Benjah-bmm27

Sometimes I accidentally omit the {{PD-user|Benjah-bmm27}} tag that I intend to include with all my uploads. An archive of all comments originally posted on this talk page regarding missing licenses can be found at User:Benjah-bmm27/licensing. Any image discussed in the archive now has a license. Other old posts are kept at User talk:Benjah-bmm27/Archive 1.

Ben 16:15, 22 April 2007 (UTC)

Hello Ben,

We notice you have made ambulance service maps. Very nice! We're just looking to do the same for a research project. Our first attempt was based on mapping LSOA and CCG to ambulance trust, where it looks like you are using counties? Would you mind us talking about the data you used? Please e-mail m.allen@exeter.ac.uk

Thanks!!

Mike Allen Michael.allen1966 (talk) 12:16, 8 February 2023 (UTC)

File:Beta-D-glucose-from-xtal-3D-balls.png

Dear Dr. Mills,

I am a permissions editor for a textbook publisher and I am currently working on a biochemistry textbook and I would like to use your image of Ball-and-stick model of the β-D-glucose molecule, C6H12O6, as found in the crystal structure. I was wondering if I could get a confirmation of public domain from you? Thank you your time and assistance.

Lauren

Hi Lauren,

I'm not Dr Mills yet, give me another four years!

I can confirm that I have released File:Beta-D-glucose-from-xtal-3D-balls.png into the public domain.

Best wishes, Ben (talk) 17:04, 25 June 2012 (UTC)

Location?

Hi Benjah - can you add a photo location to File:Alectoris-rufa-with-young.jpg, please? Thanks! - MPF (talk) 22:42, 13 August 2012 (UTC)

Category:Aspirin

Aspirin has been listed at Commons:Categories for discussion so that the community can discuss ways in which it should be changed. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this category, please note that the fact that it has been proposed for discussion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it. If the category is up for deletion because it has been superseded, consider the notion that although the category may be deleted, your hard work (which we all greatly appreciate) lives on in the new category. In all cases, please do not take the category discussion personally. It is never intended as such. Thank you!

77.184.48.22 04:56, 11 October 2012 (UTC)

A barnstar for you!

The Graphic Designer's Barnstar

Bonjour, i' m writing a book (160 pages, 300 pictures) in France about hemp agriculture…Is it possible to illustrate it with the picture of : File:L-cysteine-3D-vdW2.png Description L-cysteine 3-D | Source Derivative work of User:Benjah-bmm27 | Date 09-29-07 | Author Photohound Category:L-cysteine ... (1 100 × 979 (245 Kio)) - 22 mai 2010 à 13:53  Source Derivative work of User:Benjah-bmm27.... I have read that this picture is in the public domain... But can i have your exclusive authorisation to use it for my book…  Have you maybe an high résolution version ? i will thanks your under this photo…as a pub, which name must i write ? Thank you for your help…  Jah-ova (talk) 22:40, 1 November 2012 (UTC)

Hi Jah-ova, thanks for the barnstar! You are welcome to use File:L-cysteine-3D-vdW2.png for your book. As I have released the image into the public domain, I cannot grant exclusive rights to it - it is already unleashed on the world, if you like. I could make you a similar image at high resolution. I am quite busy with real life at the moment, what's the deadline? --Ben (talk) 09:13, 2 November 2012 (UTC)

A barnstar for you!

	The Graphic Designer's Barnstar
	i have already a 1100 x 979 in 72 dpi version, do you think it will be enough for my book ? dead line : 2 or 3 weeks... Jah-ova (talk) 22:38, 2 November 2012 (UTC)

Ask your publisher if that image size is sufficient - if not, ask me again. Best wishes, Ben (talk) 10:37, 3 November 2012 (UTC)

File:Naphthalene-numbering-2D-skeletal.png

Hi Benjah-bmm27, the numbering of the C-atoms in this image shold be corrected from 9/10 (which would be correct for saturated HCs) to 4a/8a which is common for aromatic systems. Thanks --Mabschaaf (talk) 09:01, 13 November 2012 (UTC)

Your captopril structure has an error

The factual accuracy of the chemical structure File:Captopril-3D-vdW.png is disputed

Dispute notification

The chemical structure File:Captopril-3D-vdW.png you uploaded has been tagged as disputed and is now listed in Category:Disputed chemical diagrams. Files in this category are deleted after one month if there is no upload of a corrected version and if there is no objection from the uploader or other users. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload a corrected version or simply allow the file to be deleted. In all cases, please do not take the dispute personally. It is never intended as such. Thank you! --Methano (talk) 04:53, 1 December 2012 (UTC)

Hi Methano, I've uploaded a new image, File:Captopril-from-xtal-1980-3D-sf.png, based on the crystal structure. I might just fix File:Captopril-3D-vdW.png rather than let it be deleted. Cheers, Ben (talk) 09:03, 21 December 2012 (UTC)

Image request: third form of Co₂(CO)₈

In addition to File:Dicobalt-octacarbonyl-non-bridged-3D-balls.png and File:Dicobalt-octacarbonyl-bridged-3D-balls.png/File:Dicobcalt-octacarbonyl-from-xtal-3D-balls.png, there is a third isomer of this compound discussed in doi:10.1021/ic50168a037. Could you render it in the same style as the others to complete the set? The structure is (CO)₄Co–Co(CO)₄ with each Co having trigonal–bipyrimidal geometry but each Co occupies an equatorial position on the other (unlike File:Dicobalt-octacarbonyl-non-bridged-3D-balls.png, where they are trigonal–bipyrimidal but each Co axial on the other). And it has the Co–Co conformation placing the axial axis of each Co rotated 90° from the other. DMacks (talk) 04:33, 9 December 2012 (UTC)

Ahah, found we already have a skeletal of it--File:CobaltCarbonyl.png--easier than my simply trying to describe it:) DMacks (talk) 18:52, 9 December 2012 (UTC)

Done: File:Dicobalt-octacarbonyl-D2d-non-bridged-3D-balls.png, File:Dicobalt-octacarbonyl-D2d-non-bridged-end-on-3D-balls.png. Sorry for the delay. --Ben (talk) 11:09, 21 December 2012 (UTC)

No worries, thanks for working on them. However, is the conformation correct? File:Dicobalt-octacarbonyl-D2d-non-bridged-end-on-3D-balls.png appears to have 45° dihedral but the ref says "The two cobalt trigonal bipyramids are visualized as oriented 90’ with respect to one another." That would make the ligands eclipsed along the Co–Co bond? DMacks (talk) 21:07, 23 December 2012 (UTC)

Thanks DMacks, I've fixed them now. --Ben (talk) 10:41, 31 December 2012 (UTC)

Look great! DMacks (talk) 15:02, 31 December 2012 (UTC)

User talk:Leyo#Molecules

Hi Ben. Is there anything you would like to add there? You are clearly more experienced in creating 3D images of molecules than I am. --Leyo 15:29, 12 January 2013 (UTC)

File:Dithionate-2D-dimensions.png

Just to let you know, I just tagged your structure as disputed, because there the angle is obviously incorrect. Maybe you could check, please. --Mabschaaf (talk) 20:54, 12 January 2013 (UTC)

Yes, my mistake. It should read 103° rather than 215°, which I must have copied from the S-S bond length of 215 pm and forgotten to change the value. I will update it ASAP. --Ben (talk) 12:54, 13 January 2013 (UTC)

Aspartame Error?

Hi Ben, Thank you so much for all the hard work creating the wonderful molecular models! As I was looking at the aspartame model I noticed that the nitrogen molecule on the left appears to have three hydrogens attached instead of two. Is that a little mistake? — Preceding unsigned comment added by 63.123.95.253 (talk • contribs)

This image shows the zwitterionic form. --Leyo 00:18, 15 January 2013 (UTC)

File:Phosphoric-acid-2D.svg

File:Phosphoric-acid-2D.svg has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

DMacks (talk) 11:25, 2 June 2013 (UTC)

File:Phosphoric-acid-2D-dimensions.svg

File:Phosphoric-acid-2D-dimensions.svg has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

DMacks (talk) 11:30, 2 June 2013 (UTC)

Zirconocene dichloride geometry

In your File:Zirconocene-dichloride-2D-skeletal.png, you appear to have the Cp–Zr–Cp linear (like in ferrocene) rather than bent (like your File:Zirconocene-dichloride-from-xtal-3D-balls.png). At best, it's from a special perspective (like a Fisher projection?) that makes the geometry confusing. A side perspective like File:Cp2Ti(CO)2.png is more standard from the literature I've seen. DMacks (talk) 21:48, 27 July 2013 (UTC)

Thanks for pointing this out DMacks. It was really intended to go alongside other diagrams so that, taken together, the structure is clear. See Wikibooks:A-level Chemistry/OCR (Salters)/Open-Book Paper/Discovery and development of metallocene catalysts. However, I see the image is used on various different Wikis and could be clearer, so I will make a new one. --Ben (talk) 10:57, 28 July 2013 (UTC)

Benzoylecgonine image?

Please see this Wikipedia discussion - briefly I think the stereochemistry in this image may be wrong (or the stereochemistry in the other accompanying images is wrong). Thanks. (Stillnotelf on en-wiki) -- 63.142.216.252 00:49, 30 July 2013 (UTC)

File:Ketamine-2D-skeletal.png

File:Ketamine-2D-skeletal.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Starless (talk) 19:05, 18 September 2013 (UTC)

Two very similar images

Do you know what the use-case or difference is between these diagrams of yours?

• File:NCl3-by-ED-from-CRC-91-3D-balls-web.png
• File:NCl3-by-ED-from-CRC-91-3D-balls.png

They are same dimensions and visually the same. They differ by 2K filesize but I can't figure out what that difference is. DMacks (talk) 06:27, 3 January 2014 (UTC)

I think the one ending -web was exported from Photoshop using a setting designed to optimise the image for web browsing. The actual difference is probably pretty subtle. I'm not really sure what exactly it does differently. Maybe the order in which the lines are downloaded? --Ben (talk) 11:48, 3 January 2014 (UTC)

File:Azo-coupling-A-2D-skeletal.png

And also:

• File:Azo-coupling-B-2D-skeletal.png
• File:Cumene-process-final-steps-2D-skeletal.png
• File:Cumene-process-phenyl-migration-2D-skeletal.png
• File:FITC-2D-skeletal.png
• File:Glucosinolate-skeletal.png
• File:Gold Bromide in Diels-Alder Reaction.png
• File:Gold Bromide.png
• File:Halon-1211-2D.png
• File:Hydrogen-fluoride-solid-2D-dimensions.png
• File:Nitrile-oxide-2D-B.png
• File:Nitrogen-dioxide-2D-dimensions.png
• File:Phosphonic-acid-2D-dimensions.png
• File:Potassium-metabisulfite-2D.png
• File:Propan-1-ol-2D-flat.png
• File:Propargylic Alcohol Nucleophilic Substitution.png
• File:Skeletal-formulae-example-1-hexane.png
• File:Sodium-valproate-2D-skeletal.png
• File:Tetrathionate-ion-2D-dimensions.png
• File:Tetrathionate-ion-2D.png
• File:TfOH-condensation-2D.png
• File:Thiodiglycol-2D-skeletal.png
• File:Triphenylphosphine-2D-skeletal-Smokefoot-style.png
• File:Uranyl-ion-structure.png

Hi Benjah-bmm27. Your files listed above are in Category:Chemical images that should use vector graphics. Could you please check, if the tag may be removed (in the case of high resolution PNGs), if there is already an SVG version, or if you consider uploading an updated version of higher resolution/quality on top of the old? Thank you. Leyo 13:45, 27 January 2014 (UTC)

Hi Leyo. These PNGs are all pretty hi-res. I haven't made SVG versions - I tried a while ago but the results were not good enough. If higher quality is required, I can provide that, but these images are all at least 1000 px wide or tall. Ben (talk) 14:15, 27 January 2014 (UTC)

My goal is to have the images that are of high quality or that have been replaced removed from this category. I guess that for most of your files that tag may just be removed with reference to the category description. I provided this list using VFC to be able to review all tagged uploads of yours at once. --Leyo 16:43, 27 January 2014 (UTC)

Lithium Carbonate

Hi Benjah, recently a user brought it to my attention that Lithium carbonate is the most commonly prescribed type for mood affective disorders such as Bipolar disorder. The page currently displays the chemical structure of lithium citrate instead. I think the user raised a fair point when he said lithium carbonate should be the one shown. However, I could not find much on Wikimedia Commons. I found a couple of images but no stick-ball figures or 3-D figures of the chemical structure. I found one poorer quality image of lithium carbonate's chemical structure. I am unfamiliar with the programs used to create these images. Would you be willing to help with that? I can be reached on my talk page here on Wikimedia Commons or on Wikipedia (I prefer the latter, but your choice). I hope you'll help since I think it really would be a great addition to the article and your expertise would be very helpful. Thank you! TylerDurden8823 (talk) 02:52, 28 March 2014 (UTC)

File:Dinitrogen-pentoxide-2D.png

Hello Benjah-bmm27, after a discussion in the german wikipedia we have some doubts if the angles visible in that picture are valid. At least different source seems to state different valid ones. Our best source (sorry it is a german book, but it shows a three dimentional structure) says it angle of 133° is not the NON-angle but the twisting/rotating angle between the planar NO3 units. The NON angle is given with 111.8°. Also if you have a look to table 3 in this document there is a "r" in front of the 133° values, which sounds for me like "rotating" and provide two additional angles (this document also give in the table 3 a list of different values taken from different studies). Also this source talks about rotating. Maybe the N=O=N angle is also 133°, but then it is irritating for me why N-O=N is given with 116° because 360 - 133° - 116 ° = 111°, what means one N-O=N is 111° and the other is 116° ? If N=O=N is not given directly (only indirectly as 360° - 2*116° = 128°) and the 133° is the rotating angle all would be fine, but thats only my assumption. Could you please have a look and give your opinion to that ? Thanks. Rjh (talk) 06:18, 9 May 2014 (UTC)

Hi Rjh, thanks for reminding me about this molecule! Steudel's book looks like an excellent source (I can read enough German to understand what is written there. I'll have a careful look at the other references you've kindly provided and ask some colleagues their opinion. I hope to update the image tomorrow. Best wishes, Ben (talk) 13:34, 9 May 2014 (UTC)

Any new insights so far? --Leyo 19:31, 24 May 2014 (UTC)

Hi both, the best recent reference I have found for the structure of gaseous N₂O₅ is B. M. McClelland, A. D. Richardson, K. Hedberg, Helv. Chim. Acta, 2001, 84, 1612-1624, title A Reinvestigation of the Structure and Torsional Potential of N2O5 by Gas- Phase Electron Diffraction Augmented by Ab Initio Theoretical Calculations, doi: 10.1002/1522-2675(20010613)84:6<1612::AID-HLCA1612>3.0.CO;2-K. Despite the flexibility of the molecule on account of the N-O-N=O torsion angles, the study provides accurate values for the other structural parameters. For the most stable conformation, the r_g distances are N-O 1.505(4) Å and N=O 1.188(2) Å. The alpha angles are N-O-N 112.3(17)°, O=N=O 134.2° and O-N=O 112.8°. The most stable conformation has torsion angles N-O-N=O equal to 33.7°, give or take approximately 3-4°. There is estimated to be a difference between two symmetry non-equivalent O-N=O angles of 6.7°.

What do you think of this new information? Ben (talk) 18:25, 3 June 2014 (UTC)

See File:N2O5 from McClelland et al 2001.png for a diagram. Ben (talk) 18:42, 3 June 2014 (UTC)

File:Chlordane-3D-balls.png

File:Chlordane-3D-balls.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Leyo 20:40, 27 May 2014 (UTC)

Would like to consider working together

Am a Prof in the US, without time to do figures for the chem articles I edit. Maybe we could be a 1-2 punch. You use chem draw I presume? You inorg, ochem, or struct chem in your training? Cheers, Le Prof Leprof 7272 (talk) 14:36, 28 May 2014 (UTC)

Hi Le Prof, I'm happy to do a few figures here and there. I'm pretty busy myself with my PhD, so I may not always be available, but we can discuss that on a case-by-case basis. I've done research in a variety of areas, notably organometallic kinetic and mechanistic studies, X-ray crystallography and currently organic materials chemistry. Did you have any particular projects in mind at present? Cheers, Ben (talk) 17:12, 2 June 2014 (UTC)

Glad to hear back from you; timing is perfect, just spent a half day creating a Flippin Lodge image from Heathcock's original Aldrichimica Acta article, and I can tell you, graphics is not my thing. I will begin to look about for the next best thing. Look here for a list of images I have done (very short). And stay focused, and upbeat, it's a hard grind. (You know the work of TK Hollis at Mississippi, by any chance?) Cheers, Le Prof. Leprof 7272 (talk) 23:36, 10 June 2014 (UTC)

Chip fire

Just gotta ask.....did this get put out before there was much damage...or is that a silly question? My stove fire was much smaller and it still destroyed the microwave and stove.--Amadscientist (talk) 23:25, 28 May 2014 (UTC)

Short answer: it burned itself out in a few seconds! This was actually a deliberate and controlled demonstration by an experienced secondary school science teacher. It starts out as a small metal beaker full of molten burning candle wax, and a small cup of water is added. The water sinks to the bottom of the beaker (being denser than the molten wax), comes into contact with the very hot metal surface, and immediately evaporates, ejecting the liquid wax above into the air in a plume of burning droplets. The quantities of water and wax were chosen so that all the flammable material burns away while airborne, leaving little residue or damage, except a black mark on the fireproof ceiling tiles above. The table surrounding the bunsen burner was covered in fireproof mats to prevent damage to the underlying wood. Without these and other precautions, this experiment could easily be very dangerous, as you can imagine! Ben (talk) 17:21, 2 June 2014 (UTC)

From long experience, I would have done this alone, out in a field, with no one besides myself, and a friend with the volunteer fire department on standby (if at all). Indoors? People watching? School setting? Not a chance in... well, what the picture reminds you of. And this from one who has made, used, and quenched every RLi reagent commercially available (and some not), who has done neat Et2Zn additions from cylinder at building leveling scales. I just have this thing about not killing innocents, or torching taxpayer-funded venues, if I can avoid.One has to wonder if the school principle was in the market for a new building. mdr Le Prof Leprof 7272 (talk) 23:54, 10 June 2014 (UTC)

File:Acetylacetone-enol-3D-balls.png pi-bond position

Hope you don't mind the change I made to your image--feel free to undo if so, and I'll upload it to a different name. I usually have a heck of a time getting these to go where I want in modelling software, so I just gimped it. DMacks (talk) 16:26, 2 June 2014 (UTC)

Hi DMacks, no problem, looks much better. Thanks! Ben (talk) 16:57, 2 June 2014 (UTC)

Software used for File:NaCp-chain-from-xtal-3D-balls-C.png

Hi, what software did you use to obtain File:NaCp-chain-from-xtal-3D-balls-C.png? ScotXW (talk) 10:38, 9 June 2014 (UTC)

Hi ScotXW, I forgot to add my usual line to the image description file, so here it is: "image generated in Accelrys DS Visualizer."

Do you need any further information or assistance? I've prepared a step-by-step guide to making images using this software, it's at en:User:Benjah-bmm27/MakingMolecules.

Cheers, Ben (talk) 13:23, 9 June 2014 (UTC)

First collaboration?

This is too easy, but it would see immediate use (same day insertion into articles). See this image: [1], and these sources for context [2] and [3]. Could you consider creating an image just like this (numbered and bay region labeled)? Nearly exact replica is fine, Chemdraw Evans template preferred, and I would use small bold numbers, sans serif font like Arial, and soften the colour (e.g., to a web-safe maroon like 660000 or 990000, rather than a pure red). A 3D model of your usual quality could and should eventually follow, but the flat line-angle is all that is needed immediately. Cheers, TY in advance, Le Prof Leprof 7272 (talk) 18:37, 12 June 2014 (UTC)

How's this? Ben (talk) 09:13, 13 June 2014 (UTC)

I would prefer the background to be transparent and maybe to have the atom numbers colored in blue. --Leyo 00:50, 14 June 2014 (UTC)

File:Acetonitrile-skeletal.png

File:Acetonitrile-skeletal.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Kopiersperre (talk) 15:00, 3 July 2014 (UTC)

File:Methane-2D-flat-small.png

File:Methane-2D-flat-small.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

JuTa 07:52, 13 July 2014 (UTC)

File:Methane-CRC-MW-3D-vdW.png

File:Methane-CRC-MW-3D-vdW.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

JuTa 07:56, 13 July 2014 (UTC)

Add an H to File:Glyphosate-3D-vdW.png?

Looks like this structure is seen from a perspective where only one of the phosphonic acid hydrogen atoms is visible, with the other either omitted or at best hidden behind its oxygen. Could you re-orient this structure a bit so that both can be seen, analogous to File:Glyphosate-3D-balls.png and the various skeletal diagrams in Category:Glyphosates? DMacks (talk) 18:57, 31 August 2014 (UTC)

Incorrect stereochemistry of (S)-fluoxetine

The file File:(S)-fluoxetine-3D-balls.png's geometry is currently under dispute, I asked more experienced chemists than myself before I added this dispute on this structure's commons page. The discussion I've had so far on its stereochemistry may be found here [4]. Thanks for your time. Brenton (talk) 18:31, 17 October 2014 (UTC)

Thanks Brenton, I agree with you on this. I've swapped File:R-fluoxetine-3D-balls.png and File:S-fluoxetine-3D-balls.png over. Cheers, --Ben (talk) 22:27, 17 October 2014 (UTC)

Incorrect amine chemistry of bortezomib

Hi Ben, I've noticed File:Bortezomib-from-PDB-2F16-3D-balls.png has a hydrogen attached to the position #1 nitrogen in the pyrazine ring when simple valency rules say said hydrogen should not exist which it doesn't in this 2D structure File:Bortezomib.svg. I realize this hydrogen was probably there in the original PDB but still, just thought you'd like to know. Plus out of curiosity is there a reason why you don't crop your 3D structures? By that I mean in your structures there is plenty of empty space, so I wonder why you don't just crop them as it would make it easier to fit them into drugboxes & chemboxes. Don't get me wrong, I am grateful for your images, they're great, but still giving my two cents worth on how you might improve them. Thanks for your time. Brenton (talk) 06:32, 26 November 2014 (UTC)

Hi Brenton, thanks for highlighting this issue. I'll see if I can recreate the image without the proton. I assume it was present in the PDB file, but I can't open it on this computer at present.

Regarding the space around my images, I deliberately add a 5% margin around each image to comply with en:Wikipedia:Manual of Style/Chemistry/Structure drawing#Generating PNG files. This is important as it creates white space that makes the images look neater when on the page. Do you think Chemboxes would be better without white space? If so, we can discuss it at en:WT:CHEMISTRY. Cheers, --Ben (talk) 11:15, 26 November 2014 (UTC)

Geometric basis for NAD+/NADH

You have a bunch, such as File:NAD-2FM3-skeletal-3D-balls.png that note the origin of the conformation being illustrated. I'm working on an en.wp article about their geometry and found that these:

• File:NAD-3D-balls.png
• File:NADH-3D-balls.png
• File:NADH-3D-vdW.png

do not cite or explain their origin. It seems to be pretty important for some inter- and intramolecular aspects of the reactivity (and possibly highly variable depending on what else is bound...see [[[en:Nicotinamide adenine dinucleotide#Oxidoreductase binding of NAD]] and its associated talkpage if you're interested). DMacks (talk) 19:40, 28 November 2014 (UTC)

Hi DMacks, interesting project. These three images you list are just really badly minimised structures based on skeletal formulae. I should really sort those out - thanks for letting me know. --Ben (talk) 23:03, 28 November 2014 (UTC)

Wikipedia 'List of cocaine analogues' article images needed

Hello,

I notice you make a lot of molecular structure 2D images. I am currently restricted to a library computer and cannot make images for upload.

I was wondering if you could assist me in my endeavor of adding certain images for inclusion at the Wikipedia 'List of cocaine analogues' page.

What I need is mostly those from Singh's SAR of Cocaine paper (45 pages in on the page finder; pg. 970 or so as enumerated on the paper itself: the chemical structures 183a-(through)-d, 184a & b, 185a-d, 186-188 on 'Scheme 42', on pg. 50 (974) structures 196a-o, 197a-g, 198a-e, 199a & b, 200 & 201a-e ... and more down to page 61 or so; namely N-modified analogs & such.)

Any help making these would be greatly appreciated. Nagelfar (talk) 21:46, 24 February 2015 (UTC)

DMSO geometry

Hi Ben! The accuracy of your DMSO image on double bond has been questioned. Do you have a source for the data used? I like these sort of images a lot so I hope we can put the image back with a source or perhaps we should consult the literature for other data. Thanks! V8rik (talk) 18:16, 9 March 2015 (UTC)

Hi V8rik, thanks very much for highlighting this discussion. I must have made an error, which I should be able to fix soon. Cheers! --Ben (talk) 19:04, 9 March 2015 (UTC)

File:Acetic-acid-2D-skeletal.png

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Kopiersperre (talk) 09:51, 3 May 2015 (UTC)

The factual accuracy of the chemical structure File:Cyclopyrrolone-2D-skeletal.png is disputed

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File:Iron(III)-nitrate-nonahydrate-sample.jpg

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Michał Sobkowski (talk) 09:39, 24 June 2015 (UTC)

The factual accuracy of the chemical structure File:Paroxetine-from-HCl-xtal-2D-skeletal.png is disputed

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The chemical structure File:Paroxetine-from-HCl-xtal-2D-skeletal.png you uploaded has been tagged as disputed and is now listed in Category:Disputed chemical diagrams. Files in this category are deleted after one month if there is no upload of a corrected version and if there is no objection from the uploader or other users. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload a corrected version or simply allow the file to be deleted. In all cases, please do not take the dispute personally. It is never intended as such. Thank you! --DMacks (talk) 06:07, 9 August 2015 (UTC)

Hello, Benjah-bmm27. You have new messages at Ellin Beltz's talk page. You may remove this notice at any time by removing the {{Talkback}} or {{Tb}} template.

The factual accuracy of the chemical structure File:Trifluralin-partially-based-on-xtal-3D-balls.png is disputed

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The chemical structure File:Trifluralin-partially-based-on-xtal-3D-balls.png you uploaded has been tagged as disputed and is now listed in Category:Disputed chemical diagrams. Files in this category are deleted after one month if there is no upload of a corrected version and if there is no objection from the uploader or other users. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload a corrected version or simply allow the file to be deleted. In all cases, please do not take the dispute personally. It is never intended as such. Thank you! --Ed (Edgar181) 19:24, 19 October 2015 (UTC)

... and File:Trifluralin-3D-matt-sf.png too. (I hope you're doing well, Ben). Regards, Ed (Edgar181) 19:27, 19 October 2015 (UTC)

Orbitals

Hello Benjamin! I was searching through your uploads to find general bonding and antibonding π-orbitals (like these but in your style). Do you have those? What software do you use to draw them? Thank you! — Maksim Fomich (talk) 13:22, 22 November 2015 (UTC)

Hi Maksim,

I have a few such images, for example File:Enolate-pi-MOs.png. You can find some of them at Category:Molecular orbitals. If memory serves me well, I made these ones using Spartan, but I don't have access to that particular software any more. Generally speaking, you need ab initio quantum chemistry software to generate these molecular orbital images accurately, and it costs a fair amount of money.

Best wishes,

Ben (talk) 23:14, 23 November 2015 (UTC)

Category:Benzopyrene

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Leyo 23:34, 3 December 2015 (UTC)

File:Trifluralin-partially-based-on-xtal-3D-balls.png

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Leyo 02:50, 2 January 2016 (UTC)

File:Trifluralin-3D-matt-sf.png

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Leyo 02:51, 2 January 2016 (UTC)

A beer for you!

Thanks for all the molecular models :) Btw, what Material/lighting settings do you use to make your models look like that? They are perfect :D Malmriv (talk) 13:59, 3 February 2016 (UTC)

Hi Malmriv, thanks for the brew! I use a white light and a grey light, and shine them on the model from the top right and bottom left, respectively. At least, that's my recollection - I haven't made many models recently. In the very old version of DSV I use, there aren't any materials settings, so you'll have to play around with them to try and match it. Good luck! --Ben (talk) 15:24, 3 February 2016 (UTC)

Conformation of ketamine

Your File:S-ketamine-3D-balls.png has the aromatic ring equatorial whereas your File:R-ketamine-3D-balls.png has it axial. Your File:S-(+)-ketamine-from-xtal-3D-balls.png, with lit-cited conformation, has it axial. So first, does the equatorial file have have a use? And second, that (R) file is not the same conformation as the (S)-xtal one (methylamine chain rotation compared to carbonyl) even though they are enantiomeric chemicals. Would it be more correct to replace the (R) file with an exact mirror image of the (S)-xtal one? DMacks (talk) 09:52, 16 April 2016 (UTC)

Hi DMacks, thanks for spotting this issue. The non-crystal structures were apparently just me following the skeletal formulae and making a rough model without considering cyclohexanone conformations properly. I will update the two old images, and their 2D counterparts File:S-ketamine-2D-skeletal.png and File:R-ketamine-2D-skeletal.png. I'll update the relevant articles, too. Cheers, Ben (talk) 13:24, 16 April 2016 (UTC).

File:Nitrobenzene-reduction.png

Importing what another editor wrote in an incorrect place... DMacks (talk) 15:29, 19 April 2016 (UTC)

In your diagram, you indicate Sn to be a catalyst. It's the reducing agent and gets oxidised in this reaction, so it's not really a catalyst. — Preceding unsigned comment added by Griffinsdj (talk • contribs) 12:56, 19 April 2016 (UTC) (UTC)

Thanks to you both for informing me. I actually realised this for myself earlier today - great minds, eh? I've fixed it now. Cheers. --Ben (talk) 15:55, 19 April 2016 (UTC)

File:Diazepam-3D-balls.png

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DMacks (talk) 05:30, 1 May 2016 (UTC)

Thanks for letting me know, I've commented at the entry. Cheers. --Ben (talk) 11:27, 1 May 2016 (UTC)

File:Dioxin-2D-skeletal.svg

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DMacks (talk) 14:38, 25 July 2016 (UTC)

File:Dorzolamide-2D-skeletal.png

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DMacks (talk) 03:50, 31 July 2016 (UTC)

Pd(OAc)2 x-ray structures

File:Palladium(II)-acetate-chain-from-xtal-2004-CM-3D-balls.png is a great diagram, but seems to be a less-common (or at least one of two alternative) forms of this substance. A recent C&EN (I added its cite to the en.wp article) reminded me of its interesting trimeric form, whose X-ray structure determination is also cited. Would you be able to generate an analogous 3D-balls diagram of this form? Also, a nit in the existing linear-polymeric diagram: the gray lines suggest there is Pd–Pd bonding, which I don't think is correct. Maybe a dotted line or something to illustrate this geometric alignment without implying an actual bond? DMacks (talk) 02:58, 9 August 2016 (UTC)

Hi DMacks. I can certainly make a new image or two. I included this chain form of Pd(OAc)2 in the WP article because the paper I based the image on said "it seems to be the most easily obtained form" and has "higher thermodynamic stability". However, en:Palladium(II) acetate currently implies the trimeric form is more commonly used. I'm happy to defer to consensus on which form is more important. Regarding the Pd-Pd bonds in my existing image, this was included in the original CIF. The accompanying paper says "the higher thermodynamic stability of the polymeric form is related to the mutual orientation of the [PdO4] planes of adjacent complexes, which provides stronger Pd-Pd interactions", but I doubt these are anything like as strong as a full Pd-Pd bond in, e.g., http://dx.doi.org/10.1021/ic301629m. Perhaps a dashed line as you suggest is best. --Ben (talk) 10:19, 9 August 2016 (UTC)

It seemed like the most common prep (according to the C&EN article) gave the trimer, but I haven't actually played with this Pd source since...maybe ever myself:) For the WP article, I was also hoping to match what the photo had (orange, which is apparently trimer vs linear that is described as pink). I don't have access to the full paper for the X-ray structures, but the Pd–Pd distance mentioned in the abstract did seem long compared to full bonds (such as those Inorganic Chemistry article's examples). I usually assume that unless stated otherwise or discussed with other calculations, bonds in X-ray structure publications are mostly just guessesneighbor-distance analysis:) DMacks (talk) 04:31, 10 August 2016 (UTC)

I've created new images of both forms, from a few different viewpoints for each form. The images are all now uploaded to Category:Crystal structures of palladium(II) acetate. Let me know if you think any further tweaks would help. Interesting topic, thanks for highlighting it! --Ben (talk) 10:26, 10 August 2016 (UTC)

They look great! Thanks. DMacks (talk) 07:14, 16 August 2016 (UTC)

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Jcb (talk) 00:36, 4 September 2016 (UTC)

Another fun bonding: PhLi

Our Category:Phenyllithium polymeric/crystal diagrams have an infinite ladder, where each ipso is sigma bonded to the previous and next Li as well as the Li forming the rung. But the cited ref says that it's more like discrete [PhLi]₂ dimers, only to "two rungs" of the ladder, with the Li then bonded to a larger portion of the pi face of the further Ph groups. That is, not just to ipso along the ladder rail, but also ortho (I took a try at File:Phenyllithium chain from xtal eta3.png) and possibly a long interaction with meta and para as well. Just for kicks I decided to learn to use Mercury (free version) to see if I could do it myself, but am not sure how to specifically change the color or thickness of these C–Li bonds for the non-sigma-like interaction. Any ideas how to do that? As a fallback, I managed to bond to the centroid of each such ring rather than to any of the C in it, but figured I'd keep using this as a learning example and ask your experience:) DMacks (talk) 02:59, 5 September 2016 (UTC)

Hi DMacks, thanks for looking into this structure. I've managed to get Mercury to do what we want, so I've updated the original image accordingly. To get it to work, I right-clicked on every bond I wanted removed and selected 'hide'. I then added 'contacts', in this case between C and Li, between 2.3 and 2.9 Å, intramolecular (> 0 bonds). Hope this info is helpful for future images - let me know if anything is unclear. Cheers, Ben (talk) 08:52, 5 September 2016 (UTC)

Looks great. And I managed to reproduce that method. Thanks! DMacks (talk) 02:39, 6 September 2016 (UTC)

Category:Thioic_acids

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DMacks (talk) 19:37, 19 September 2016 (UTC)

Image request

Hi! I've seen that you created File:Cotunnite-3D-balls.png. Could you please recolor atoms to replace the chlorine color with that of barium? According to Russian Wiki (and they put three refs next to the sentence saying this), Ba₂Pb shares its crystalline structure with PbCl₂.--R8R Gtrs (talk) 18:14, 29 October 2016 (UTC)

File:Bifluoride-elpot-3D-vdW.png doesn't look symmetric

The right fluorine looks smaller than the left one. Is the molecule in this diagram rotated so that the right one is actually further away (one smaller due to perspective, not due to chemical fact)? Or are the two F not equivalent (one smaller because it really does have a reduced vdW radius)? DMacks (talk) 23:06, 27 November 2016 (UTC)

Hi DMacks, sorry for the slow reply. Yeah, this is just a slightly rotated molecule. --Ben (talk) 19:01, 22 March 2017 (UTC)

Your link at the VX structures is dead

I added this source to those images:

• John H, Balszuweit F, Kehe K, Worek F & Thiermann H (2015) "Toxicokinetic Aspects of Nerve Agents and Vesicants" in Gupta, Ramesh C. , ed. Handbook of Toxicology of Chemical Warfare Agents (2nd ed.), Cambridge, MA: Academic Press, pp. 817−856, esp. 823 [Fig.56.1] ISBN: 0128004940.

Feel free to replace with a better one, in particular the one you used to verify/corroborate and OR you did. Meanwhile, this can go into the article using the image. Hope all is well in your career. Have left my Prof position, nor in private sector. Cheers, Le Prof Leprof 7272 (talk) 15:54, 22 March 2017 (UTC)

Thanks Le Prof. I'll keep the dead link just in case it is later possible to find the original source. Thanks also for the new reference. --Ben (talk) 19:04, 22 March 2017 (UTC)

picture of polymeric SO3?

Hello, I highly appreciate your pictures of molecular and crystal structures on Wikipedia. I would find it very useful if you could insert a picture of the polymeric form of SO3 (so-called "alpha" form, which is apparently the most stable form. Thank you!

--Signo (talk) 10:27, 20 April 2017 (UTC)

File:Potassium-superoxide-unit-cell-3D-ionic.png

Hi, I highly appreciate too your molecular pictures and I have a question about this file. Could you give me the reference which allowed you to build it? In fact, I seach for the space group of potassium superoxide crystals. Thank you in advance! --Titou (talk) 13:59, 22 May 2017 (UTC)

Hi Titou, thanks very much! The paper I used to build the model was http://scripts.iucr.org/cgi-bin/paper?a01469 (I think). The space group was chosen as F4/mmm by Kasatochkin and Kotov in 1937, although I'm unsure if modern conventions change that. There are apparently also several other possible polymorphs, according to http://www.e-periodica.ch/digbib/view?pid=hpa-001:1976:49::63#63. Good luck. Ben (talk) 17:02, 22 May 2017 (UTC)

VO(acac)₂ ligand tilt

Hi Ben,

I came across File:Vanadyl-acetoacetonate-3D-balls.png, which does not have any stated source for the geometry, and then looked at File:Vanadyl-acetylacetonate-from-xtal-3D-balls.png, which does. The former seems to have the two acac almost coplanar with each other and the vanadium atom creating a visually noticeable pucker in each V–acac ring, whereas the latter seems to have each ring more planar and the two rings at angles to each other. Is this just an illusion in the uncited image? DMacks (talk) 04:19, 1 June 2017 (UTC)

Hi DMacks,

Thanks for pointing out these two images. The one based on X-ray diffraction is the one to trust. The first image (without a reference) was cobbled together by me based on a cartoon representation of the structure, probably in Greenwood & Earnshaw. I recommend replacing all instances of the former image with the latter.

Best wishes, Ben (talk) 11:38, 1 June 2017 (UTC)

I did the replacement and set a deletion-request for the non-Xray one... DMacks (talk) 14:43, 1 June 2017 (UTC)

File:Vanadyl-acetoacetonate-3D-balls.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

DMacks (talk) 14:42, 1 June 2017 (UTC)

Brilliant, thank you. Is it easy to do? I could check my other uploads and make sure the best version is used. --Ben (talk) 15:36, 1 June 2017 (UTC)

Replacing one image with another across all wikipedia sites is trivial (as long as it's not likely to be a controversial change:). It's one of the side features of having the admin bit here on commons. Ping me if you need anything. DMacks (talk) 04:21, 8 June 2017 (UTC)

File:Ethylene-2D.png

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DMacks (talk) 06:16, 30 November 2017 (UTC)

Wiki Science Competition 2017 closes on December, the 15th

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File:L-proline-3D-balls.png

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69.9.54.26 00:49, 17 December 2017 (UTC)

A barnstar for you!

	The Graphic Designer's Barnstar
	Thank you for making great illustrations of molecules! It really helped me in my final presentation! Respublika Narodnaya (talk) 15:04, 3 April 2018 (UTC)

Category:Boc_protecting_group

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ChemNerd (talk) 15:47, 9 April 2018 (UTC)

Readability issue with allicin image

The image in question; notice the way that (unless you are using very large thumbnails, or the problem has been since fixed) the S=O bond looks like a S-O bond.

Hi! I noticed a readability issue with the File:R-allicin-3D-balls.png file. Because of the angle that the image is taken from, the double-bond between the sulfur and oxygen in the thiosulfinate blends together and one stick very nearly occludes the other. While at full scale the bond is clearly a double bond, when the image is zoomed out—as it is on the wikipedia:Allicin page—the bond looks like a single bond. I tried to resolve this myself, but I couldn't find a good pdb file for allicin (the only one I found in the first few Google results for "allicin pdb", from ChemConnections, didn't have the right bond angles as shown in your image; the oxygen-sulfur bond was in plane with everything else, whereas your image shows it as being slightly away from the plane) and therefore couldn't make a proper image. This is the original post I made on Talk:Allicin on the English Wikipedia. ThinkingCat (talk) 09:39, 28 May 2018 (UTC)

Seeking permission to use your "File:Buckminsterfullerene-perspective-3D-balls.png" image

— Preceding unsigned comment added by Mice of Mu (talk • contribs) 16:14, 27 August 2018 (UTC)

I am writing to seek your permission for the inclusion of your image "File:Buckminsterfullerene-perspective-3D-balls.png" in a book to be published by Robert M. Hazen: Symphony in C: Carbon and the Evolution of (Almost) Everything. The book is written for a public audience to help them understand the important role carbon plays in our lives.

I was wondering if you could confirm the image is in the public domain?

Thanks for your time! --Mice of Mu (talk) 16:11, 27 August 2018 (UTC)

Hi Mice of Mu,

Yes, no problem - the image is in the public domain.

Best wishes,

Ben (talk) 12:09, 30 August 2018 (UTC)

Thanks Ben.

Cheers,

--Mice of Mu (talk) 13:50, 30 August 2018 (UTC)

Aromaticity in File:Trazodone-from-HCl-xtal-3D-balls.png

Hi Ben,

This image has an aromatic pyridine ring, but the other structures of en:Trazodone appear to have an exo-imine-like substituent. It seems like the resonance structures that give a π bond along the ring-fusion edge would be fairly minor (a urea nitrogen lone pair shifted away from the carbonyl to make it N+). Even in en:2-Pyridone, where the aromatic tautomer is neutral N, there is little to none of that tautomer present in the solid state. Could you check the full cited ref (doi:10.1107/S0567740879003964), which I cannot access, to see if it comments on the electronic nature of this ring? DMacks (talk) 03:05, 18 September 2018 (UTC)

Hi DMacks,

Thanks for the message. I had a look at the paper and found the following relevant comments:

The bond lengths associated with N(8) of the TPN nucleus and the aromatic N of pyridine are similar. The average bond length about N(8) is 1.387 (3) Å while that for pyridine is 1.392 (1) Å (Sørensen, Mahler & Rastrup-Andersen, 1974). The bond lengths associated with the five-membered ring are similar to other 1H-1,2,3-triazolo structures (Pfirkfinyi, Kfilmfin, Argay & Schawartz, 1977, and references therein).

The bond lengths in the pyridine ring do vary a bit – the average length of the six C-C and C-N bonds in the ring is 1.382 Å, with the shortest bond 3% below this average at 1.337 Å and the longest bond 3% above the average at 1.421 Å. The exo-imine-like bond (pyridine ring C to sp² N) is 1.308 Å, compared to the N-N bond at 1.384 Å. The shorter bonds are exactly where you'd expect based on the exo-imine-like resonance structures.

So I think you're right, the image would be better if the bond order representation was changed. I haven't used the software that made this image originally for a long time, but I'll see what I can do. Ben (talk) 20:39, 11 October 2018 (UTC)

OK, I've found a new way to put these sorts of image together. How about this?

--Ben (talk) 00:01, 23 November 2018 (UTC)

The factual accuracy of the chemical structure File:Neuraminic-acid-3D-balls.png is disputed

Dispute notification

The chemical structure File:Neuraminic-acid-3D-balls.png you uploaded has been tagged as disputed and is now listed in Category:Disputed chemical diagrams. Files in this category are deleted after one month if there is no upload of a corrected version and if there is no objection from the uploader or other users. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload a corrected version or simply allow the file to be deleted. In all cases, please do not take the dispute personally. It is never intended as such. Thank you! --Mykhal (talk) 12:04, 20 November 2018 (UTC)

I agree the polyol chain is in the wrong stereohemical position. File:Neuraminic-acid-3D-sticks.png is the same (compare to the rest of Category:Neuraminic acid). DMacks (talk) 12:35, 20 November 2018 (UTC)

Thanks for letting me know. I've prepared an alternative image, based on experimental data:

--Ben (talk) 00:07, 23 November 2018 (UTC)

S,S-Jacobsen's Catalyst

Hi Ben,

Is there a chance you could provide me with the mol/pdb/xyz file for the S,S-Jacobsen's Catalyst model you have uploaded. I understand that you may by this time completed your PhD and so this request might be impossible.

Thanks,

Ben — Preceding unsigned comment added by BS-284 (talk • contribs) 17:01, 6 March 2019 (UTC)

Hi BS-284,

I don't have the file I used to make this image to hand, but it should be simple to recreate.

The original CIF is available at http://scripts.iucr.org/cgi-bin/sendcif?cf1320sup1.

You can download the Mercury app from the CCDC (https://www.ccdc.cam.ac.uk/solutions/csd-system/components/mercury/) and save the CIF as a mol/pdb/xyz.

Cheers,

Ben (talk) 16:00, 10 March 2019 (UTC)

File:Trimethylsilyl-chloride-3D-balls.png

File:Trimethylsilyl-chloride-3D-balls.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

DMacks (talk) 01:29, 1 April 2019 (UTC)

Category:Grignard_reagents

Grignard reagents has been listed at Commons:Categories for discussion so that the community can discuss ways in which it should be changed. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this category, please note that the fact that it has been proposed for discussion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it. If the category is up for deletion because it has been superseded, consider the notion that although the category may be deleted, your hard work (which we all greatly appreciate) lives on in the new category. In all cases, please do not take the category discussion personally. It is never intended as such. Thank you!

DMacks (talk) 04:58, 4 April 2019 (UTC)

Ketamine (hydrochloride) crystal structures

Hi Ben,

File:Ketamine-free-base-enantiomers'-conformations-2D-skeletal.png is a great teaching example of conformational effects on optical rotation! Looking at the crystal-structure images you uploaded, File:S-(-)-ketamine-from-xtal-3D-balls.png is cited to the salt and has the conformation of the salt, but the N only has one H. Could you double-check if I'm reading this all correctly, and regenerate the crystal image if necessary? DMacks (talk) 05:48, 8 May 2019 (UTC)

Hi DMacks,

I deleted the extra proton manually. At the time, I don’t think there was a crystal structure available of the free base.

Do you know if one has been published since?

Ben (talk) 09:51, 8 May 2019 (UTC)

Looks like some guy named "Ben Mills" thinks so, having uploaded File:S-ketamine-3D-balls.png. I agree the "free base in the •HCl conformation" might be useful to have (I renamed it File:S-ketamine-from-HCl-xtal-3D-balls.png to clarify what it is), but also having the actual salt is useful if it wouldn't be too much trouble. I could do it (I assume you used Mercury?), but not sure I would have the matched style settings you had used. DMacks (talk) 14:40, 11 May 2019 (UTC)

Haha no wonder I thought there might be such a thing out there. The style is actually pretty tricky to recreate these days, I'd need to boot up a very old PC with DS Visualizer still installed. We could recreate the entire thing in Mercury - what do you think? --Ben (talk) 21:01, 13 May 2019 (UTC)

File:Acetic-anhydride-2D-skeletal.png

File:Acetic-anhydride-2D-skeletal.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

DMacks (talk) 00:54, 11 September 2019 (UTC)

File:Acetylene-2D.png

File:Acetylene-2D.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

DMacks (talk) 12:24, 16 November 2019 (UTC)

File:Water-2D.png

File:Water-2D.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

GKFX^talk 23:58, 26 March 2020 (UTC)

File:Lewisite-3D-vdW.png

File:Lewisite-3D-vdW.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

DMacks (talk) 04:05, 23 April 2020 (UTC)

How to create good looking 3D images of molecules

Hello Benjah-bmm27, I have read your tutorial "How to make 3D images of molecules" to make very good looking 3D images of molecules. I have downloaded and installed BIOVIA Discovery Studio Visualizer and I'm wondering if you could help me to adjust the lighting settings in order to create good perspectives and colours. At the moment, the molecules look very bright and there seems to be to much light which gets reflected by them. The problem is that I have applied your settings, but the molecules do not seem to look exactly like e.g File:Alpha-D-glucose-from-xtal-1979-3D-balls.png which was created by you. Perhaps you could help me to fix those problems. Thanks in advance, Chem Sim 2001 (disc) 11:53, 18 May 2020 (UTC)

Hi Chem Sim 2001,

I'm not exactly sure why you're getting this result, but I suspect it's because Discovery Studio Visualizer has been updated significantly since I wrote the tutorial.

You could try decreasing the brightness of the light sources, e.g. replace white with light grey and light grey with dark grey.

Ben (talk) 10:54, 23 May 2020 (UTC)

Hello Ben, thanks for your response. I think I have fixed the issue. An example can be seen here. Have a nice evening, Chem Sim 2001 (disc) 20:18, 26 May 2020 (UTC)

File:Carbon-tetrabromide-2D.png

File:Carbon-tetrabromide-2D.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Chem Sim 2001 (disc) 20:49, 16 June 2020 (UTC)

Light settings in CCDC Mercury

Hello Ben, could you tell me which light settings you are currently using in CCDC Mercury 3.8, the programm you are using to create ball-and-stick models. Thanks in advance, Chem Sim 2001 (disc) 19:50, 11 September 2020 (UTC)

Hi Chem Sim,

I think I use the default settings. I have lights 1 and 2 enabled, lights 3 and 4 disabled. Light 1's diffuse colour is light grey and its specular colour is white. Its position is x=1, y=1, z=1. Light 2's diffuse and specular colours are a darker grey and the position is x=-1, y=0.2, z=1. For both lights, the diffuse ambient colour is dark grey.

Hope this helps,

Ben (talk) 16:49, 15 September 2020 (UTC)

@Benjah-bmm27: Thanks for your response. I'm using the default settings as well. Do you switch the style to Publication before exporting the image? Chem Sim 2001 (disc) 19:19, 18 September 2020 (UTC)

Hi Chem Sim, yes - publication style. --Ben (talk) 21:31, 29 September 2020 (UTC)

Rhenium (II) compounds

category nonsense

this was a nonsense edit! This is never a rhenium (II) compound. ReB2 is an intermetallic alloy/compound.

Best regards, --Alchemist-hp (talk) 21:33, 29 November 2020 (UTC)

It's down as Re(II) in en:Template:Rhenium_compounds, but fair point: the electronegativities of Re and B are very similar. --Ben (talk) 00:10, 30 November 2020 (UTC)

Kernowite

The mineral w:Kernowite is similar to Liroconite. Can you adapt File:Liroconite-unit-cell-3D-bs-N17-M25.png and create a Kernowite diagram please? Mjroots (talk) 20:59, 23 December 2020 (UTC)

It would look exactly the same, but with iron atoms where the aluminium atoms are. Although the lattice parameters will probably be slightly different. The difficulty is the actual data for kernowite has not been published yet - it's due early next year. I'll see if I can find some details tomorrow to make something evidence-based. --Ben (talk) 00:51, 24 December 2020 (UTC)

Yes, that's what I was looking for. Just change the iron to aluminium and we've got it. Don't think we need worry too much about actual data not having been published. Mjroots (talk) 05:26, 24 December 2020 (UTC)

OK, all sorted. If/when the data for kernowite is published, I can update the image. --Ben (talk) 10:50, 24 December 2020 (UTC)

Grave errors in structure Cyanocobalamin-3D-sticks.png

Dear Ben,

When I did a major revision of "Vitamin B12 total synthesis" in February last year, I left its original first figure "Cyanocobalamin, also known as Vitamin B12" unchanged (and uncontrolledǃ). Recently, a retired professor who did a lot of work on vitamin B12 and derivatives informed me that this modelled structure, i.e., your file Cyanocobalamin-3D-sticks.png in Wikimedia Commons, contains several grave errors. These errors are hard to discern in the picture size used in this B12 article, but became more obvious when I enlarged the original from Wikimedia Commons: The central chromophore is NOT a corrin at all: only ring B (top left) is a pyrroline ring (but with the position of its propionic side chain above instead below, and the acetic acid side chain shows a C-O instead a C=O group); "rings" C (top right), D (lower right), and A (lower left) are not 5-membered rings, each missing a bond; the configurations (up/down) of the side chain in "ring C", and of both methyl groups as well as the acetic acid side chain in "ring A" are all wrong; the Co-CN group is linear, not with an angle as shown.

Your Commons entry also contains a second, older structure which shows all the hydrogens; this leads to so much overlap and clutter that I can only say that this one does contain four pyrrolenine rings, but I dare not to comment on the correctness of the structure much beyond that.

I replaced your structure in "Vitamin B12 total synthesis" with one I created from a x-ray crystal structure analysis of vitamin B12 (Dorothy Hodgkin, 1964; Wikimedia Commons: Vitamin_B12_hydrate.png); although this must be correct "by definition", I had the structure checked by the aforementioned colleague - just to be on the safe sideǃ

Regards, Easyloc (talk) 11:32, 9 January 2021 (UTC)

Thanks for highlighting these issues. There are two root causes: (1) I failed to draw a few key C-C bonds to complete the corrin ring, and (2) it looks like I accidentally or unreasonably minimised this partially literature-based structure with molecular mechanics in an attempt to generate missing hydrogen atoms. The heavy atom positions are (I think) based on the reference, http://www.3dchem.com/vitaminb12.asp. Whatever I actually did in 2008 (I can't remember exactly), you're right it needs correcting so I will do that now. --Ben (talk) 13:09, 9 January 2021 (UTC)

File:Nitrilium-ions-2D.png

File:Nitrilium-ions-2D.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

W_I^KImaniac 16:34, 30 January 2021 (UTC)

Languague versus computer language, blanc versus hyphen

Hello, Benjah, As a chemist, and since short filemover, I became aware of your extensif work on chemical images, a great job. You puzzled out your titles, but they have become a puzzle for the incidental reader. Computer language did not allow blancs, so in adresses they were replaced by symbols like _ or hyphen - . In the early years of wikipedia, file titles were treated a little bit like computeradresses, so symbols and short coding were not uncommon and initially, blancs were avoided. But the file titles have developed to become real image titles, written in real language and using blancs as text dividers between words. The hypen then is no longer a symbol, but has a defined typographic meaning of trait-d'union. In your file titles you use the hyphen correctly as trait-d'union in chemical names, but also wrongly as text-divider where it should be a blanc. From a didactic point that is confusing, those who read your file titles must search which hyphen is a trait-d'union and which hyphen is used as a text or word divider. No need to change old file titles, but I invite you to use in the future blancs instead of hyphens if a word divider is needed. At least, the name of the chemical compound should be a entity separated from the other info in the title. Your titles become more self-evident with a combination of appropriate blancs and hypens (and possibly a comma or a point). Please consider this for the future. Kind greetings --Havang(nl) (talk) 05:26, 2 March 2021 (UTC)

Hi Havang, thanks for taking the time to explain your point of view on this. I have considered your arguments but I don't agree. I don't see hyphen-separated image filenames as a problem. They have technical benefits, such as being able to double click any part of the filename and select all of it. Normal spaces stop this working. It is not possible to give a full description of the image in the filename, so I use the image description template extensively. There is also the issue of consistency. I want a consistent file naming system for all my images. It is not practical to rename the thousands of files I have already uploaded. Is there any Commons policy on filenames that I need to comply with, or is it purely my choice as the creator? --Ben (talk) 14:07, 2 March 2021 (UTC)

Hello, I was absent a day. See Commons:File naming. Criteria: meaningful and helpful, and possibility of translation. Your repeated hyphen has only the meaning of forming composite non-words. Separating at least the chemical name from the image code by a blanc en not a hypen has great advantage in being more meaningful, making translation possible and does not basically affect your titling system. Greetings. --Havang(nl) (talk) 16:49, 4 March 2021 (UTC)

Transparent backgrounds

Hoa112008 is now indef'ed. Among other behaviors, their didn't even bother responding to your polite "Overwriting images I've uploaded" comment on their user-talkpage, but continued to do it several more times since then. I spot-checked, and it seems like "only" converting to transparent backgrounds, so it's not the more-severe COM:OVERWRITE violation. Let me know if you'd like me to do a more detailed check of their edits. DMacks (talk) 16:24, 13 March 2021 (UTC)

Thanks for letting me know, DMacks. I've seen a few users start similarly (serious CIR issues) and become valuable contributors over time. It's a shame Hoa112008 didn't respond to any of our attempts to initiate a conversation. Thanks for checking, I too have mainly seen the backgrounds thing. I don't really mind about backgrounds per se but Hoa112008's editing process seemed to make the images grainy. I'll go through the edits and see if there's anything significant worth fixing. Ben (talk) 12:01, 14 March 2021 (UTC)

Mixed-valence silver-oxide crystal

Hi Ben,

Could you help improve the en:Silver(I,III) oxide crystal-structure image? It contains both Ag(I) and Ag(III) but the image we have (File:AgO.png) does not distinguish between them. I thought about simply editing the graphic to re-color one. But because it's only a unit-cell, we don't see all the bonds--it is not easy to see the different coordinations of them. According to the enwiki article, half of the silver atoms should only be coordinating two two oxygens (linear geometry), but I I can't find any Ag with two visible bonds to O.

I don't have access to doi:10.1016/0022-1902(60)80231-X that has the coordinates to be able to figure out alternate perspectives or cell styles that might help:( DMacks (talk) 04:29, 8 July 2021 (UTC)

Hi @DMacks: happy to create an image or two for this compound. It looks there are monoclinic and tetragonal polymorphs, but they look similar structurally. I'll explore it a little. --Ben (talk) 10:45, 8 July 2021 (UTC)

OK, all sorted – images now available at Category:Silver(I,III) oxide. --Ben (talk) 09:44, 9 July 2021 (UTC)

Your Ball and stick model re Adrenaline perhaps needs checking

Dear Ben Ive left a comment on the talk page. Thanks — Preceding unsigned comment was added by 2A00:23C8:3D03:D300:4557:8AA4:4A7:55E7 (talk) 17:38, 10 July 2021 (UTC)

Thanks, I've replied at en:Talk:Adrenaline#Ball_and_stick_model. --Ben (talk) 23:05, 11 July 2021 (UTC)

Category:Salts and esters of sulfur oxoacids

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Palosirkka (talk) 15:54, 22 February 2022 (UTC)

File:Technetium-heptoxide-3D-balls.png

File:Technetium-heptoxide-3D-balls.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Nucleus hydro elemon (talk) 04:37, 14 March 2022 (UTC)

A barnstar for you!

	The Original Barnstar
	Уважаемый Benjah-bmm27, благодарю за Ваш вклад в дело создания моделей молекул химических веществ. Мои наилучшие пожелания! Вадим Дмитриевич (talk) 12:12, 2 April 2022 (UTC)

File:Sec-butyllithium-2D-skeletal.png

Hi Ben. When I first saw File:Sec-butyllithium-2D-skeletal.png I thought it depicted all four sec-butyl groups with bonds to one lithium atom and the other three lithium atoms have no bond to any sec-butyl group. Then I realized that I was probably misinterpreting the image. So I wrote a description for other readers. Can you check and confirm that what I wrote is accurate, and correct it if it is not? Thank you. Marbletan (talk) 14:13, 29 April 2022 (UTC)

Looks great, thanks Marbletan! Ben (talk) 19:43, 29 April 2022 (UTC)

Notification about possible deletion

Some contents have been listed at Commons:Deletion requests so that the community can discuss whether they should be kept or not. We would appreciate it if you could go to voice your opinion about this at their entry. If you created these pages, please note that the fact that they have been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with them, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Affected:

• File:Enone-2D-skeletal.png

And also:

• File:L-threonine-2D-skeletal.png
• File:L-isoleucine-2D-skeletal.png

Regards, Marbletan (talk) 19:00, 30 May 2022 (UTC)

Thanks!!

For your contribution on chemical structure. ShazidSharif (talk) 16:36, 6 October 2022 (UTC)

Strobilurins

Hi Benjah-bmm27. Back in 2006 you uploaded a bunch of files related to the article en:Strobilurin which I have contributed to more recently. In doing so again today I realised that the structure you provided for strobilurin A, for example, is wrong. The story is a little complicated but is described at en:azoxystrobin, which was mostly drafted by me. The problem is that the original publications were shown later to have the incorrect stereochemistry of one of the double bonds. A good review reference for this is "Strobilurins and Oudemansins" in (1999) Drug Discovery from Nature, Springer, pp. 320–334 ISBN: 3540648445. With your assistance, I'd like to fix Wikipedia to reflect the correct structures. I can generate .svg files using chemical drawing software and Inkscape and this might be an opportunity to replace your .png graphics. What do you think? Michael D. Turnbull (talk) 15:40, 19 October 2022 (UTC)

Hi Mike, feel free. I based this on a structure in an A-level textbook: (2000) Salters Advanced Chemistry: Chemical Storylines (second ed.), Heinemann Educational Publishers, p. 205 ISBN: 0-435-63119-5. I still have a copy, just checked it and the incorrect (E,E,E) structure is there. I can't find what source I used for the structures of the other strobilurins but they include stereochemical ambiguity. Ben (talk) 18:50, 21 October 2022 (UTC)

OK, thanks. I'll start to work on the .svgs and upload them with the same filenames as yours but, obviously, they won't overwrite what you have. Later we'll have to work out whether any of yours are being used deliberately to show the "wrong" structures. If not we can replace their use in articles with my .svg. There will be no need to delete your files, we can just alter their descriptions, since they are perfectly valid chemistry, albeit not of the natural products. Michael D. Turnbull (talk) 19:05, 21 October 2022 (UTC)

I've updated the en:Strobilurin article with my new .svg files. I checked what your files were being used for and concluded they were all in different language versions of the same article, which meant I decided to overwrite your .png files with new .png derived in Inkscape from my .svg. That meant that the corrections could ripple through to the other Wikis. There are a couple of oddities: the best source is the review doi:10.1007/978-3-662-10378-4_5 by Anke, who did most of the original work, which says that strobilurin D and G are in fact the same structure and seems to say that strobilurin F may be two compounds, F1 and F2. Hence I changed your .png for G to be the same as D although it might be best to remove the duplication (which would mean also editing the foreign Wikis to remove G altogether). I'll try to go back to the original publications to find out what the full story for F is. Meanwhile, I've left your .png as-is. Michael D. Turnbull (talk) 14:00, 24 October 2022 (UTC)

It turns out that there are indeed two "F"s that were confused. One is File:Strobilurin F2.svg and the other is File:Strobilurin H.svg, where the OMe in the aromatic ring is replaced by OH. Your file File:Strobilurin-F-2D-skeletal.png had both substituents, which is incorrect for any of the natural products. I think it might be best for you to request deletion of that file. Other than that, everything looks good to me now. Michael D. Turnbull (talk) 14:52, 24 October 2022 (UTC)

Category:Cyclooctasulfur

Cyclooctasulfur has been listed at Commons:Categories for discussion so that the community can discuss ways in which it should be changed. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this category, please note that the fact that it has been proposed for discussion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it. If the category is up for deletion because it has been superseded, consider the notion that although the category may be deleted, your hard work (which we all greatly appreciate) lives on in the new category. In all cases, please do not take the category discussion personally. It is never intended as such. Thank you!

DMacks (talk) 11:08, 31 December 2022 (UTC)

Crystal structure of File:Sb2O4 structure.jpg

Hello Benjah-bmm27, I was wondering if you could create a new crystal structure of File:Sb2O4 structure.jpg. The problem is that we need a new high-quality version of this compound at de:Antimon(III,V)-oxid on the german Wikipedia. Thanks in advance, — Chem Sim 2001 (talk) 11:35, 2 April 2023 (UTC)

Hi Chem Sim 2001, thanks for the request. I've uploaded a set of images to Category:Antimony tetroxide. Hope you're well. Ben (talk) 14:23, 6 April 2023 (UTC)

Hi Ben, I'm fine thanks. They're really great and of high-quality, thanks a lot. Best regards, — Chem Sim 2001 (talk) 17:59, 6 April 2023 (UTC)

Using Avogardo 1.2 and CCDC Mercury to create 3D models

Hi Ben, I have read your updated version of en:User:Benjah-bmm27/MakingMolecules. I'm using CCDC Mercury 2022.3.0 provided by the license of my university for a couple of years now. However, I was not able to really figure out how you create those nice looking images. Since I'm very interested in enhancing the quality of the chemical structures (both 2D and 3D) here on Commons and on the German Wikipedia homepage, I downloaded Avogardo 1.2 and watched some tutorials about the basics.

As an example, one year ago I have created File:1,2-Dichlorobenzene-Mercury-3D-bs.png by simply searching the structure at CCDC, import it to Mercury and export it as a high-quality .png-file. However, especially salts like File:Beta-Sb2O4-xtal-b-2x2x2-3D-bs-17.png I don't know how to create them and add the box for the unit cell.

So my questions are: Do you always start with Avogardo and then export the file to Mercury for better visalization? How do you implement the crystal information like bond lengths, angles, cell parameters to Avogardo/Mercury from a certain literature paper? Why do the bond lengths, e.g C-H, from your files (for instance File:Acrolein-s-trans-GED-MW-3D-bs-17.png) bond differ from my ones (see File:1,2-Dichlorobenzene-Mercury-3D-bs.png).

If you have the time I'm really looking forward to hearing from you. Regards, — Chem Sim 2001 (talk) 10:02, 15 April 2023 (UTC)

Hi Chem Sim, great questions - I can probably update that making molecules guide with a bit more information.

For crystal structures, I use the following menu options: Calculate > Packing/Slicing... > Pack. You can toggle 'Show cell axes', and adjust the multiples of the a, b and c axes you want to display. You can choose whether to display only those atoms that fit within the limits you've chosen, or you can extend it to molecules where the centroids or any of the atoms fit. You can then rotate the model by hand or use the a/b/c/a*/b*/c*/x-/x+/y-/y+/z-/z+/x-90/x+90/y-90/y+90/z-90/z+90 buttons to reorient it. You can also hide specific atoms and bonds by selecting them, right clicking and choosing Show/Hide > Hide. There are ways of doing this to all atoms of a given element or other selections using the Selection menu then the Display > Show/Hide options.

I don't always use Avogadro, some structures just display correctly automatically in Mercury. I mainly use Avogadro to adjust the bond orders (e.g. adding in double or triple bonds that Mercury hasn't automatically detected) and to simplify crystal structures to molecular structures (e.g. choosing one of several molecules in the asymmetric unit).

I do sometimes edit the .mol2 file directly to get the bond orders right, e.g. changing C-C bonds in an aromatic ring from bond order 1 to bond order 'ar'.

I do not usually adjust the bond lengths, angles and cell parameters myself. I get them from WebCSD or crystallography.net. I the past I have extracted crystallographic data from papers manually and created my own CIF files, which is tedious but possible. CIFs are meant to be human-readable so you can in principle write them by hand, but I wouldn't recommend it. Just put the literature reference (ideally the DOI) into WebCSD and you'll most likely get what you need.

The bond lengths probably aren't generally different between your images and mine, they might just look different because I have adjusted the atom radii. I use the Display > Styles > Ball and Stick setting... options. I tend to set the atomic radii to 0.17 times the van der Waals radius - I felt this looked a bit cleaner for large molecules that the default Mercury setting of 0.25 times. That's why my images' filenames often end in -bs-17.png.

You do sometimes get slightly different bond lengths from different techniques: X-ray and neutron diffraction, gas electron diffraction, microwave and IR spectroscopy and even microcrystal electron diffraction. The biggest discrepancy is bonds to hydrogen determined by X-ray diffraction – these tend to underestimate the bond length by about 10% because the X-rays scatter off electron density and in such a light atom as hydrogen, the density is concentrated between the nuclei of the hydrogen atom and the other atom it is bonded to, rather than concentrated primarily around the hydrogen nucleus (the proton). See e.g. https://doi.org/10.1002/chem.201604705. So the same molecule might look like it has shorter C–H bonds if I use X-ray data and longer C–H bonds if I use neutron or microwave data. The neutron or microwave data is likely to be more accurate.

Hope this helps! Ben (talk) 13:45, 15 April 2023 (UTC)

Hi Ben, thanks for your detailed explanations. I tried to apply your suggestions to an example using File:Alpha-Sb2O4-xtal-b-2x2x2-3D-bs-17.png as a kind of template. Here is the result. I have found the Calculate > Packing/Slicing... > Pack options and tried to play around with them a bit.

Can you tell me which settings you use for the unit cell box and where I can adjust them? Compared to your file, the thickness slightly differs from my file and I think it's another font.

Adjusting the atom radii to 0.17 also worked for me and I think it look much better compared to the default 0.25 setting. :-)

Thanks so much for all your help and time! Regards, Simon (— Chem Sim 2001 (talk) 17:20, 15 April 2023 (UTC))

File:Iminium-2D.png

File:Iminium-2D.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Alfa-ketosav (talk) 20:43, 24 August 2023 (UTC)

File:Imine-2D-skeletal.png

File:Imine-2D-skeletal.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Alfa-ketosav (talk) 20:55, 24 August 2023 (UTC)

File:Alkene-(general)-skeletal.png

File:Alkene-(general)-skeletal.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Alfa-ketosav (talk) 20:58, 24 August 2023 (UTC)

Category:Organoiodine_compounds

Organoiodine compounds has been listed at Commons:Categories for discussion so that the community can discuss ways in which it should be changed. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this category, please note that the fact that it has been proposed for discussion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it. If the category is up for deletion because it has been superseded, consider the notion that although the category may be deleted, your hard work (which we all greatly appreciate) lives on in the new category. In all cases, please do not take the category discussion personally. It is never intended as such. Thank you!

DMacks (talk) 06:45, 27 November 2023 (UTC)

Antimony-pentafluoride-tetramer-3D-balls.png

Dear Benjah. It seems the picture misses 4 atoms of Fluor. See for example PtF5solid.tif Reing (talk) 16:43, 1 December 2023 (UTC)

File:L-isoleucine.png

File:L-isoleucine.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Alfa-ketosav (talk) 16:27, 11 December 2023 (UTC)

File:Butyric-acid-2D-skeletal.png

File:Butyric-acid-2D-skeletal.png has been listed at Commons:Deletion requests so that the community can discuss whether it should be kept or not. We would appreciate it if you could go to voice your opinion about this at its entry. If you created this file, please note that the fact that it has been proposed for deletion does not necessarily mean that we do not value your kind contribution. It simply means that one person believes that there is some specific problem with it, such as a copyright issue. Please see Commons:But it's my own work! for a guide on how to address these issues. Please remember to respond to and – if appropriate – contradict the arguments supporting deletion. Arguments which focus on the nominator will not affect the result of the nomination. Thank you!

Alhadis (talk) 06:21, 17 January 2024 (UTC)

Errors in two of your files

Hi Ben. It seems that in both File:Trimethylsilylmethoxyacetylene-3D-vdW.png and File:Trimethylsilylmethoxyacetylene-3D-balls.png, there is a mismatch between the file name/description and the depicted chemical structure: Me₃Si vs H₃Si. If you agree that there's an error, can you correct the images? Thanks, Marbletan (talk) 15:28, 6 February 2024 (UTC)

Hi Marbletan, thanks for pointing out these errors. I suppose I must have accidentally drawn a silyl group instead of a trimethylsilyl group back in 2008 when I made the images. Unfortunately, I don't have access to the paper with the structural parameters and the software used to make the images is no longer supported. If anyone can send me a copy of the paper (https://doi.org/10.1007/BF00607512) I can redraw the images in Mercury. Thanks again. Ben (talk) 12:18, 17 February 2024 (UTC)

Thanks for having a look. Unfortunately, I don't have access to the paper (at least not legally - it's viewable via w:Sci-Hub). But if the files can't be updated, perhaps they can simply be renamed. I suspect the geometry of silyl vs trimethylsilyl is inconsequential and they could be used to illustrate the geometry of the SiCCO group either way. Marbletan (talk) 13:18, 19 February 2024 (UTC)

Good idea, I've done that. Thanks. Ben (talk) 12:31, 21 February 2024 (UTC)

Humble request..

Hi, First of all thank you for your pictures of the PdS-structure. I used to work on Pd-P-S phases a long time ago. I am retired now and I was writing some article about that for af.wikipedia. I wonder if you would be willing (and able) to produce some pictures for the compound PdPS as well. There does not seem to be anything on commons and it is an interesting structure. I'd do it myself if I had the software but I don't.

PdPS crystallizes with orthorhombic symmetry, space group Pbcn (D2h-16)) and lattice constants a= 13.3045 (37), b= 5.6777 (5), c= 5.6932 (5) A,~, Z= 8.

The selenide PdPSe is isostructural

(a=13.569(4), b=5.824(1), c=5.856(1))

Pd is in 8d: x=0.11372(2); y=0.25292(5); z=0.15907(5)

P is in 8d x=0.41818; y=0.12975(20); z=0,28111(19)

S is in 8d x=0,3494(8); y=0.36324(18); z=0.04553(17)

It has an interesting double layer structure with [SPPS] (4-)-ions connecting the two layers coordinating to Pd2+ ions in a more or lesssuare planar arrangement

ReferenceJeitschko, W. (1974). "The structure of PdPS and the crystal chemistry of late transition-metal dipnictides and dichalcogenides". Acta Cryst. B 30: 2565-2572. DOI:10.1107/S0567740874007606. is accessible through the Wikipedia library under Wiley.

̴̴ Jcwf (talk) 02:23, 12 April 2024 (UTC)