User talk:Jynto

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Citrulline
Please read the edit notes on your citrulline. Not only was your previous image incorrect, it was laid out in a non-intuitive manner. We are trying to help readers see molecules, and so it would be great if you could flip your image. Would that be possible? Thanks,
 * Understood and done - I can see this avoids confusion between the two ends of the molecule (which are deceptively similar in citrulline). It was a pedantic point to make, but thanks for making it anyway. Please sign your posts. Ephemeronium (talk) 22:43, 27 January 2010 (UTC)
 * I am sorry to have come across as pedantic or reproving. Keep up the good work.--Smokefoot (talk) 13:37, 29 January 2010 (UTC)

BrF3
I recommend against depicting structures of complex molecules with "lone pairs" of electrons. The idea of such isolated localized lone pairs is a highly simplified fiction that is provided students, but it is a simplification. If you plan to do a lot of this kind of drawing, I encourage you to engage a broader group of consultants, perhaps at the Chem project page. No one can argue about the placement of the atoms so the angular and distance aspects are great, but nonbonding electrons are not visualized by the usual diffraction experiments. --Smokefoot (talk) 19:42, 1 May 2010 (UTC)

Question
Can you explain what this means? (i.e. jpeg artifacts) It's my first FP nomination and I'm somewhat clueless. ;-) APK  whisper in my ear  14:31, 15 June 2010 (UTC)
 * Oh, that means small squares are visible at high resolution, because the image (as a jpeg) is highly compressed, and some information about the image's detail has been lost. This is a more extreme example, from the article on compression artifacts. The jpeg artifacts come from the original image, that is I couldn't find a less compressed on on the NASA website. Of course all jpeg images contain some loss of information, but to varying extents. --Ephemeronium (talk) 15:45, 15 June 2010 (UTC)
 * Ah, gotcha. Thanks.  APK  whisper in my ear  16:26, 15 June 2010 (UTC)

Question 2
Hi Jynto. I think that there is a little mistake in one or you illustration for Totrazuril. There is a methyl group in one of the Nitrogene in the molecule.

Here is the molecule https://commonchemistry.cas.org/detail?cas rn=69004-03-1

I just wanted to let you know :) have a nice day ! — Preceding unsigned comment added by 195.228.162.62 (talk) 09:06, 24 April 2023 (UTC)

Due reward
Thank you so much. Because of your kindness, I was motivated to produce another image for that article. I hope you like it. Thank you again. --Ephemeronium (talk) 12:02, 26 August 2010 (UTC)

Recent images
Hi there

Thanks for your recent images. I was wondering - did these structures come from X-ray diffraction data, or were they optimized computationally? Or are they simply 3-D renditions of 2-D structures? --Rifleman 82 (talk) 22:21, 17 December 2011 (UTC)

I'm sure I've been asked the exact same question. The answer is, there is no data. It's energy-minimized, and not very accurate at that. I make sure the shape of the molecule settles into something that looks plausible, usually by clicking the button a load of times. --Ephemeronium (talk) 00:13, 18 December 2011 (UTC)

Thanks. I think it doesn't matter for most compounds, but I was thinking about tetraphenylcyclopentadienone. I'm not quite seeing the propeller geometry I expect? As a crystalline solid, a crystal structure is probably preferable. --Rifleman 82 (talk) 00:54, 18 December 2011 (UTC)
 * If you do not have some data driving these structural drawings, I recommend against making them in general. What you are doing is close to being original research - you are implying knowledge that you are creating, not reporting.  Also, I cannot imagine what anyone really learns from most space-filling models.  We discussed models on the chemistry pages:  Wikipedia talk:WikiProject Chemicals).  In any case, those are one editor's views.  Good luck.--Smokefoot (talk) 02:26, 19 December 2011 (UTC)

I respectfully disagree. Molecular models are not meant to be the gospel truth, and no one expects them to be. Most of the other molecules on Commons are drawn without data, including Ben Mills' early stuff. I do believe it's a step above what many other sites use, which are automatically generated molecules. Notice how the PubChem model of aniline shows the nitrogen as fully planar, while the on Commons shows it as slightly pyramidal. Concerns like these are a nitpick, and data-based models are a luxury. I don't believe you meant to insult my work, so I won't take it personally. --Ephemeronium (talk) 03:07, 19 December 2011 (UTC)
 * I agree that this drawing business is not worth fighting about. Best wishes with your efforts.  --Smokefoot (talk) 10:57, 19 December 2011 (UTC)


 * These models look pretty for sure, but unless they depict the geometry in a realistic fashion, I don't see how they are superior to the line drawings if all they depict well is connectivity.


 * The structure you uploaded of tetraphenylcyclopentadienone caught my eye; I remember its calculated structure was propeller-like; your picture depicts the phenyl groups at the 2 and 5 positions to be coplanar with the pentadienone ring. A quick search yielded I'm not sure how your program does it, I'm guessing some sort of molecular mechanics. I suspect that delocalization is poorly represented, or neglected entirely. --Rifleman 82 (talk) 09:57, 19 December 2011 (UTC)

I can make exceptions in the cases where the simulated structure has some blatant errors, but only if they are called to my attention. I will probably end up doing this for tetraphenylcyclopentadienone. Just to confirm, in the real conformation, are the phenyl rings completely perpendicular to the plane of the central five-membered ring? Or are they just less coplanar than my structure depicts them? If this is a problem, I could get hold of a student edition of Spartan for $50, which uses the Hartree–Fock method and basis sets, whatever those are. Ben Mills uses it for his calculated molecules. I still believe my images show more than just connectivity. They depict the molecule intuitively, in a way that can be understood by the non-chemist, who would likely be baffled by skeletal formulas. Ephemeronium (talk) 04:56, 22 December 2011 (UTC)


 * I've replaced your image of tetraphenylcyclopentadienone with crystal structures. I feel that experimental data should be used wherever possible.
 * If you want to buy Spartan for yourself, go for it. But I don't think you should feel obliged to buy it for the sole purpose of editing in WP. Many educational institutes have access to that or some other computational chemistry program (Gaussian, perhaps?) via site license.
 * Hartree-Fock calculations should give you good bond lengths and angles for most simple organics. If you are going to that trouble you should do a frequency calculation to make sure you are not sitting on top of a saddle point, and you might need to apply a little chemical intuition to make sure you are at the lowest energy conformation. --Rifleman 82 (talk) 22:02, 22 December 2011 (UTC)

See Talk:Dibutyltin oxide for an example of why it's important not to guess structures. n-Bu2SnO is not a monomer. You could probably have guessed that with a little experience of structural chemistry. The double bond rule is useful to bear in mind. Sn=O bonds are not really any stronger than Sn–O bonds, so given the option, tin will choose to polymerise and increase its coordination number. --Ben (talk) 00:29, 24 December 2011 (UTC)

Name change
I am requesting a rename on Commons. My current Commons name is Ephemeronium. Ephemeronium (talk) 20:41, 11 February 2012 (UTC)

Slow down please and ask around
You are a really active editor - way to go. I do fear that we might be misleading readers inadvertently through your drawings. I'd ask around. A good place to consult the group is Wikipedia talk:WikiProject Chemicals. Friendly (usually) and helpful editors there, including some very experienced organickers. --Smokefoot (talk) 17:42, 27 September 2012 (UTC)

MDMA image
I notice there is a back-and-forth over the MDMA image. I believe Lazord00d supports the other image because it shows the double bonds on the carbons. Perhaps you and he should discuss this. Sizeofint (talk) 19:18, 8 January 2015 (UTC)

MDMA image
I noticed you reverted a change I made to an image in the MDMA article, but the only reason given is that in your opinion "there was nothing wrong with "insert person's name" image." The reason I made the change is because the current image does not show double bonds the same way as the 2d formulaic image above it. Can you provide a reason why this is not an improvement? Your inclusion of the image authors personal name makes me wonder about what is actually behind the change to be honest.

Regards

Lazord00d (talk) 19:40, 8 January 2015 (UTC)

I understand that dictates that we draw our skeletal formulas with localised double bonds, but I don't see why this should carry through to the molecular models as well. You know the benzene ring is delocalised, so many programs show it with a dotted line (the same goes for higher polycyclics). I think it is the job of 3D models to show a more 'lifelike' view of a molecule, which means realistic geometry and so on. But you seem to think that it should be a perfect representation of the skeletal formula. By that token, should they omit hydrogen and carbon atoms as well? I fear there are problems to this approach, like when a skeletal formula dictates that you must twist the 3D model into an energetically unfavourable conformation, but I digress.

Since you twisted my arm, I'll go ahead and say it: I think Ben's model is better. I say this out of no personal bias, as I can assure you I have no relationship with Ben Mills outside of Wikipedia. I just think his molecules are really good. They are, for lack of a better term, aesthetically pleasing.

Jynto (talk) 20:34, 8 January 2015 (UTC)

Actually it's the omission of atoms that is why I prefer all 3d models to formulaic. At no point did I say anything about 3d models being identical to 2d, that would defeat the purpose of having them. But the fact that the ring is delocalized isn't known to everyone and an encyclopedia should not require foreknowledge of a subject on the part of the reader. However you just admitted that your change is based on your opinion primarily so the facts are moot. Since you twisted my arm, I'll just say that opinion-based changes aren't the preferred method of editing a reference text. I feel like there's probably something to that effect somewhere in this place's SOPs or whatnot.

Laterz

Lazord00d (talk) 22:45, 8 January 2015 (UTC)

Based on opinion, but justified by fact. Isn't that how all decisions are made? I don't see how using the dotted line for an aromatic ring is leaning on the reader's foreknowledge any more than depicting it as three discrete bonds is. I think the reader is smarter than you give them credit for. A single bond with a dotted line is easily interpreted as one and a half bonds. And if they see three double bonds in one image and six dotted lines in another, they would most likely assume these structures are equivalent. I myself have picked up plenty of chemistry knowledge this way. It was images like this one which taught me that furan rings are aromatic, without having to learn some rule about 4n+2 pi electrons. And when skeletal formulas showed the discrete structures of biomolecules, while molecular models depicted them as ions under physiological conditions, I quickly learned that these forms were still the same chemical.

I can't quite put my finger on why three discrete bonds is wrong for molecular models. It's just messy. Those bonds could be in one of two positions on the ring. Does that mean there's positional isomerism? It's almost suggesting that the molecule itself has discrete double bonds, which is simply not true, but that's what it's suggesting. Even a reference drawing has subtext, and readers will pick up on that.

Or we could just compromise with a space-filling model, since those don't show the bond order.

Jynto (talk) 23:49, 8 January 2015 (UTC)

You can do whatever. Once I find that a topic is being policed by individuals and held to standards that are simply their opinion, that's my cue to roll out. At that point the topic is compromised and no longer being edited with fact in mind, it's now about what some person thinks is good in their opinion. It's unfortunate because this place could be a great reference if it weren't for that. Happens a lot too, my patience for it is pretty thin.

Lazord00d (talk) 00:07, 9 January 2015 (UTC)

On second thought, after viewing your personal page it's clear to me by the fact that we contribute similar content that this isn't about scientific fact or what's in the best interest of readers of all ages at all. You're not wanting to share the stage. I really wish people could grasp that this is supposed to be a collective effort, not a "get off my turf" scenario. When your rebuttals do not contain substance, only opinions about how you feel that all models should be as "aesthetically pleasing" (in your opinion) as yours are (again in your opinion), I see nothing in your statement that contains any substantial advantage over a more direct model. Opinions suck to be quite honest with you. I'm only interested in fact and improving the appeal to readers of all ages and skill levels, both things that are slightly more important to our efforts here at Wikipedia than the aesthetics of your molecules. The one I posted translates directly to the formulaic model, I fail to see how that doesn't help anyone see the direct translation from formula to atoms, regardless of their knowledge. The very idea lacks substance and seems like a half-hearted effort to justify your changes.. Just calling like it is and edit war or not I'll be reverting it back sooner or later.

Laterz

Lazord00d (talk) 07:25, 9 January 2015 (UTC)

Those are bold claims to make based on one edit. And after seeing my userpage you think you have enough information on me to make inferences about my character. Have you considered a career in journalism?

I won't make an edit without good intentions. I target most of my edits on articles that don't already have molecular models. And while I occasionally replace models on a judgement call basis, no one yet has been this touchy about me removing theirs. I never said the MDMA article was my "turf". But in light of all you said, I will now think twice before I edit any article that has your image in it.

I can't claim to understand what goes on in your mind by looking through my computer screen, but I invite you to reflect upon yourself. You might be leaning on the same or similar biases to the the ones you accuse me of.

Good day

Jynto (talk) 11:29, 9 January 2015 (UTC)

You think they're bold? I don't. I see routinely from lots of users. Very possessive folks given the public nature of this place. So I don't think they're in the least bold. But whatever, the reason I seldom edit here anymore is because someone is always offended by the edits, regardless of the explanation. Total crock if you ask me.

Laterz

Lazord00d (talk) 14:11, 9 January 2015 (UTC)

Naked Na+?
It looks like your new Na dtc structure has naked Na+. That kind of image is problematic for many chemists, and it is probably worth discussing with others how to depect such species. For me, naked Na+ is a fiction to be avoided if possible.--Smokefoot (talk) 18:40, 9 January 2015 (UTC)

I can see the dilemma. As far as I'm aware, there is no 'proper' way to depict the sodium counterion. All the crystal structures I've seen show it unbonded and 'floating'. Is it the position or the size of the sphere that's bothering you? I could show it off to the side, so as not to imply any certain interaction with the anion's structure, or even in a separate image like what I did here.

Now that I think about it, it's probably the size that's the issue. For most elements, I sized them in proportion to their van der Waal's radii, and used a standard size of 1.8 A for elements that don't have a vdW radius, with a few exceptions. But the sodium and potassium ions just looked so big - at 2.27 and 2.75 A respectively, and they probably get even bigger down the group. I assumed these sizes referred to sodium and potassium metal, and the ionic radius was probably closer to the truth. So I chose ten of the most electropositive elements (six from group 1, four from group 2) and sized them according to their ionic radii. If you look at my 'periodictableane' (not an IUPAC recommended name), you can see the inconsistency in these two groups.

What I'm getting at is that I should maybe depict these ions at their van-der-Waal's radii? I don't know what that would mean for rubidium and caesium, but they would most likely be huge. Or should I just use the standard 1.8 A?

Alternatively, I could leave out the sodium ion altogether. But then it would feel inconsistent if I did not do the same for compounds with a chloride counterion. I think I need a second opinion. Which of these options do you find most appealing?

Jynto (talk) 22:13, 9 January 2015 (UTC)

Well, what do you think? Jynto (talk) 11:46, 14 January 2015 (UTC)

Bipy is transoid
Heads up on your drawing project, 2,2'-bipy is transoid. An important aspect of its coordination chem. Thanks, --Smokefoot (talk) 14:27, 24 May 2015 (UTC) Uploaded a new version, uses crystallographic data. Still leaving the cisoid version up as that one best represents it as a ligand. - Jynto (talk) 19:18, 24 May 2015 (UTC)

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Deoxymiroestrol rendering?
Would it be possible if I could have a 3D rendering of the molecule deoxymiroestrol? I would like one which is in portrait orientation with the light shining down on it (so the light is shining the "long way" down the molecule as opposed to down across it the short way), if that's doable.

Much appreciated!

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