei=jk0RUcCQDsaX0QWt3oGgBQ&ved=0CDcQ6AEwAQ#v=onepage&q&f=false. The full quote is thus:

It should be mentioned that the "discovery of conducting polymers" in connection with polyacetylene is an exaggeration not only because of the example of polyaniline described above since polypyrrole was prepared even earlier. Australian researchers have published a series of papers entitled "Electronic conduction in polymers" in 1963. They prepared iodine-doped polypyrrole by pyrolysis of tetraiodopyrrole, which showed rather good conductivity. They cited the paper by Szent-Györgyi and Isenberg, who had prepared a charge-transfer complex of pyrrole and iodine even earlier. Very deep is the well of the past.

Ben (talk) 18:31, 5 February 2013 (UTC)
Thanks for the info. I've created a RFC on the issue here. --Noleander (talk) 18:59, 5 February 2013 (UTC)

Ph2Se2[edit]

What an eye you have. Nice work.--Smokefoot (talk) 18:48, 12 February 2013 (UTC)

Thanks very much! What's happening with Proctor related things? It seems there's a bureaucratic stalemate. Ben (talk) 19:15, 12 February 2013 (UTC)
See
I'm not even interested in Proctor, nor chemistry, nor baldness ... yet it has occupied way too much of my time the past 2 weeks. Oh, well. --Noleander (talk) 19:19, 12 February 2013 (UTC)

Request for mediation accepted[edit]

The request for formal mediation of the dispute concerning Peter Proctor, in which you were listed as a party, has been accepted by the Mediation Committee. The case will be assigned to an active mediator within two weeks, and mediation proceedings should begin shortly thereafter. Proceedings will begin at the case information page, Wikipedia:Requests for mediation/Peter Proctor, so please add this to your watchlist. Formal mediation is governed by the Mediation Committee and its Policy. The Policy, and especially the first two sections of the "Mediation" section, should be read if you have never participated in formal mediation. For a short guide to accepted cases, see the "Accepted requests" section of the Guide to formal mediation. You may also want to familiarise yourself with the internal Procedures of the Committee.

As mediation proceedings begin, be aware that formal mediation can only be successful if every participant approaches discussion in a professional and civil way, and is completely prepared to compromise. Please contact the Committee if anything is unclear.

For the Mediation Committee, AGK [•] 11:55, 19 February 2013 (UTC)
(Delivered by MediationBot, on behalf of the Mediation Committee.)

Thanks[edit]

Ben, thanks for the note. I should have looked. This wayward editor is keen to do drawings so my idea was to at least get work on interesting solids. The associated higher skills involve making sure that the images are instructive vs a jumble of atoms. You might make some suggestions at my page or his. For example, for molecular crystals we might want the packing in non-space filling format or even not even a unit cell. In other cases we want multiple unit cells in various directions. And, as you pointed out, another key skill is searching for existing images, which you have now disclosed.

Did you see the Bristol-esque phosphine that I started yesterday? Cheeers, --Smokefoot (talk) 16:13, 24 February 2013 (UTC)

No problem, I think the editor did in fact use one of the pre-existing images. Certain illustrators here (Jynto, Ccoil etc) had a habit of making nearly identical replicas of existing images, either because they hadn't thought to search for them, or because they wanted to have their specific lighting scheme applied to all molecular images!
The best depiction for a given crystal structure really does vary on a case-by-case basis, as you say. I'm happy to offer advice. I'll keep an eye on both talk pages.
I did notice Phosphatrioxa-adamantane. Very nice! I don't work in that particular area but many people here do. Another interesting class of phosphine ligands I've seen worked on here are phobanes (e.g. Pringle et al, J. Am. Chem. Soc. (2009) 131, 3078–3092). I don't know the field well enough to know if these are particularly notable or just a current Bristol topic, but maybe you can offer an outside perspective.
Cheers, --Ben (talk) 08:35, 25 February 2013 (UTC)

File:Ben-Mills-23-August-2007.jpg listed for deletion[edit]

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File:BenMills.jpg listed for deletion[edit]

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Xylindein[edit]

Hi, I'm trying to make a model and 2D schema of xylindein. I'm making it in ChemDraw, but generated name is not equal as name here. My source files and CDX document are here. Could you please told me what is wrong? I'm not that good in chemistry. Thank you. Dominikmatus (talk) 12:15, 3 March 2013 (UTC)

Hi Dominik, everything looks fine. ChemDraw probably uses a different name-generating algorithm to ChemicalBook. There are many ways of naming most molecules. Have you seen Donner et al, Tetrahedron (2012) 68, 2799–2805? --Ben (talk) 13:18, 3 March 2013 (UTC)
Good, thank you. Yes I seen in, but not read it. Dominikmatus (talk) 15:48, 3 March 2013 (UTC)
I created page Xylindein, if I made some mistake, please correct it. :) Dominikmatus (talk) 22:14, 3 March 2013 (UTC)

Request for mediation rejected[edit]

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Decalin melting point[edit]

In the article on decalin you added a "racemate" melting point, but the isomers of decalin are symmetric molecules. You were probably referring to a mixture of 50% cis- and 50% trans-decalin. Could you fix that please? Icek (talk) 14:18, 24 October 2013 (UTC)

Thanks for the heads up, I've updated the page. --Ben (talk) 10:18, 26 October 2013 (UTC)

deep fry fire picture[edit]

Hi. On that photo where there was a huge chip-fire from deep-frying, did the house burn down or no? Just wondering and concerned :) 76.220.66.126 (talk) 04:35, 1 November 2013 (UTC)

No, it was in a laboratory, well suited and designed to cope. I wouldn't recommend trying it at home. Ben (talk) 07:33, 1 November 2013 (UTC)

Sodium nitroprusside[edit]

Hi, I saw your image at https://en.wikipedia.org/wiki/File:Sodium-nitroprusside-2D.png and I wanted to ask how you created it because I'd like to be able to do structures like it myself. Thanks for your time Fuse809 (talk) 22:47, 20 November 2013 (UTC)

I used ChemDraw, but there are many other such apps - have a look at the article Molecule editor for a list. --Ben (talk) 10:23, 21 November 2013 (UTC)

Request for help, Flippin-Lodge angle[edit]

Ben, earlier you did a nice job putting a preliminary figure into the FL angle article. Can you look at the overly long legend, and see if a figure revision might be done, to allow the legend to be shortened? In particular, you had a hard job then in presenting a 3D definition as a 2D figure. If we want to make clear that the angle measured is of the projection of the nucleophile onto the carbonyl plane (a point I have defined as Nu-dagger, because this was an available, relatively visible symbol in the chart) -- how to do this? I am hoping for several cycles of improvement to the article, but a better figure would go a long way... Cheers. LeProf — Preceding unsigned comment added by 50.179.92.36 (talk) 17:14, 14 December 2013 (UTC)

I should also say that we have a figure for a paper in preparation that I could send you, that could form the basis for the figure, if there is a way to get things to you. Note, I can;t just take the figure into WikiCommons, because it will be copyrighted when ultimately appears. However, the image could contribute to your ideas (both for FL,and for BD). Leprof 7272 (talk) 19:23, 14 December 2013 (UTC)

Hi Leprof, interesting article. If you send me the figure you have in preparation for your paper, I will make a draft of a new figure for Flippin-Lodge angle and we can modify it until it's suitable. You can email me through the "email this user" link in the tools menu on the left hand side of the page. Cheers, Ben (talk) 10:29, 15 December 2013 (UTC)

Cheers. Got it. As soon as it is ready. Leprof 7272 (talk) 08:06, 23 December 2013 (UTC)

Geometric detail in Cu(II)(H2O)6[edit]

Do you remember if commons:File:Hexaaquacopper(II)-3D-balls.png is based on a published geometry or was minimized by you? The description doesn't have a lit cite. Jahn–Teller effect uses it as an example with specific literature-value Cu–O distances, and I'd like to make sure the image matches. DMacks (talk) 17:15, 16 December 2013 (UTC)

I think I just made a model using the Cu-O distances from Greenwood and Earnshaw. I can make a new one from a specific crystal structure if you like. --Ben (talk) 18:13, 16 December 2013 (UTC)
Any structure bsaed literature values for this actual ion would be great. Maybe doi:10.1021/ic950857a? Looks like H-bonding has a major effect as well, I usually forget to even think about ligand/ligand interactions like that. DMacks (talk) 15:06, 17 December 2013 (UTC)
Or even G&E is fine...anything that would give that image a citeable ref for those key bond-lengths. DMacks (talk) 18:40, 17 December 2013 (UTC)

Actually, now I think about it, it was probably this book by Mark Winter. I'll check for you and update the ref. Cheers. Ben (talk) 19:09, 17 December 2013 (UTC)

About making figures...[edit]

Hey Ben!

I would like to be able to produce figures like f.ex. figures 1, 3 ad 5 in this paper: http://download.springer.com/static/pdf/560/art%253A10.1007%252Fs11244-006-0090-x.pdf?auth66=1391092148_2b62948438393cb067c9525beec262c1&ext=.pdf. Do you think that's possible with the recipe you have given? I wanted to draw specific surface terminations of bulk crystals but I am not sure if there exists CIF files for these. But if that's possible do you know about an alternative program to Accelrys Discovery Studio Visualizer 2.0 that is compatible with mac and would be able to do the same things?

Regards,

Logiarnarson (talk) 14:44, 28 January 2014 (UTC)logiarnarson

I know a of few programs for Mac that could do this well, none of which are free. I have CrystalMaker for Mac, and could make them for you. I'm pretty busy at the moment, so it might be a while. Have a look online for Mac crystallography software. CCDC's Mercury might be useful, even though it's primarily for molecular crystals. --Ben (talk) 14:48, 28 January 2014 (UTC)


I'll take a look at these programs, thanks for the reply! — Preceding unsigned comment added by Logiarnarson (talkcontribs) 15:02, 29 January 2014 (UTC)

Notification of automated file description generation[edit]

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WT:CHEMS#Stereochemistry of norbornene derivatives[edit]

Hi Ben. The discussions involved images you uploaded. Please have a look. --Leyo 23:44, 15 February 2014 (UTC)

Your submission at Articles for creation: Bristol ChemLabS (March 3)[edit]

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Lithium carbonate[edit]

Sounds terrific, thank you for getting back to me so quickly. TylerDurden8823 (talk) 19:49, 28 March 2014 (UTC)

Just wanted to follow up with you, how are things progressing? TylerDurden8823 (talk) 22:06, 6 April 2014 (UTC)

Hi Tyler, sorry for the massively long delay - I'm in Japan at present. I uploaded the image but forgot to tell you about it. It's here: File:Lithium-carbonate-xtal-1979-Mercury-3D-sf.png. Best wishes, Ben (talk) 09:51, 21 April 2014 (UTC)

Not to worry my friend, there's no need to apologize. I appreciate the hard work you put in to make the image. I'll move it to the Bipolar disorder page soon. Thanks again! TylerDurden8823 (talk) 05:58, 23 April 2014 (UTC)

A beer for you![edit]

Export hell seidel steiner.png This is a cup of beer for you to drink (maybe even do an exploding experiment with it)! ZYjacklin (talk) 03:35, 29 July 2014 (UTC)
Cheers mate! Ben (talk) 08:08, 29 July 2014 (UTC)

3D images request[edit]

Can you make 3D molecular images of paullinic acid, docosahexaenoic acid, and stearidonic acid? The image could be either space-filling or balls-and-stick, or maybe both, PNG format would be the best. Thanks a lot.--ZYjacklin (talk) 05:33, 30 July 2014 (UTC)

Yes, I can do those. It's on my to-do list, I'll let you know when I've done them. Cheers. --Ben (talk) 08:49, 31 July 2014 (UTC)
Thanks a lot, Ben. :)--ZYjacklin (talk) 11:42, 31 July 2014 (UTC)

All done, let me know of any errors. Cheers. --Ben (talk) 17:36, 5 August 2014 (UTC)

Those images are very great!--ZYjacklin (talk) 09:20, 6 August 2014 (UTC)

2,4-dithiapentane and Dimethyl-sulfide 3D-balls images[edit]

Hi Ben, I’m working on a book about truffles but the publisher said your images on Wikipedia of the two truffle flavor molecules are too small for print: could you supply me with larger versions?

Thanks much, Zach Pg1945 (talk) 13:03, 19 August 2014 (UTC)

Wikipedia talk:Articles for creation/Bristol ChemLabS concern[edit]

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Butadiene MO diagram[edit]

Just a note to say that I have inserted your MO diagram for butadiene in the article on Antibonding (soon to be moved to Antibonding molecular orbital if there is consensus.) The article previously used benzene as a polyatomic example, but I have put butadiene first specifically because your diagram shows the concept of antibonding orbital very clearly. Dirac66 (talk) 02:43, 18 September 2014 (UTC)

Your draft article, Wikipedia talk:Articles for creation/Bristol ChemLabS[edit]

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Drawing of 3D models[edit]

Hi, as my animated 3D models have their limitations, especially when it comes to epileptics and other people with neurological disorders as they interfere with their ability to view them, I'd like to know how to create models like yours, mostly for my own Wiki (from Wikia). I know you used Accelrys Visualizer and I have viewed this guide of yours [3] but seeing how it was last edited by you some 6 years ago the latest version of Accelrys Visualizer is significantly different and I have no idea as to how to draw a structure like this one [4] of (R)-thalidomide you made. This [5] is what I get from trying to create a 3D model of racemic fluoxetine (R and S enantiomers shown) after customizing it as much as I can; trying to make it as close to the format of your (R)-thalidomide model I linked. Any ideas how I could make it closer to your model? I especially like the delocalization of the electrons on the phenyl rings you do. Brenton (contribs · email · talk · uploads) 04:21, 8 October 2014 (UTC)

Hi Brenton, the best thing to do is just play around with all the settings. Look for all the settings you can change under Preferences, and by right clicking particular atoms, bonds, the background, etc. I could download the latest version and create a how to guide, but it would take me a lot of time. A word of caution: it is easy enough to create 3D models of molecules based on the skeletal formula, but there are many ways you can create a misleading representation when you move to 3D. The best way is to base your model on experimental data, normally always X-ray crystallography for molecules larger than five or six atoms. According to your user page, you are a science student, so I'm reasonably confident I could give you some further guidance on how to find such experimental structures if that's what you'd like to do. --Ben (talk) 08:35, 8 October 2014 (UTC)
I know about crystal structures it's just not always possible for one to find the one required, especially seeing how my university doesn't grant me access to many crystallography journals. For example, for (R)-fluoxetine and (S)-fluoxetine I am yet to see any crystallographic structures for either one, sadly. My carbons atm are grey, any idea as to how to make them black like yours were? I know I'm using a newer version but still I'm stuck there. Same with delocalization, I have no idea. Could you at least tell me what you did when you did yours in your older version? Like did you go into preferences to represent the electrons as delocalized? Do you remember what specific option you had to modify in order to get the phenyl ring represented in terms of a delocalized charged? I understand you're busy so I think I will take my questions to Chemistry StackExchange or Accelrys forums. Brenton (contribs · email · talk · uploads) 13:12, 8 October 2014 (UTC)
Hey, this is something I think should be pretty simple and fast for you to do for me, do you know anywhere I can find a complete table (including the blends of RGB required) of CPK colours for all elements found in drug molecules (like hydrogen, carbon, lithium, oxygen, nitrogen, sodium, fluorine, chlorine, iodine, phosphorus, sulfur, potassium, boron, magnesium and calcium)? Every chemistry software I have seen except Accelrys seems to use different CPK colours than are deposited into the latest version of DS Visualizer, hence I'd like to know what the RGB blends are meant to be. For example you used some sort of yellow colour for fluorine in the (S)-fluoxetine 3D model [6] you created using Accelrys whereas Accelrys uses a sky blue colour blend by default for fluorine, or at least its latest version does. I have tried Google to get the answer but all the lists I have found have been incomplete, in fact they never even included fluorine in their colour scheme. Brenton (contribs · email · talk · uploads) 11:18, 9 October 2014 (UTC)

Hi again Brenton. I would start with the help menu in DSV. I think the colour palette is in Preferences. I Googled "crystal structure of fluoxetine" and found various papers, including Robertson et al, J. Med. Chem., 1988, 31, 185–189. If you need any help extracting the relevant information from there, I can help. I've actually already made images for both enantiomers and deposited them at commons:Category:Fluoxetine, so I don't think we need new images for this particular molecule. I haven't found one specific set of CPK colours that are used everywhere, but I based my own colour palette on a combination of DSV's default colours and the colours of Molymod molecular models. If you open that palette in Photoshop or similar, you can extract the RGB settings for each colour/element. Alternatively, if you click 'edit' at User:Benjah-bmm27/MakingMolecules#Colour_palette, you can see the hex codes for each one. Let me know if I can help further. --Ben (talk) 11:27, 9 October 2014 (UTC)

How do you make the background of these images transparent? I know how to set the background to white but not transparent. For example in File:Venlafaxine-3D-balls.png you have a transparent background to your structure. Brenton (contribs · email · talk · uploads) 07:20, 10 October 2014 (UTC)

I do that in Photoshop. I usually set the background to a colour that isn't used for any of the elements, such as light blue. Then I replace it with transparency and save it as a PNG in an image editor. --Ben (talk) 16:30, 10 October 2014 (UTC)

I just found another question for ya, I saw for File:Cocaine-from-xtal-1983-3D-balls.png you cited that 1983 paper and I'm scratching my head as to how you created the 3D structure from the coordinates given. Using those coordinates and trying to create a XYZ file (which had 43 for the first line, cocaine 1983 for 2nd line just to give ya an idea that I am following the correct format) I get this structure http://i.imgur.com/7paFRgE.png in Accelrys, rofl. As I'm pretty new to this I thought I'd ask your help. Brenton (contribs · email · talk · uploads) 00:01, 18 October 2014 (UTC)

Here's the XYZ file I have if you're wondering:

43
Cocaine 1983
C          0.5419        0.1631       0.7095
C          0.4579        0.2047       0.5345
C          0.3080        0.1713       0.5168
C          0.2903        0.0286       0.5727
C          0.3950        0.0004       0.7409
C          0.3870        0.1080       0.8678
C          0.4858        0.2192       0.8450
C          0.1028        0.2512       0.3219
C          0.0323        0.2713       0.1411
C          0.0857        0.2213       0.0238
C          0.0189        0.2435       -0.1419
C         -0.0995        0.3166        -0.1875
C         -0.1528        0.3671      -0.0719
C         -0.0880        0.3462      0.0951
C          0.5172        0.1331      0.4127
C          0.7261        0.1009      0.3465
C          0.6418        -0.0439     0.8543
N          0.5324        0.0158      0.7182
O          0.2257        0.1933      0.3470
O          0.0560        0.2836      0.4306
O          0.4616        0.0531      0.3097
O          0.6481        0.1713      0.4393
H          0.6210        0.1840      0.7230
H          0.4640        0.2980      0.5170
H          0.2820        0.2340      0.5830
H          0.1930        0.0110      0.5730
H          0.3050        -0.0240     0.4930
H          0.3850        -0.0960     0.7770
H          0.4090        0.0810      0.9760
H          0.2870        0.1410      0.8610
H          0.4440        0.3140      0.8150
H          0.5560        0.2330      0.9400
H          0.1580        0.1680      0.0530
H          0.0640        0.2050      -0.2240
H          -0.1470        0.3330      -0.3060
H          -0.2320        0.4140      -0.103
H          -0.1280        0.3810      0.186
H          0.7330        0.0190      0.3810
H          0.8130        0.1470      0.3710
H          0.6990        0.1060      0.2370
H          0.7250        -0.0340      0.836
H          0.6470        -0.0070      0.961
H          0.6230        -0.1410      0.861

What you need here instead of Cartesian coordinates (xyz) is coordinates in terms of the lattice constants of the unit cell. You also need the crystallographic space group and various other details from the article. I don't have enough time today to explain it all, but I can do so tomorrow. Watch this space! Ben (talk) 10:59, 18 October 2014 (UTC)

Methylphenidate[edit]

Hey, how did you get the d-isomer of methylphenidate from [1]? It only provides the l-isomer. Brenton (contribs · email · talk · uploads) 22:12, 6 November 2014 (UTC)

1. Froimowitz, M; Patrick, KS; Cody, V (October 1995). "Conformational analysis of methylphenidate and its structural relationship to other dopamine reuptake blockers such as CFT". Pharmaceutical Research. 12 (10): 1430–4. doi:10.1023/A:1016262815984. PMID 8584475. 
Hi Fuse809, I've moved this question to its own section for ease of navigation. I assume you're referring to the following pair of images, File:Dextromethylphenidate-based-on-hydrochloride-xtal-1995-3D-balls.png and File:Levomethylphenidate-based-on-hydrochloride-xtal-1995-3D-balls.png. I simply took the l isomer and inverted it. For a crystal of a pure enantiomer rather than a racemic mixture, the crystal structures of the two enantiomers should be identical in all respects, except for the chirality of its space group. Therefore it is legitimate to infer the structure of one enantiomer from the other simply by inversion. --Ben (talk) 12:20, 7 November 2014 (UTC)
Yep, they're the structures. How did you do the inversion, software wise? Was it with the CrystalMaker you mentioned on the description pages of these two structures? Brenton (contribs · email · talk · uploads) 13:12, 7 November 2014 (UTC)

I think I actually did it in DSV. You can select a molecule or atom, right click and choose invert. Or maybe it's in one of the menus. Let me know if you find it. --Ben (talk) 15:39, 7 November 2014 (UTC)

Yeah I found how to invert their chirality (sorry for the delay I found out months ago). I was interested in what you had for theta min and max (which should be in your CIF file as _cell_measurement_theta_min & _cell_measurement_theta_max, respectively) for this experiment because I couldn't find one in this paper. Brenton (contribs · email · talk · uploads) 01:13, 2 May 2015 (UTC)

I hate to inform you of an error.... but a quick heads up![edit]

I love all your images, they're absolutely fantastic.

I quick proofing note, on the article Tetrahydrocannabivarin (THCV) on which you are listed as one of two authors, I couldn't help but notice the molecule rendered is not in fact delta-9 or delta-1 (dibenzopyran and monoterpenoid numbering, respectively) THC, but is the chiral enantiomer. If you quickly look at the THCV page, you will see the skeletal structure and the 3D rendered image give opposite information about the two chiral centers (6a and 10a for dibenzopyran, 3 and 4 for monoterpenoid). I don't know what software you use, but this should be a routine fix.

Anyway keep up the good work, sorry to be a nuisance! :-)

example: http://www.digammaconsulting.com/minorcannabinoids/thcv.html — Preceding unsigned comment added by 50.185.26.18 (talk) 23:51, 18 October 2014 (UTC)

Thanks for the notification. It turns out this image was made by User:Jynto. They took an old image of THC that I had made and flipped it horizontally before modifying it, inverting the chirality. I would take it up with Jynto but it seems a new image has been created. Thanks again. --Ben (talk) 11:00, 7 November 2014 (UTC)

I'll see if I still have the paper. It might have been an electronic copy that expires after a few days. The image is actually based on a calculation that used the crystal structure of the HCl salt of pethidine as a starting point, but the two substances are different and will have slight differences in structure. --86.160.152.210 (talk) 12:01, 25 November 2014 (UTC)

Coordinates for pethidine[edit]

Hi, where did ya get the coordinates for File:Pethidine-PM3-based-on-xtal-1974-3D-balls.png? I know you cited that 1974 journal article but you didn't provide a doi, or any link just the abbreviated journal title in which it was published, date, pages and volume which weren't enough for me to find it through Google. Let me guess you had to get a paper copy of it through your university in order to get your coordinates? Brenton (contribs · email · talk · uploads) 19:54, 20 November 2014 (UTC)

Hi Fuse809, yes I believe I had to get hold of the original paper on an inter-library loan through my university library. I couldn't find the original paper online anywhere, hence why I didn't provide a link. Do you need the coordinates? --Ben (talk) 18:24, 24 November 2014 (UTC)
Yes, please. Brenton (contribs · email · talk · uploads) 04:45, 25 November 2014 (UTC)

It turns out the paper is now online, at http://dx.doi.org/10.1002/recl.19740930609. Do you have access to that? The cell parameters are space group P21/c, a = 22.62 Å, b = 11.53 Å, c = 11.83 Å, β = 90°. It'll take a little while to get the coordinates again. Do you want the coordinates from the original crystal structure of the HCl salt or of the calculated structure that the image is based on? --Ben (talk) 12:12, 25 November 2014 (UTC)

I do not have access to that article, unfortunately, so the coordinates of the calculated structure and the original would be nice. Thanks for your effort, btw. Brenton (contribs · email · talk · uploads) 12:43, 25 November 2014 (UTC)

Your opinion?[edit]

I'd be interested to have your input on this discussion about the value of 3D models for non-conformationally restricted compounds. Input on the style that should be used for ball and stick models would also be useful.Testem (talk)

3d models... more 3d models[edit]

Ben right? Pretty sure you've seen every word I've typed on the matter. So why are you asking me? Folks around here seem like they figure they run this show, and that's just super hilarious to me in it's ridiculousness. Please go read the stuff I've already written.. not trying to develop carpal tunnel endlessly defending something I've already defended over and over. For me it's really just about consistency and not only consistency with the formulaic models but across all of wikipedia. I don't care who makes the models, but in the interest of cleaning up the look and keeping the info as simple to understand as possible I took the initiative. I've made a great many new models and have replaced some old ones. Strangely (lol) all I've heard from are the other people who are submitting 3d models.. hmm. Wonder what that's all about?!?!

Lazord00d (talk) 02:53, 16 January 2015 (UTC)

So you're telling me that all of these other models I see around here are ALL backed with some sort of research data individually? And this is cited? I'm pretty sure that the 2d model contains enough information to create an accurate 3d model..

Lazord00d (talk) 02:37, 16 January 2015 (UTC)

Lol so yeah the link I found on your images ([http://dx) is proving confusing to my web browser.. hmm. Wonder what that's all about?!?!

Lazord00d (talk) 02:43, 16 January 2015 (UTC)

Haha AND FURTHERMORE your models all have little tiny thumbnails that lack definition. My models have big, thick, juicy, and amazing thumbnails. Just saying, since they're so much more enormous and huge it's easier to feel their presence, to see the veins of richness in their design lol... well you get the picture :-D

Lazord00d (talk) 02:47, 16 January 2015 (UTC)

Just to let you know: I nominated a bunch of inappropriate ball-and-stick models for deletion. --Leyo 01:00, 17 January 2015 (UTC)

In my opinion, high quality and chemical accuracy is more important than consistency. But considering a very large number (ca. 6000) of these images were done either by me or in the style that I use (notably by Jynto), it would be best for consistency to use my style. I've given full instructions for other editors on how to do that at User:Benjah-bmm27/MakingMolecules. You could easily improve your contribution to WP articles by making your models in this style, with aromatic dashed bonds. And please use crystal structures for the actual atomic coordinates where available. --Ben (talk) 21:03, 17 January 2015 (UTC)
Responding to your other points above: I can't say every single model is based on experimental data, but a high proportion of my ones are. You can spot ones that are based on crystal structues if they have -xtal- and a year in the file name, such as File:Cocaine-from-xtal-1983-3D-balls.png. "I'm pretty sure that the 2d model contains enough information to create an accurate 3d model" - no this is absolutely not the case. The relationship between the 2D connectivity and 3D structure of molecules varies between being simple and very complicated, depending on the molecule. See Molecular geometry for starters. For an extreme example of a complicated relationship, see Protein folding. . The link you're having trouble with is http://dx.doi.org, see Wikipedia:Digital Object Identifier for details. No idea what you mean about thumbnails, those can be generated automatically from the full size image. --Ben (talk) 18:47, 18 January 2015 (UTC)\\

Must be nice to be able to appoint your style as the "official" Wikipedia molecular model style.. regardless thanks for the reply and explanation. A point critical to my position is that the depiction of aromatic rings with either dashed bonds or alternating is not a real issue for the majority of our readers. They are both equivalent, as they can both be found in use in many other references.

Lazord00d (talk) 19:20, 21 January 2015 (UTC)

I wouldn't normally ask anyone to copy my style, I'm happy for there to be a variety of styles. But since you are keen on consistency, I would say the easiest way to be consistent is to go with the existing majority. It's not a big deal to me. What is a big deal is replacing images that are based on high quality, peer reviewed experimental data from the scientific literature with ones that are not.
Regarding alternating single and double bonds in benzene rings, you just don't see this very much is 3D models. It's a convention in chemistry not to do it. Let's just stick to the convention, because that's what encyclopaedias do.
I saw your reference to the Springer Materials database (e.g. http://www.springermaterials.com/docs/substance/MJRKAJZYCIWMFSIA.html). I believe these structures are generated automatically from the 2D structures using an algorithm that is reasonable most of the time for simple molecules without any unusual bonding, but (i) is not directly based on experimental data, and (ii) has the capacity to be quite wrong in some cases. For example, compare the calculated N-N bond of 0.147 nm at http://springermaterials.com/docs/substance/TRLILWZBHSHSZXRA.html with the experimental value of 0.186 nm cited at dinitrogen trioxide. This is just the first example I came across, many others would have similar issues. I have sent an email to Springer asking where these structures come from and I will let you know of their reply.
It's not that your images are awful, they're ok. but they could be both consistent with the existing predominant style, and more importantly, based on literature structural data. This is now the gold standard for structures on WP and there's no reason you can't adhere to it. I can show you how to do it if you're keen to contribute.
As an aside, the reason I think I have some authority on molecular structures on Wikipedia is my education: I have a master's degree in chemistry, my final year project was on determining the structure of molecular solids by X-ray crystallography, and I am coming towards the end of a PhD in materials chemistry. You may be more of an expert in this topic than I am - if so please say so and we can talk in more technical detail. That's not to say that my opinion should trump yours just because of my background, obviously not: the arguments we make have to be considered on their merits. But it takes time to go through point-by-point why there are some issues with your structures and the reasons why certain sources are not reliable enough for this kind of structural information. It will also take some time to teach you how to use the literature to get accurate structures, if you don't already know, but I am more willing to do that because it will lead to a better outcome in the long run. Arguing endlessly and getting nowhere is a waste of time for you and me.
In a nutshell:
  1. Do you know more about molecular structure than you're letting on?
  2. If not, would you like a quick introduction to doing it properly?
Ben (talk) 00:37, 23 January 2015 (UTC)

Nomination for deletion of Template:Massa2nd[edit]

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Custom Pictures Request[edit]

Ben, I love your pictures. They really help students understand molecular geometry. Do you have the time to create the following five pictures: A linear, trigonal planar, tetrahedral, trigonal bipyramidal and a octahedral ; each having all blue terminal atoms? I would sincerely appreciate it! HAZMAT001 (talk) 05:23, 6 March 2015 (UTC)

Also these 6 withOUT any lone pairs (yellow spheres). Please again with terminal atoms as blue spheres: bent, trigonal pyramidal, see-saw, T-shape, square planar, and square pyramidal. Thank you very much. — Preceding unsigned comment added by HAZMAT001 (talkcontribs) 06:12, 6 March 2015 (UTC)

Hi Hazmat001,
I assume you're referring to the images in the table at VSEPR theory#AXE method. It would take me a long time to make these again, but in different colours. The best way for you to get the images you want is probably to take the existing images and simply modify the colours in some image editing software like Photoshop. You can highlight the white terminal atoms and change them to blue. I'm pretty busy at present so I probably won't get round to doing this any time soon. You might be able to ask for help in modifying the graphics here on Wikipedia. I've seen various help desks over the years where editors offer to do such manipulations.
Out of interest, why do you need blue terminal atoms?
Best wishes, Ben (talk) 18:33, 6 March 2015 (UTC)

Hi Ben. Thank you for your quick response, and for your suggestions. I wanted to remove the distinction between terminal atoms and lone pairs when just describing and naming geometry. Many students are having trouble going from electron pair geometry to molecular geometry. Using terminal atoms to describe/name geometry confuses my students. You're pictures are great, and I would like to use them in some of my study guides. May I have your permission to use them? HAZMAT001 (talk) 09:45, 9 March 2015 (UTC)

Hi Hazmat. OK, that's fine. My images are all in the public domain, so, legally speaking, you're free to use them with or without permission. However, it's kind of you to ask and of course you have my permission to use them. Good luck with your students! --Ben (talk) 18:45, 9 March 2015 (UTC)

Thank you Ben! In your previous edit, you said that I might be able to ask for help in modifying the graphics here on Wikipedia and that you've seen various help desks over the years where editors offer to do such manipulations. Sorry to ask for more, but can you explain how I do this? HAZMAT001 (talk) 08:54, 10 March 2015 (UTC)

I had a look but can't find the page I've seen in the past. Try asking at Wikipedia:Help desk - they should point you in the right direction. Best of luck. --Ben (talk) 10:08, 10 March 2015 (UTC)

Nomination for merging of Template:Infobox UK Fire and Rescue[edit]

Template:Infobox UK Fire and Rescue has been nominated for merging with Template:Infobox fire department. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Thank you. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 11:08, 12 March 2015 (UTC)

Error in XeF2 article[edit]

Hello, I saw that you specialized in diagrams. Unfortunately the picture under "aromatic fluorination" in the article xenon difluoride is incorrect as it shows not oxidation but reduction of a nitro group to an amino group by XeF2. 70.187.88.4 (talk) 20:53, 15 April 2015 (UTC)Guest

EROS for XeF2 has this example with the nitro remaining unchanged. I could envision ways it might not, but that's not relevant here:) DMacks (talk) 22:02, 15 April 2015 (UTC)
SciFinder's only hit is EROS, and also lists the other positional isomers as products. I don't have it handy to look for the actual lit ref for this example or to see just how major (I don't doubt that meta is major) it is. DMacks (talk) 22:15, 15 April 2015 (UTC)
I could have been more clear. What I mean is that the nitro group should be untouched while the aromatic ring is oxidized. Instead the nitro group is reduced. Reduction of the Nitro group by XeF2 should not occur.
I corrected the image to retain the nitro group in the product. -- Ed (Edgar181) 14:42, 16 April 2015 (UTC)

Nomination for deletion of Template:Infobox UK Fire and Rescue[edit]

Ambox warning blue.svgTemplate:Infobox UK Fire and Rescue has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Zackmann08 (talk) 02:16, 19 April 2015 (UTC)

A kitten for you![edit]

Red Kitten 01.jpg

Very helpful, you can check out what I made on the page for Pentafluorobenzoic acid.

DFliyerz (talk) 03:42, 28 April 2015 (UTC)

Creating 3D models for freebase using crystallography data for the salt[edit]

Hi, Ben. I've asked a question on Chemistry StackExchange that I think you might be better suited to answer, here it is. See many structures you create for Commons are based on xtal data for a molecule's salt instead of the freebase molecule you usually are depicting in the structure and I was simply wondering if there's any corrections required for such structures or will simply removing the unwanted atoms in Accelrys DS Visualizer suffice. Thanks for your time in advance. Brenton (contribs · email · talk · uploads) 15:52, 23 May 2015 (UTC)

Hi Brenton, good question. In most cases (for example, mescaline), protonation of the amino group should not make a great deal of difference to the structure of the rest of the molecule. Nonetheless, if you take the crystal structure of a salt and digitally deprotonate it, you should say so in the image description. As an additional measure, I usually indicate the origin of the structure in the filename, so I would call such an image something like "mescaline-from-HBr-xtal-3D-balls", or File:Trazodone-from-HCl-xtal-3D-balls.png. That way, if anyone is unsure what the image actually represents, they can find out. Some chemical intuition / experience is required to recognise molecules that are likely to have significantly different protonated and deprotonated structures, in which case other structural data should be sought. --Ben (talk) 10:38, 25 May 2015 (UTC)

Nickel selenide[edit]

Hi, before I caption the image in chembox could you please confirm which form of Nickel selenide you used to make the image File:Nickel-arsenide-3D-unit-cell.png? The compound has various stoichiometric and nonstoichiometric forms and I don't want to miss-label it. Cheers --Project Osprey (talk) 09:02, 26 June 2015 (UTC)

Hi Project Osprey, this is stoichiometric NiAs, probably from http://www.chemtube3d.com/solidstate/_NiAs(final).htm.
Let me know if you need any more details. --Ben (talk) 12:11, 26 June 2015 (UTC)
Thank you! I notice that the elements weren't coloured according to the CPK coloring system, so I had to make an educated guess as to what was what (you might what to check my work), out of interest is there a different colouring system you tend to use? --Project Osprey (talk) 12:58, 26 June 2015 (UTC)
I use User:Benjah-bmm27/MakingMolecules#Colour palette, which is based on the Accelrys DS Visualizer palette, itself based on CPK, and has colours for other elements not included in the CPK scheme. Arsenic, antimony and bismuth are all shades of purple in that colour scheme, so I've updated the legend at nickel selenide.
Cheers! --Ben (talk) 13:11, 26 June 2015 (UTC)

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Asking for further information[edit]

Hi Ben,

Could you please give me more information about adjusting the lightning of the molecules in DS visualizer?

Such as Specular,Shininess,and diffusion.


Thank you.

--ابراهيم زين العابدين (talk) 14:32, 12 January 2016 (UTC)

Hi there,
The process I use is described at User:Benjah-bmm27/MakingMolecules. In particular, the lighting settings I use are shown in an image: http://www.benjamin-mills.com/DS-lighting.png.
I haven't used the latest version of DSV that includes options to adjust the specular and diffuse reflectance, so I can't help you there I'm afraid.
Try playing with the settings and see how it looks.
Good luck,
--Ben (talk) 17:30, 3 February 2016 (UTC)

Thank you very much! , The image helped me a lot. ابراهيم زين العابدين (talk) 19:32, 6 February 2016 (UTC)

Mirtazapine ball-and-stick model[edit]

Mirtazapine ball-and-stick model.png

Hello, Ben. Could you please explain me in simple language what's wrong with my mirtazapine model? The only difference I found between our models is that yours depicts (S)-(+)-enantiomer and it's flipped vertically, whereas mine portrays (R)-(−)-mirtazapine. Hydrogen atom positions were calculated automatically in Accelrys DS Visualizer 4.1 (I used Clean geometry tool). 3D image on PubChem [7] shows pretty similar structure, I mean the positional relationship of mirtazapine «wings» and its piperazine fragment. Thank you in advance. --vaccinationist (talk|edits) 15:17, 15 February 2016 (UTC)

PS. And also, ranitidine, cimetidine, captopril, etc.

Hi Vaccinationist.
The difference is, if you click on my images, you will find they have a link to the paper they are based on. The positions of all heavy atoms are derived directly from the single-crystal X-ray diffraction data. Therefore, my structures can be trusted to be and are seen to be correct. I believe this is an important principle of Wikipedia.
The work you've done adding structures to articles that did not previously have them is great, it really benefits the articles. The ones I have changed are ones I remember making X-ray-based structures for in the past. These images are the gold standard for Wikipedia articles and should only be replaced by new images if those new images are based on XRD or other accurate experimental structure determination methods from the peer-reviewed scientific literature.
From the description at File:Mirtazapine ball-and-stick model.png, it seems you've drawn the molecule based on the skeletal formula and minimized it in DS Visualizer. If this is not the case, you should update the image description with the source of the atomic coordinates, such as DFT calculation, X-ray diffraction experiment, rotational spectroscopy data, or similar.
In general, it is not necessary to replace existing images of molecular structures in articles unless there is something wrong with them. Top of list is factual errors, such as wrong connectivity, missing atoms, wrong enantiomer, and so on.
I've made several thousand images of 3D molecular structures based on X-ray diffraction data, so to save time and maintain high standards in this area, every editor considering adding or changing the image of a structure in a WIkipedia article (in whatever language) should check my contributions and those of others first to see if a suitable image already exists. The best way to do this is to check the appropriate categories at Wikimedia Commons. In this case, that would be Commons:Category:Mirtazapine.
If you would like to discuss this in further detail, I'd be happy to do so.
Best wishes,
Ben (talk) 15:57, 15 February 2016 (UTC)
So, if I understood you correctly, I shouldn't use Clean geometry tool anymore, for it generates wrong atom positions? --vaccinationist (talk|edits) 16:59, 15 February 2016 (UTC)
It's much more complicated than that. Clean geometry is often OK for generating hydrogen atoms where the heavy atom positions are known, but it doesn't sound like you're using literature structures to start with. What level of expertise do you have in molecular geometry? Depending on your answer, I can point you in the direction of appropriate sources of data, or advise you where to learn more so you can use verifiable, high quality sources. --Ben (talk) 17:11, 15 February 2016 (UTC)
Please excuse my tardy reply. Well, I'm afraid I'm quite far from molecular geometry. I am M.D., psychiatrist, mostly working with inpatients suffering from treatment-resistant diseases. My work here on Wikipedia is just a hobby. But I will be very happy to get high-quality sources to redraw some of my structures so they can represent molecular orientation more accurately. Thank you! --vaccinationist (talk|edits) 15:41, 18 February 2016 (UTC)
Hi Vaccinationist, thanks for the info — no need to rush your replies, as you say Wikipedia is a hobby and it can definitely wait. I imagine you have a reasonable background in chemistry as a result of your medical training, so you're certainly in a position to grasp the main principles that determine the precise structures that molecules adopt. I'll give you a quick summary of the problem and how we address it.
The clean geometry button in DSV uses a highly simplified model of molecular geometry to make a reasonable estimate of the 3D structure of a molecule based on which atoms are connected. It's a good first start, but it cannot hope to account for all the intricate interactions between the electrons in a molecule. There are much more sophisticated models and software out there, but they take much more time and computer power than DSV does. Such software is expensive (typically hundreds to thousands of dollars/pounds/euros) and requires some expertise to use.
Even if we used very sophisticated computational chemistry methods to calculate the structure of molecules to illustrate Wikipedia articles, our images would run the risk of being considered original research because they have not been through the peer review process of the scientific literature. This could be a problem because it's easy to make mistakes with these calculations, even for experts. Worse still, even the most sophisticated calculations can be wrong – nature often surprises us – so we always prefer an experimentally-determined (i.e. real life rather than calculated) structure if possible. Furthermore, Wikipedia is founded on the principle of reporting what other verifiable sources state rather than its editors trying to determine the truth themselves. There's some flexibility here, since contributors to WP regularly upload their own photos of plants and animals, landscapes, buildings, people and so on. However, molecular geometry is easy to get wrong and important to present accurately, so we encourage the use of experimentally-determined structural information from the peer-reviewed scientific literature.
In practice, if you want to make an image of the 3D structure of a molecule to add to a Wikipedia article, you should carry out the following steps in order:
  1. Check Wikimedia Commons to see if a suitable image (based on a scientific journal article) already exists – if so, add the image to the article (but check the article's talk page first to see if the image was previously removed for any reason)
  2. If there is no suitable existing image, search the scientific literature to see if the structure of the molecule has been determined. One place to start is Google Scholar. Search for something like "mirtazapine structure" or "crystal structure of mirtazapine". Find a suitable reference that gives the structure.
  3. Use the structural information in the paper to generate a 3D model in your software, then orient the model so it clearly shows the key aspects of the structure and (if possible) matches the existing 2D structural formula
  4. Upload your image to Commons and add it to the Wikipedia article
You are certainly capable of doing steps 1, 2 and 4. I suspect step 3 will be difficult without a degree in chemistry, crystallography or a closely-related discipline, or some intensive training and access to specialist databases. It is possible to learn just enough to extract the structural data without that broader chemistry perspective, but it's much better if you have an expert to point out any mistakes. I can help you with step 3, as I have a background in this sort of thing.
A final important point: many of the drug molecule you are interested in have not had their structure published in the open literature. Some may never have been determined. In that case, it is acceptable to make an image using your approach up until now: draw it in DSV and use the clean geometry function. However, the structure should be checked by a chemistry expert (e.g. someone from WP:CHEMS) and possibly compared to the published structures of related molecules. Those of us who have experience of molecular geometry will notice an unlikely structure by eye immediately, so it's not an onerous task.
If you want to try out this process, tell me a molecule you're in drawing and I'll help you prepare an image the rigorous way!
Best wishes,
Ben (talk) 16:34, 18 February 2016 (UTC)
Thank you so very much for such a circumstantial answer, Ben! I definitely will follow your algorithm in my future work and ask your advice in need. Cheers! :3 — Dmitri (Vaccinationist) (talk|edits)

Welcome back[edit]

I take it that things in the lab are going well since you've been MIA here! If you ever get time, there has been a fair bit of work done and needed at chirality, which was a collection of random factoids. Cheers,--Smokefoot (talk) 19:03, 15 February 2016 (UTC)

Nice to see you again, Smokefoot!
Yeah, it's been busy. Lots of stuff about to reach the surface. Nearly done, though.
I think I could add a perspective to chirality, I'll have a think and make some proposals on the talk page.
Cheers,
Ben (talk) 21:06, 15 February 2016 (UTC)

My hasty reversion[edit]

Sorry, I restored your addition at Silicon sulfide. My bad — Andy W. (talk · contrib) 18:10, 18 April 2016 (UTC)

No problem, thanks for letting me know! --Ben (talk) 18:14, 18 April 2016 (UTC)

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Asbestos model[edit]

Hi Ben,

Do you happen to have a 3D model of Chrysolite? Jander8786 (talk) 18:51, 14 February 2017 (UTC)

Hi Jander8786, do you mean peridot or chrysotile?
Ben (talk) 19:06, 14 February 2017 (UTC)

Nomination of Dilithium (Star Trek) for deletion[edit]

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Could you make a few 3D/ball and stick structures for me?[edit]

Firstly trithiapentalene, the first reference in the article should have sufficient information in it. More later when I find good sources for their structures. --OrganoMetallurgy (talk) 22:57, 26 June 2017 (UTC)

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The Arbitration Committee is the panel of editors responsible for conducting the Wikipedia arbitration process. It has the authority to impose binding solutions to disputes between editors, primarily for serious conduct disputes the community has been unable to resolve. This includes the authority to impose site bans, topic bans, editing restrictions, and other measures needed to maintain our editing environment. The arbitration policy describes the Committee's roles and responsibilities in greater detail.

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