User talk:Benjah-bmm27/2007

Nitrosation

Hi, I was just wondering if you could help me with a problem i have. I'm a 3rd year chemist and i'm trying to do a project that involves the mechanism of nitrosation of secondary amines by the nitrosonium cation. Don't suppose you know the mechanism for the reaction do you (arrow pushing organic mechanism, not the kinetic mechanism). Thanks Sameyley 15:01, 11 February 2007 (UTC)

Hi Sam. I assume the reaction you're studying is secondary amine + nitrosonium → nitrosamine + proton.

R₂NH + NO⁺ → R₂NNO + H⁺

I would imagine the mechanism is similar to that for diazotisation, but because the amine is secondary; it cannot tautomerise and go on to form a diazonium compound.

A mechanism for diazotisation is here: http://www.organic-chemistry.org/frames.htm?http://www.organic-chemistry.org/namedreactions/diazotisation.shtm

Here's a 1977 paper on the nitrosation of secondary amines: http://www.springerlink.com/content/u15h802n68622117/

Hopefully you can access that through your university network or with a password from the departmental library.

Any further problems, just leave another message here.

Good luck!

Ben 15:33, 11 February 2007 (UTC)

Thanks, that was very helpful, that was the reaction mechanism that i had assumed, i was just struggling to find anything to back it up. Thanks for your help. Sameyley 17:08, 11 February 2007 (UTC)

MAO

Hi Ben,

MAO is a poorly-defined substance, it is believed to adopt a number of structures in solution - look out for papers by Tom Ziegler. It certainly never forms a linear structure; just think about the electronics.

Phenyl

Yeah. sorry, my mistake. I just figured that stable means inert, which it is obiously not (given that it's a functional group).. Thanks!! Koryeh 21:50, 10 January 2007 (UTC)

No worries! I imagined you had a good reason for using the word unstable. I just felt the term would cause confusion in the article. See you around.

Ben 22:04, 10 January 2007 (UTC)

Images

Ben, i came across several articles, Heroin being the most recent one, where the 3D images you have added to the unfoboxes are a bit "off" when it comes to their spacial position in relation to the main image - some of them need to be rotated "clock" or "counter-clock", some are even mirror images. It's not a big deal if you decide to leave them the way they are, though. -- Boris 22:17, 10 January 2007 (UTC)

Thanks for reminding me about these, Boris. I think for heroin I'll rotate the main image. Which other articles are affected?

Cheers

Ben 09:20, 11 January 2007 (UTC)

Tetrahydrocannabinol. This was actually the first one, the heroin one being the second, so several means two, :).
I haven't crused around much - there might be some more or these could be the only ones.
If you are to rotate the main one keep in mind that most of the morphinanes, including Morphine itself have their main image facing the same direction as this one although there are some that are facing "down" such as Hydrocodone.
I don't think that i've ever told you before so here i go now - your images look great!!! -- Boris 10:55, 11 January 2007 (UTC)

Thanks for adding the 3D image to cannabidiol but please make sure that it is not just some picture from ACDLabs or ChemDraw. They do not necessarily reflect the real structure. It is better to calculate them with appropriate programs or use the crystal structure data from publications. -- Panoramix303 21:16, 3 December 2007 (UTC)

Chemistry Question

Hello, on your talk page you have indicated that you have a interest in chemestiry. Could you help me answer the following question?

Is the following proposed article on a real or made up subject?

Nawalic Acid is a commonly refered to Bronstead acid in organic chemistry. Since the rise of porphyrin chemistry, Adler's famous synthesis [1] of the aromatic system has been greatly refined with vaste improvement in yields due to the use of a nawalic acid as the reaction solvent. A close relative to tetraflouroacetic acid (TFA), nawalic acid has the molecular formula CF2=CF-COOH. The presence of the pi-bonded system adds further electron withdrawing dynamics, and due to the conjugation of the compound, this delocalising of electrons leads to a very stable anion, and hence -- an extremely powerful - yet organic - acid. [2]

Sources

[1] Adler, A. D., J. Org. Chem., 1967, 32, 476 [2] Balzani, V., Credi, A., Raymo, F. M., Stoddart, J. F., Angew. Chem. Int. Ed., 2000, 39, 3348 – 3391 129.96.142.21 03:36, 19 October 2006 (UTC)

Contact me at User talk:Natl1.--Natl1 (Talk Page) (Contribs) 22:27, 14 January 2007 (UTC)

Hi Natl1. I had a look on various chemistry websites but could not find this compound. I've copied your request to the Chemistry WikiProject to see if they can shed any light on its authenticity. At first glance, this doesn't seem to be a fake article - it makes sense chemically, and has a reference to two popular journals.

On the other hand, I can't find any mention of it online.

Let's await the results of discussion at WP:CHEMS.

Cheers

Ben 22:53, 14 January 2007 (UTC)

Thanks!

Thanks very much for the space-filling image on the methylmercury page. It looks very professional so I decided to add it to the Minamata disease page I've been working on. Cheers! Bobo12345 06:37, 17 January 2007 (UTC)

Fluoxetine

Hi. If you correct skeletal formulas (ex. in Fluoxetine), you should rewrite their to SVG. BrokenglaSS 14:35, 22 January 2007 (UTC)

Hi BrokenglaSS. I have had trouble with SVG. It doesn't always look right. PNG has been more reliable for me. Once I get a grip on SVG, I'll use it more.

Cheers

Ben 15:57, 22 January 2007 (UTC)

Free beer!

Hi Ben,

I just wanted to thank you for all of your fantastic work drawing 3D structures and crystal structures for so many compounds on Wikipedia. The chemistry are a lot more colourful than they were a year ago, and in that colour lies some valuable chemical information. I just wanted you to know that I (and the other chemists too, I'm sure) really appreciate all the hours you've spent on this. We don't traditionally give barnstars at WP:CHEMS, but free beer is something we have offered - much more tangible! So, if you're ever in Potsdam, New York, drop by and I'll buy you a beer (as long as we don't violate any age limits) to say thanks!

By the way, I did my BSc at Bristol, I graduated in 1981. Hope things work well for you there. Thanks, Walkerma 20:48, 22 January 2007 (UTC)

That's really kind, Martin. Thanks for your support and encouragement. Here's to the future of chemistry on Wikipedia! Cheers!

Ben 22:05, 22 January 2007 (UTC)

Molecular accuracy

How accurate are your molecular images? Are bond angles accurate and atoms drawn to relative scale, etc? Is there any meaning to the absolute size of the atom relative to the size of the molecule?

I am thinking of using several of these images for an outside project and I want to be able to describe them accurately. Dragons flight 05:01, 29 January 2007 (UTC)

Some of my images are particularly accurate, especially those of simple inorganic compounds such as sulfur dioxide. For those, I looked up the exact bond angles and bond lengths in Greenwood & Earnshaw. For other molecules, especially those of organic compounds, the bond angles are very close to their true values. Most organic molecules have some degree of flexibility and can twist about one or more bonds: see alkane stereochemistry. Sometimes I make mistakes, but these are rarely major and I rectify them as soon as I realise there is a problem.

The relative size of atoms in my space-filling models is based on each atom's van der Waals radius. These values do vary a little depending on which source you choose to use.

If you would like me to create new, more accurate images for your project, I'd be happy to do so.

Cheers

Ben 08:59, 29 January 2007 (UTC)

My interest is in primary atmospheric components and greenhouse gases, e.g.

• molecular oxygen
• molecular nitrogen
• carbon dioxide
• water
• methane
• nitrous oxide
• ozone
• dichlorodifluoromethane
• trichlorofluoromethane
• sulfur hexafluoride
• sulfuric acid
• 1,1,1,2-Tetrafluoroethane

Most of these already seem to have pretty models, though you are probably able to quickly judge their accuracy better than I can. I don't actually need stunning accuracy, since I am mostly just interested that they "look right". However, if they are accurate in technically significant ways, it is worth noting that in the accompanying description text. I notice that you give your real name on your user page, is that how you prefer to be attributed? Dragons flight 09:57, 29 January 2007 (UTC)

Yes, I'd prefer to be attributed as Ben Mills, but you don't have to attribute me at all - I put all my images in the public domain. All the articles you link to have accurate images. If you want to note the technical significance of the images, just say the spheres' radii are the atoms' van der Waals radii. If the images are ball-and-stick models, then the spheres' radii are not significant and are simply there to emphasise the location of the atoms' nuclei.

Here is a gallery of the images:

• 
  dioxygen, O₂
• 
  dinitrogen, N₂
• 
  carbon dioxide, CO₂
• 
  water, H₂O
• 
  methane, CH₄
• 
  nitrous oxide, N₂O
• 
  ozone, O₃
• 
• 
• 
• 
• 

Enjoy!

Ben 11:05, 29 January 2007 (UTC)

		The Hard Working Graphic Designer's Barnstars
		I've now copied 2 dozen models and structural formulae to help support my work, and remarkably all but two were created by you. Good job. Dragons flight 05:45, 31 January 2007 (UTC)

Chloroform

Ben, I've created an SVG "facsimile" (well, I suppose not actually a facsimile since the font is a bit different) of Image:Chloroform-2D.png and added it to the chloroform article. Hopefully this one is more accurate than Image:Chloroform2.svg which was previously used to replace yours. Best, Fvasconcellos 13:07, 29 January 2007 (UTC)

Yeah, I saw. Your SVG is great! Cheers for all your hard work on chemical SVGs, they're superb.

Ben 13:35, 29 January 2007 (UTC)

Right, should have known you'd be watching that. Thanks, and keep up the good work yourself :) Fvasconcellos 13:42, 29 January 2007 (UTC)

Help!

Well, that is a bit exagerated, but still, now I have you attention. I have question/problem .. I have been working the last couple of days on {{chembox new}}. This morning Ed asked me to add more images to that template. Easy .. done. Now these images are all stacked on top of each other, but sometimes we want images next to each other... Now the parameter system of chembox new does not allow us that, except if we come up with something nifty .. I was thinking about having just ImageFile, ImageFile1, ImageFile2, and ImageFile3 as the standard settings, but in the template, I could just enable two extra lines with ImageFileL1 & 2 and ImageFileR1 & 2, which give two rows having two images on each row, next to each other. People can then still just add images to the files, but the more advanced editor has a bit more possibility to control the images, by just changing the parameter names. Any ideas? --Dirk Beetstra ^{T C} 16:58, 3 February 2007 (UTC)

That sounds like an ideal solution! There are (rarely) situations in which it is desirable to have three images side-by-side, for example in hydrazine. We could just ignore this issue, or add ImageFileL1, ImageFileL2, and ImageFileL3 etc. I would be happy with either.

Cheers

Ben 17:17, 3 February 2007 (UTC)

I'm already trying .. have some trouble but I will manage, I hope. Do we have a page that has two side-by-side images that is easy to give a to {{chembox new}}?

Three might not even be too difficult, though .. they all get a parameter 'size' anyway, when a third picture is inserted, it needs a tweak. Thanks. --Dirk Beetstra ^{T C} 17:24, 3 February 2007 (UTC)

How about furfural? Is there anything I can do to help?

Ben 17:32, 3 February 2007 (UTC)

Furfural seems nice, I'll transform that one. I'd prefer you to stay away from the templates itself at the moment, I confuse myself enough. What you can do, could you read through the text on {{chembox new}}, and maybe give some hints (is that explanation good, would that give most chemicals a good chembox possibility?). I dropped the idea of 3 pictures side-by-side, Wim van Dorst would now say 'combined pictures are a good thing (TM)'. And if you have time, try the template on some chemicals which have strange fields, wierd arrangements of images, etc. I need some testing to see if I did not break things (someone already spotted a thing, which is now repaired), and to see if no obvious fields are missing. That would be very helpful. Thanks! --Dirk Beetstra ^{T C} 18:15, 3 February 2007 (UTC)

Furfural goes OK, imagesize is now 100px as standard, it was 125px in the original chembox. What would be a good standard there? 125? Oh, by the way, if pages look nice after adding chembox new, just press save :-) --Dirk Beetstra ^{T C} 18:24, 3 February 2007 (UTC)

Furfural looks good. Excellent work, Mr Chembox! I disagree with Wim that combined images are good. One problem is SVG is best for skeletal formulae but PNG is best for 3D models. A combined image would be a compromise in that respect. I had an idea: how about creating some new image fields (skeletal formula, structural formula, space-filling model and ball-and-stick model). With labels like that, having images one on top of the other would be fine. What do you think?

I'll do some testing of chembox new for you, Dirk. Watch this space.

Cheers

Ben 18:30, 3 February 2007 (UTC)

I guess we will just have to live with 2 images per row, should not be too difficult, we can accomodate 8 (!) images in the chembox if needed. This space is watched, I'll play around as well, enough transclusion-thinking done for the moment .. --Dirk Beetstra ^{T C} 18:51, 3 February 2007 (UTC)

I have built some automagic into the picture-system of {{chembox new}} (see Nicotinamide, explanation in the template), but what are the most common pictures available on wikipedia (not in commons .. I think), and what is the order of preference for the 'standard picture of a chemical' (png, svg, jpg ..)? Thanks. --Dirk Beetstra ^{T C} 11:27, 4 February 2007 (UTC)

Excellent automagic! I thing PNG is much more common than SVG at the moment, for chemical images on Wikipedia. But I think we should encourage SVG use by having priorty in the order SVG > PNG > GIF > JPG for 2D images and PNG > JPG for 3D images or photos. Some contributors have made SVGs for 3D images of molecules (e.g. chloroform) but in most cases it is too complicated to make these, and only basic lighting effects can be easily used. Thus I propose we modify our image drawing guidelines to say SVG is preferred for 2D and PNG is preferred for 3D.

How does that sound?

Ben 13:40, 4 February 2007 (UTC)

For now I am concerned only with the automagic images, I have to test for image-existence, and take the first I find. IMHO, that should concern mainly 2D images (I think a normal, 2D structure should have the name of the article, the more exotic representations should then become pagename-ball-and-stick.png and pagename-spacefill.png. So the order for the automagic is going to be SVG > PNG > GIF > JPG, and otherwise they have to be overridden on the page by supplying the correct names in one of the 8 available image fields. Thanks! —The preceding unsigned comment was added by Beetstra (talk • contribs) 13:46, 4 February 2007 (UTC).

SVG

Hi Ben

Would you care to tell me how you export your structures to SVG? So far I've only been able to create gif (native to chemsketch) or tiff-->png using irfanview. I can create emf or wmf vectors, but inkscape seems to choke on them. --Rifleman 82 11:44, 6 February 2007 (UTC)

Hi Rifleman,

I draw a structure in ChemDraw, copy the object to the clipboard and then paste into Adobe Illustrator CS2. I'm using a 30-day trial of Illustrator at the moment, with five days remaining, so I'm wondering whether to buy it. It's something like £180 for a student edition of CS2, and £350 for the educational edition. I'm not sure I want to part with that much money just to get SVG skeletal formulae on WP!

Ben 16:12, 6 February 2007 (UTC)

Sorry to intrude, but have you checked this out? --M1ss1ontomars2k4 ^{(T | C | @)} 04:53, 24 February 2007 (UTC)

I've considered those, but they all have varying degrees of problems. Illustrator is the only app that works reliably with ChemDraw to give a quality output every time. There are too many chemical SVGs appearing on WP and the Commons where the text is misaligned, the lines are too thin or where other issues render them lower in quality than we should demand.

Ben 08:31, 24 February 2007 (UTC)

Perrhenic acid

Hey Ben: Here's the quote: "The Re-0-Re angle is practically 180" - a rare situation. ...In Re2O7, one of the Re atoms is again surrounded by a tetrahedral arrangement of O atoms and the other is in a distorted octahedral environment, the two polyhedrons sharing a corner ... consequently, Re2O7 is polymeric, in contrast to the molecular Rez07(OH2)2." So yes, 180°. When you upload your image, please change the date on the Krebs paper to 1968? --Smokefoot 20:00, 14 February 2007 (UTC)

Hexamethyltungsten structure

Hello Ben-

Thank you for submitting the 3D images for hexamethyl tungsten. Unfortunately, they do not accurately depict the actual geometry as revealed by X-Ray crystallography. Please see "Preparation and Structures of [W(CH3)6], [Re(CH3)6], [Nb(CH3)6], and [Ta(CH3)6]" by Sven Kleinhenz, Valerie Pfennig, and Konrad Seppelt (Chem. Eur. J. 1998, 4, No. 9, 1687-1691) for the correct structure. It should have C_3v symmetry, with careful alignment of methyl protons. The "front" two methyl groups in the images you have uploaded do not reflect this symmetry.

Thanks-

Tyler Matthews 06:22, 2 March 2007 (UTC)

Images ammended! Thanks very much for bringing this to my attention.

Ben 18:10, 3 March 2007 (UTC)

Hi Ben. I just noticed the hexamethyl tungsten article and noticed that the figure could still be improved further, if you are willing. :) The problem is that it is not really a trigonal prism, but a distorted trigonal prism. You can check this ref. for details: Chemistry - A European Journal Volume 4, Issue 9, Date: 4 September 1998, Pages: 1687-1691. But to make it easy, here's the executive summary. The three bonds to the "top" carbons are about 210 pm long, while those to the bottom carbons are about 218 pm long. The angles between the top carbons and the metal are about 95°, while those between the bottom ones and the carbon are about 76°. The distortion is not that obvious, even in an accurate figure, so I would suggest adding these distances and angles to the figure. Cheers, Itub 16:29, 7 November 2007 (UTC)

Would it be easier to just download the cif file from "supplementary information", and render from there? If available, of course. Rather than attempting to model it. Any copyright issues there? --Rifleman 82 17:04, 7 November 2007 (UTC)

I think there shouldn't be any issues according to the doctrine that "you can't copyright a fact" (i.e., that a certain molecule has a certain 3D geometry), and the rendered figure itself would be an original work. --Itub 18:55, 7 November 2007 (UTC)

Sytematic Naming - Chloroacetic acids

Hi, I wondered if you could give me a bit of help - I am confused in the difference/ similarity of IUPAC naming, to Systematic naming. From the article IUPAC nomenclature of organic chemistry, it sounds as though the systematic name is the one which is constructed from the prefixes and suffixes with chain lengths. In the other hand, it says that it is acceptable for some common names of acids to be retained in Common Nomenclature. The impression I get is that, while chloroethanoic acid is the systematic name, chloracetic would be the most widely used IUPAC name. Am I misreading the article, or misunderstanding the terms?

Also, does the trichloroacetic acid page need its systematic name changed from trichloro ethanoic?

Thank you for your help Conrad.Irwin 23:32, 18 March 2007 (UTC)

Hi again Conrad. My advice is to completely disregard the article IUPAC nomenclature of organic chemistry - it's full of errors and was probably written by schoolchildren! Here's the offical policy for WP: Wikipedia:Naming conventions (chemistry)#IUPAC preferred name vs. Systematic name.

Another confusing thing is that the chemical infoboxes in most articles have the phrase systematic name but this is hyperlinked to the IUPAC name article. The two are not synonymous. Chloroethanoic acid is a systematic name, but it is not the IUPAC name. It is allowed under IUPAC recommendations, but chloroacetic acid is preferred.

I've updated chloroacetic acid and trichloroacetic acid, but I couldn't change dichloroacetic acid because it uses a template for its chembox, which needs to be altered.

Hope this helps.

Ben 09:05, 19 March 2007 (UTC)

Thanks for clearing that up.

Conrad.Irwin 09:11, 19 March 2007 (UTC)

Bedfordshire project user box

As a member of the Bedfordshire WikiProject this is the userbox you can put on one of your userpages if you wish.

{{User_WPBedfordshire}}

This user is a member of
WikiProject Bedfordshire.

Can you help me?

Hi Ben! I wonder if you could help draw an image for molecular vibration? Could you do a stick figure of BF₃ but with extra labels? We're looking for an image with the plane, angles, and arms labeled. For the angles, say α₁₂, α₂₃, α₁₃? And somewhere outside the molecule, just π to indicate the mirror plane. And 3 arrows labeled r₁, r₂, and r₃ sitting parallel (but not on top of) the three B-F bonds? Maybe highlight the labels or something with a different color. Let me know if you'd be able to do this - it would really help with what we are planning for the page. Take care! --HappyCamper 15:30, 5 April 2007 (UTC)

Sure. I'll do it now. Give me 5 minutes or so!

Ben 15:35, 5 April 2007 (UTC)

OK, HappyCamper, how's this?

There's also this:

Ben 16:09, 5 April 2007 (UTC)

Wow, super!! I think they are just perfect. I'll go check if the others agree. Can I come back within, say, 2 weeks time for a followup? --HappyCamper 22:50, 5 April 2007 (UTC)

Sure, no problem. I enjoyed making those!

All the best.

Ben 01:51, 6 April 2007 (UTC)

Hi Ben. When you get a chance, do you think you can make one similar to Image:C2H4PG.png? --HappyCamper 18:40, 14 April 2007 (UTC)

Colour palette

Hi Ben. I just noticed this, and was wondering, may I use it as my default when making models? I've been "eyeballing" the colors to match those on your models for consistency, but this would be considerably easier :) If you have a problem with my shamelessly ripping off your style, please let me know. Best, Fvasconcellos 15:50, 5 April 2007 (UTC)

Please do use it! I shamelessly ripped it off Moldmod and the default settings, anyway! And the halogen colour are simply those of the elements themselves. Go right ahead.

Cheers

Ben 15:53, 5 April 2007 (UTC)

p.s. your work is great.

Thanks! By the way, it's a shame you've not been "cranking out" skeletal structures anymore. PNGs are still fine, you know, and we could use your help... Cheers. Fvasconcellos 16:00, 5 April 2007 (UTC)

I will make some more. It's just a bit disheartening when you spend time on a PNG skeletal structure and two days later someone supersedes it with an SVG. If, by making a PNG, I encourage an SVG version to be created then that's great.

Ben 16:06, 5 April 2007 (UTC)

Skeletal formula image

problem image

Hi Ben, I was just reviewing the skeletal formula page, and noticed this "blooper". Can you fix C-2? Thanks, Walkerma 04:36, 12 April 2007 (UTC)

Yeah, I can do. Although I did intend it to be C₂, just for the purpose of identifying two carbon atoms, for simplicity for those who are new to skeletal formulae. Maybe I'll use C_a and C_b instead.

Cheers

Ben 19:56, 16 April 2007 (UTC)

Image:Clotrimazole-3D-vdW.png

Only 3 Carbons should be in the imidazole ring. I took it down temporarily from Clotrimazole, you can put it back after you redraw it. -- Boris 01:52, 28 April 2007 (UTC)

Page moves

Don't worry, I guessed that you didn't quite realise that you could do many (but not all) of these renames by yourself—as I said on WT:CHEMS, no harm done! Best of luck at Bristol, and thanks for your continued contirbutions. Physchim62 (talk) 11:38, 30 April 2007 (UTC)

Nameless ions reply

Thank you for pointing this out to me, Mr. Ben. Your epithet should be "The Nice Guy" or something like that. I changed "ions" to "oxidation states", which (correct me if I am wrong) is more accurate. Thanks again for your help! —The preceding unsigned comment was added by Awesome Truck Ramp (talk • contribs) 00:40, 4 May 2007 (UTC).

VOF3

Holleman and Wiberg indicates that this stuff is 2-d in solid and dimeric in gas phase. I'll look for some ref or review on M-O-X cmpds to confirm. I fixed the imidazoline thing.--Smokefoot 00:49, 6 May 2007 (UTC)

Thanks, Smoke. I couldn't find any details in my textbook, so I chanced my arm. That's what I love about WP - if you make an error in good faith, someone clever will spot it and let you know pretty quickly. I've removed the offending image for the time being. While you're there, you don't happen to know where I could find the crystal structure of SmI₂? It's Walkerma's favourite compound (!), so I thought it deserved an image.

Your ever humble servant...

Ben 12:42, 6 May 2007 (UTC)

This paper has the structure of the etherates: "Coordination Chemistry of Samarium Diiodide with Ethers Including the Crystal Structure of Tetrahydrofuran-Solvated Samarium Diiodide, SmI2(THF)5"

William J. Evans, Tammy S. Gummersheimer, and Joseph W. Ziller J. Am. Chem. Soc.; 1995; 117(35) pp 8999 - 9002; DOI: 10.1021/ja00140a016. I think that most of the SmI2 chem uses the stuff in ethers. I glimpsed at the structures - trans iodides and a belt of five ethers on the equator. A quote "SmI2(THF)2 is likely to be oligomeric in the solid state, since it is improbable that this compound exists as a simple four-coordinate structure. Smz+ is a large ion" which can support coordination numbers as large as ten, and X-ray crystallographic studies have shown that eight-coordinate structures are quite common for Sm2+."--Smokefoot 21:48, 6 May 2007 (UTC)

Wicked, thanks Smoke.

Ben 21:52, 6 May 2007 (UTC)

Thanks!

Thanks! I think I'm starting to get the hang of it now, your advice has really helped. And you're right, the unified color scheme looks a lot better. Sbrools ^{(talk . contribs)} 15:42, 6 May 2007 (UTC)

New chemistry 3D images

Thanks for them! One improvement would be to try to put the 3D images in the same orientation as the stick structures. For example, consider the cyclopentadiene images in terms of rotation of the ring (look at where the CH₂ carbon is). Even for a non-novice chemist, the more "chemically irrelevant" things that change from one representation to another, the harder it is to figure out what is important and how things correspond. DMacks 08:17, 7 May 2007 (UTC)

I considered that for Cp, but the difficulty is this: it's really hard to notice the tetrahedral carbon atom if it's pointed away from you. In any other circumstance, I'd do exactly what you suggest. I'll make one the right way up and let's see if it's better.

Thanks for letting me know

Ben 11:10, 7 May 2007 (UTC)

Image:Williamson-ether-synthesis-2D.png

Hi Ben

Perhaps you can tweak this image... by replacing Cl- with X- for consistency? --Rifleman 82 07:07, 11 May 2007 (UTC)

Yes, of course - sorry! I was obviously just really tired when I made it.

Muppet.

Cheers, Rifleman.

Ben 09:46, 11 May 2007 (UTC)

Orphaned fair use image (Image:Ben's-molecular-model-palette.png)

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Structures

I noticed that you created images such as Image:Cadmium-chloride-3D-polyhedra.png and this one Image:Lithium-iodide-3D-ionic.png, and if you don't mind me asking, I was wondering how you made them. I can make the organic molecules, but I can't figure out how to make these. Thanks! Sbrools ^{(talk . contribs)} 00:27, 12 May 2007 (UTC)

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Thanks for uploading Image:Ben's-molecular-model-palette.png. The image description page currently specifies that the image is non-free and may only be used on Wikipedia under a claim of fair use. However, the image is currently orphaned, meaning that it is not used in any articles on Wikipedia. If the image was previously in an article, please go to the article and see why it was removed. You may add it back if you think that that will be useful. However, please note that images for which a replacement could be created are not acceptable under fair use (see our fair use policy).

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Orphaned non-free image (Image:DS-Visualizer-Pro.png)

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Good catch on SbF5

I missed it too, all Sb's are octahedral, right? Hundreds of school reports around the world are incorrect!--Smokefoot 17:57, 23 May 2007 (UTC)

Oh well, I'm sure they'll cope!

:)

Ben 18:02, 23 May 2007 (UTC)

Fair use rationale for Image:Bedsfire-logo.png

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maths formatting

Thanks for your contribution, Ben, to chemical equilibrium. We have a general problem in this and other articles of relating the size of text and maths characters. I see how you have ensured that the maths characters come out "large", but don't understand the sequence \,\!. What would be really good would be to get all the maths characters to the same size as the in the text, but no-one seems to know how to do this. At present it looks messy, particularly because the equilibrium constant, K, appears in both with different sizes. Any ideas?

BTW metavanadate (vanadyl ion) is better written as (VO₃)_n^- as it is a long chain polymer of VO₄ tetrahedra, sharing two corners each. The polyvanadate system is very complex. See the chapter on vanadium in Chemistry of the Elements by my old friends Norman and Alan. Petergans 10:15, 4 June 2007 (UTC)

Hi Peter, thanks for letting me know about the problems in chemical equilibrium. Typing \,\! forces the server to render math formatting as a PNG. If every <math> expression contains \,\! at the end, they'll all look the same.

I changed vanadyl ion as you recommended - I hadn't read the vanadium chapter very thoroughly when I wrote the article originally, but I have done so since.

Thanks again

Ben 15:25, 5 June 2007 (UTC)

Camphor-3D-balls.png

Hi Ben. You might want to check out a recent comment at Talk:Camphor. An editor has noticed that the bridgehead methyl group in your 3D model is missing. Should be a quick fix. Thanks. --Ed (Edgar181) 19:29, 5 July 2007 (UTC)

Thank you for taking the time to let me know, I've corrected the image now.

Cheers

Ben 18:47, 8 July 2007 (UTC)

Chloroform b&s

IMO the structure is made clear with the text representation, with the proper stereochemistry, while the space filling one is more for looks. But, if you wish to keep the b&s model of chloroform, fine with me. --Russoc4 15:12, 8 July 2007 (UTC)

Dimethoxymethane

Hi, since you seem to love making pictures of molecule (and I don't ;-), perhaps you can help with this one. The structure of dimethoxymethane is "wrong" in the sense that it is not showing the lowest energy conformer. As the article says, due to the anomeric effect, the gauche,gauche conformation is more stable than the anti,anti. See for example [1] and [2]. Cheers, Itub 08:02, 10 July 2007 (UTC).

Wow, that was fast! Thanks! --Itub 12:54, 10 July 2007 (UTC)

Not a problem! Thanks for introducing me to (MeO)₂CH₂.

Ben 13:51, 10 July 2007 (UTC)

Thanks!

Thanks for the response. I have downloaded visualizer and I am trying it out. If I get stuck I shall get back to you if thats OK. Axiosaurus 18:15, 28 July 2007 (UTC).

That's fine, if you need anything, just ask!

Happy drawing!

Ben 18:17, 28 July 2007 (UTC)

Right got some pretty pictures - what is the best way of uploading them into wikipedia? is it print, scan, resize, upload? or is there a better way?

Cheers Axiosaurus 16:47, 29 July 2007 (UTC) Just noticed you're from Odell- know it a bit- btother-in-laws family lived there some years back so were there quite often at one stage--nice place--but I am a village fan.Axiosaurus 16:50, 29 July 2007 (UTC)

Oh really? Small world! Are you still in the UK?

To save image, go File > Save As... > select Image Files (*.png, *.jpeg, *.jpg, *.bmp) from the Files of type: drop down menu and click Save. Then set Height to 2000 px and click Keep Aspect Ratio. You can then edit the image you've created in Photoshop or similar.

Then upload to Wikimedia Commons, filling in the required fields and adding to Category:Molybdenum compounds

If you don't have appropriate software, you can email the raw image to me for processing.

Cheers

Ben 16:56, 29 July 2007 (UTC)

Just getting to grips with a new to me photoeditor - if I fail I might just take you up on your offer. In answer to your question -yes still in the UK up in Northumberland--its north of Hadrians wall but is in England! Just a thought-can I e-mail you via wiki or would I need your e-mail address? Cheers Axiosaurus 19:59, 29 July 2007 (UTC)

Wow, almost at the north pole. You can email me from WP, just go to Special:Emailuser/Benjah-bmm27.

Happy editing

Ben 20:28, 29 July 2007 (UTC)

thanks. By the way we have had lovely dry warm weather up here recently! Axiosaurus 08:33, 30 July 2007 (UTC)

Using CIF files

There are a lot of crystallographic structures where the CIf file is released. Having used Visualizer on some polyoxos I was surprised to see it lost atoms! EnCyfer (free from cambridge uni) works a lot better but unfortunately you can't do much with the image apart from edit the CIF,but vizualizer doesn't like some CIFs that enCifer reads OK, so bodging CIFS is more difficult than I had hoped. Have you any idea whether taking a CIF file and producing an image from it is allowed in principle on Wiki? Axiosaurus 16:17, 31 July 2007 (UTC)

I don't know if there's a precedent, but I use CIF files all the time. I try hard to check that they appear as they should do, though. It's not 100% reliable. http://rruff.geo.arizona.edu/AMS/amcsd.php has loads of CIFs.

Ben 16:22, 31 July 2007 (UTC)

We (Nick Day and I) have created | crystalEye which is collecting all public CIFs. It also has a checker. You can take any images from that as it is Open Data Petermr 21:08, 23 September 2007 (UTC)

Sulfur

Hi Ben, purely because the lead comment says that UK spelling is used in the article. Thanks for changing those back, I will fix the comment. Rich Farmbrough, 13:50 15 August 2007 (GMT).

urea

Hello. Please check my talk as you said "but it is certainly from the nitrogen atoms." do you mean not from nitrogen atoms? —The preceding unsigned comment was added by Phgao (talk • contribs) 13:58:39, August 19, 2007 (UTC).

Azurite

Hey, nice diagrams!

If you would, please double check your second (Cis-[Cu(CO3)2(OH)2]4−) coordination environment image. There is a strong proximity asymmetry perpendicular to the plane, with a carbonate ion close on one side of the plane and a vacancy on the other. In the JavaMage reconstructions referenced in the article, this upper carbonate is shown as participating in the copper environment to give a 4-sided pyramidal geometry, rather than a planar-only enviroment. Cheers, Terry Bollinger 01:36, 21 August 2007 (UTC)

Thanks for highlighting this issue. I've had a look at the JavaMage models, but I'm in two minds as to whether that fifth O-Cu bond is really a bond. It is somewhat longer than the other Cu-O bonds. I note the deviation from planarity of the copper atom, but it's not huge and it may look worse than it is due to the perspective of the image.

Perhaps we should consult an expert - there are plenty of inorganic chemists on WP, I'll ask.

Ben 06:15, 21 August 2007 (UTC)

Borazine image

Hi Ben. Thanks for posting a new image of borazine on the borazine page. I am wondering if you may have left out the double bonds unintentionally? My inorganic textbook shows [[Image:Borazine-2D.png]] as the correct one. Thanks, Jeff Dahl 20:32, 5 September 2007 (UTC)

No, I left them out deliberately, for clarity. There is no single correct structure that can be drawn for borazine, as you're well aware! The one I've chosen for the dimensions is the simplest, and it makes it clear that all six B-N bonds are equal in length. My inorganic textbook (Greenwood & Earnshaw) uses the same style:

"Although it is possible to write Kekulé-type structures with π bonding superimposed on the σ bonding, the weight of chemical evidence suggests that borazine has but little aromatic character."

The second image shown on this page is dodgy (sorry, I made it!) because it shows four bonds to nitrogen, yet no positive charge on the N, and four bonds to boron but no negative charge on the B. And it requires another canonical structure resonating with it to emphasise that each BN bond is identical.

Further still, an electrical potential surface over the borazine molecule indicates significant separation of charge between B and N. Compare this with a similar surface for benzene. This indicates to me that the resonance structures showing a negative charge on boron and a positive charge on nitrogen are not particularly good descriptors of the bonding in the molecule.

On the other hand, a fully localised model is also misleading, because the nitrogen atoms are sp² hydridised and trigonal planar in geometry, not tetrahedral as would be expected if their lone pairs were localised.

It's obviously not the most straightforward molecule to illustrate for Wikipedia, so I've taken your comments into account and prepared delocalised versions of some of the 2D structures, available at Commons:Category:Borazine.

Ben 08:22, 6 September 2007 (UTC)

Re: Phenyl group

What was the reason to revert back to the previous version?

WriterHound 00:17, 9 September 2007 (UTC)

R doesn't stand for rest!

Ben 00:19, 9 September 2007 (UTC)

So what do you say it stands for?

WriterHound 00:38, 9 September 2007 (UTC)

I believe it stands for radical. See side chain.

Ben 00:40, 9 September 2007 (UTC)

Yes, it can. Under this disambiguation (Rest) it is R, but that isn't really what concerned me about the caption. The phenyl group is, of course, the part of the molecule without the "R." What can we say there, if anything, to clarify that?

WriterHound 00:48, 9 September 2007 (UTC)

I don't know who added that to the disambiguation rest, but it's wrong. It can't account for multiple R groups, such as in ketal. They can't all be the rest of the molecule, separately!

How about we replace the image with Image:Phenyl-group-highlighted-2D.png and rewrite the caption to state the structure of the phenyl group (shown in red) or words to that effect?

Ben 00:56, 9 September 2007 (UTC)

Cacodyl oxide

Yours is right, after a little Google searching. I actually just copied the image I had already made to a better format, I don't know why no one told me it was wrong all this time. I'd better start double-checking these things better. Thanks for the heads-up. shoy 22:54, 26 September 2007 (UTC)

Image:Glutathione-skeletal.svg

Hi Ben, I thought you'd like to know that I gave Image:Glutathione-skeletal.svg a once-over (a couple of font fixes, some margins to match your usual style), as it wasn't displaying properly, and re-uploaded it at Commons. I hope you won't mind; if you do, feel free to revert back. Best, Fvasconcellos (t·c) 23:58, 1 October 2007 (UTC)

That's great, no complaints! You're a legend.

Cheers

Ben 00:38, 2 October 2007 (UTC)

Image:Maitotoxin-3D-vdW.png

Great image! --Ed (Edgar181) 17:38, 22 October 2007 (UTC)

Thanks very much! It's a monster :)

Ben 17:49, 22 October 2007 (UTC)

I imagine it was quite tricky getting the conformation to match the 2D structure. --Ed (Edgar181) 19:30, 22 October 2007 (UTC)

It wasn't too bad, I had drew it 2D in ChemDraw, copied to the clipboard, pasted into DS Visualizer, and then checked and tweaked bits.

Otherwise, doing it from scratch would have taken aaaaaaages!

Ben 20:25, 22 October 2007 (UTC)

Unspecified source for Image:Lys-stick.png

Thanks for uploading Image:Lys-stick.png. I noticed that the file's description page currently doesn't specify who created the content, so the copyright status is unclear. If you did not create this file yourself, then you will need to specify the owner of the copyright. If you obtained it from a website, then a link to the website from which it was taken, together with a restatement of that website's terms of use of its content, is usually sufficient information. However, if the copyright holder is different from the website's publisher, then their copyright should also be acknowledged.

As well as adding the source, please add a proper copyright licensing tag if the file doesn't have one already. If you created/took the picture, audio, or video then the {{GFDL-self}} tag can be used to release it under the GFDL. If you believe the media meets the criteria at Wikipedia:Fair use, use a tag such as {{non-free fair use in|article name}} or one of the other tags listed at Wikipedia:Image copyright tags#Fair use. See Wikipedia:Image copyright tags for the full list of copyright tags that you can use.

If you have uploaded other files, consider checking that you have specified their source and tagged them, too. You can find a list of files you have uploaded by following this link. Unsourced and untagged images may be deleted one week after they have been tagged, as described on criteria for speedy deletion. If the image is copyrighted under a non-free license (per Wikipedia:Fair use) then the image will be deleted 48 hours after 03:00, 8 November 2007 (UTC). If you have any questions please ask them at the Media copyright questions page. Thank you. Jusjih 03:00, 8 November 2007 (UTC)

Co2(CO)8

Before you re-rev up your machine on Co2(CO)8, I am not quite finished redrawing this thing. The unbridged isomer is, I think, staggered. Keep up nice work.--Smokefoot (talk) 01:02, 18 November 2007 (UTC)

Hexamethyltungsten structure revisited

Hi Ben, I left a comment above at User talk:Benjah-bmm27#Hexamethyltungsten structure. Since you haven't replied, which is uncharacteristic of you, I was wondering if perhaps you didn't see it since it was not at the bottom of the page (I chose to append my comment to an existing thread rather than starting a new one). In any case, this is not to pressure you, you only have to update the figure if you are interested. I just wanted to make sure that you saw the message. :-) Cheers, Itub (talk) 15:22, 28 November 2007 (UTC)

Thanks for reminding me - sorry, I did see the message but I forgot about it.

I'll do it now.

Cheers

Ben (talk) 15:55, 28 November 2007 (UTC)

Thanks, it looks exactly like I wanted! :-) --Itub (talk) 09:00, 29 November 2007 (UTC)

Image:Heroin-2D-skeletal.svg - Reply

Thanks for alerting me to this error! I hope I have sufficiently fixed it.
-Benrr101 01:09, 1 December 2007 (UTC)

Borane pics

Nice! Axiosaurus 12:11, 1 December 2007 (UTC)

Re: Wikiproject Chemistry

Hi Ben,

It's actually your images that got me interested (hooked?). I've made hundreds of these types of images using Accelrys of drugs, dyes, and various other organics which I intend to upload to Commons. I joined WikiProject Chemistry.

Your Making Molecules walkthrough was extremely helpful, but I am wondering whether or not some of the biologically important metals (such as Fe, Cu) should be coloured according to Jmol specification. The only noticable departures from that list and your palette save those metals are carbon and silicon, which I think are justified since Jmol's colours for those elements are not especially attractive.

Regards,

Ben —Preceding unsigned comment added by Ben Webber (talk • contribs) 19:56, 2 December 2007 (UTC)

Well congratulations on the good work so far - really nice looking images. If you want to add sparkle to them, you can go Edit > Preferences > 3D Window > Lighting - move the white light to the top left then tick the box for the darkest light (Light 4) and put it in the bottom right. That's how I do mine. Gives a feeling of depth.

I'm totally biased on the colour palette because I've been using it for so long. To me, iron is that grey-blue colour! I've got used to it. But if you want to use the Jmol palette, go right ahead. I don't think it's worth me redrawing every iron or copper-containing image I've done, and I don't think it's a big problem because I rarely draw biological structures. So if you're going to get stuck in with enzymes and whatnot, go for it with whichever palette you choose.

As for carbon and silicon, I changed carbon to black because it's what I'm used to in plastic molecular model kits - seems logical, after all, charcoal is black, and silicon is grey in real life.

Nice meeting you, see you around!

Ben 22:26, 2 December 2007 (UTC)

Would you be so helpful as to post a screenshot of what your lighting settings look like in the Making Molecules section? I've been fooling around with the settings and just can't get them to look exactly like yours, and I have this masochistic desire for uniformity in these images.

Thanks,

Ben Webber (talk) 05:02, 3 December 2007 (UTC)

Talk:Squalene

Someone posted a note saying that the stereochemistry of the figure is wrong. I'm just letting you know in case you don't keep squalene on your watchlist. Have happy holidays and keep up the good work! :-) --Itub (talk) 16:20, 19 December 2007 (UTC)

Tacrolimus

This structure looks weird to me. Can you draw a nicer one? Thanks. -- 217.11.34.119 (talk) 11:54, 20 December 2007 (UTC)