SubDural12

Welcome to Wikimedia Commons, SubDural12!

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Tip: Categorizing images

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Hello, SubDural12!

Tip: Add categories to your files

Thanks a lot for contributing to the Wikimedia Commons! Here's a tip to make your uploads more useful: Why not add some categories to describe them? This will help more people to find and use them.

Here's how:

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CategorizationBot (talk) 11:04, 15 January 2011 (UTC)

• Image:Cyproheptadine3.png was uncategorized on 14 January 2011 CategorizationBot (talk) 11:04, 15 January 2011 (UTC)
• Image:Cyproheptadine2.png was uncategorized on 14 January 2011 CategorizationBot (talk) 11:04, 15 January 2011 (UTC)

Alcohol.png

Hi SubDural,

Loving the images of molecules you've been uploading.

I saw one, File:Alcohol.png, that contains a mistake. The carbon atom should be tetrahedral, but you've drawn it in a highly unstable inverted geometry.

File:Alcohol spacefill.png also has the same problem.

Let me know if you need any tips.

You might like to get involved with Wikiproject:Chemistry. There are loads of experts there, most have PhDs, you might find it interesting.

Ben (talk) 14:06, 16 January 2011 (UTC)

Thanks Ben,

I appreciate your comment. I see what you mean, I am perplexed as to why BK Chem would translate this way in DS3. That was very percipient. I believe that I first created the molecule as methanol and then I saved it as a .mol file. This is so I could color the hydrogen atoms tan, and label them as remainders. This should not have caused an error, but it did. Well, it has now been fixed! I'm glad that you pointed this out BEFORE I posted it on the main page. Also, I hope you don't mind that I robbed your color idea for remainders. May I ask what atom you used for the remainder (instead of hydrogen) in your rendition of carboxylic acid? I noticed the bond length to be a bit shorter than hydrogen's. Also, I might be using Wikipedia's "talk" function incorrectly. I am still learning how to "code" here. Please inform me of any mistakes.

SubDural12 (talk) 19:45, 16 January 2011 (EST)

Use whatever colours you think look good, I don't mind at all!

I think I did just use a hydrogen for File:Carboxylic-acid-group-3D.png. C-H bonds are generally shorter than most others. There's a "minimize energy" button in DS, that might be a useful check for you.

Using that button would also avoid the situation you have in File:Benzhydryl2.png, which is in an unrealistic conformation. Two hydrogen atoms are very close together and a space-filling model will show that they're occupying much of the same space - the steric repulsion would be large, so the two benzene rings would twist out of plane to avoid each other. Such issues are arguably minor, but to avoid having to redraw too many images, I base mine on experimental data - crystal structures and the like.

Ben (talk) 08:44, 17 January 2011 (UTC)

Ben,

These errors are not arguably minor to me. On the contrary, they make a big deal to me. What I do not understand is this "minimize energy" button. Are we talking about "dreiding energy," the option under the macromolecules tab? I also believe that I have seen some people use a feature called "bond order from 3d" to delocalize electrons. Is this a correct allegation?

Any time you spot one of my errors, don't hesitate to let me know. I appreciate it, and so does Wikipedia.

SubDural12 (talk) 14:48, 17 January 2011 (UTC)

Yeah, try that button. Search the help files if that doesn't work. Further help is available at https://community.accelrys.com/community/discovery_studio.

Ben (talk) 15:47, 17 January 2011 (UTC)

I was thinking about what you said about the chemistry wikiproject, and I decided to add a couple pages that were not yet made. I think it would be beneficial to have someone more educated than me in wikipedia and chemistry to help me out be checking them over. I have not added the pages yet, but I plan to add some information on the tocotrienol molecules. They are very similar to the tocopherols, with the exception that they are more potent antioxidants. The pages do not exist yet, but they will be Alpha-Tocotrienol, Beta-Tocotrienol, Gamma-Tocotrienol, and Delta-Tocotrienol.

SubDural12 (talk)

A good method for beginners is to write a draft of the article(s) in your user space. Put a slash after the URL of your user page, then give it a name (e.g. en:User:SubDural12/tocotrienols). Then you can get used to the formatting, get comments from the experts, and avoid the risk of deletion!

People there are very helpful if you respond to their suggestions.

p.s. The structure of diphenylmethane itself has been determined: J. Org. Chem. (1981) 46, 4975–4979. I've made the structure into a PDB for you if you want to make a new image: http://www.benjamin-mills.com/Wikipedia/diphenylmethane-from-xtal-1981.pdb.

Ben (talk) 18:29, 17 January 2011 (UTC)

I appreciate the image you have made for me. However, I do not have access to the Journal of Organic Chem. I do, however, have access to Medline with full text. I found this article: http://www.ncbi.nlm.nih.gov/pubmed?term=16095369. I see that for C2-C3-H14 you have 118.96 degrees, for C2-C3-C4 you have 122.03 degrees, for C8-C1-C2 you have 112.42 degrees, and for H24-C1-H25 you have 109.46 degrees.

At The Journal of Chemical Physics, it was listed as follows: For C2-C3-H14 they have 120 degrees, for C2-C3-C4 they have 120 degrees, for C8-C1-C2 they have 118 degrees, and for H24-C1-H25 they have 115.75 degrees.

I am new to the measuring of molecular structure dissolved in crystal, so I am unsure if diphenylmethane dissolved in a nematic liquid crystal is the ideal method of analysis.

Would you please help me understand this?

SubDural12 (talk) 08:07, 20 January 2011 (UTC)

That J. Chem. Phys. paper seems to describe an extremely unusual method for determining molecular structure. I'd ignore it if I were you. Stick with X-ray crystallography, it's the gold standard for structure determination. For small, gas phase molecules, spectroscopy is often used to determine molecular structure. Microwave (rotational) and infrared (vibrational) spectroscopy are common, and ultraviolet (electronic) spectroscopy is sometimes appropriate.

Ben (talk) 20:31, 20 January 2011 (UTC)

3D geometry problem

File:Phenylpropanolamine spacefill.png appears to have the H on the O and one of the H on the N colliding--that would be a pretty unlikely geometry for that molecule. Same type of issue in File:Methylphenidate2.png, where the methoxy O is overlapping an H on the aryl ring--I doubt that the carboxyl is coplanar with that ring--and maybe also another H on the aryl ring is overlapping an H on the other ring. The conformations of most organic molecules are often not the same as the way they are drawn in skeletal diagrams:( DMacks (talk) 19:59, 11 February 2011 (UTC)

Thanks, DMacks.

I've been meaning to get around to this for a while now, and I actually totally forgot. I appreciate your perspicacity.

SubDural12 (talk) 20:21, 11 February 2011 (UTC)

Molicule Program

I wish to know what program or programs you use to render the various molicule pictures you have on wikipedia and on commons. --71.88.23.164 16:48, 4 May 2011 (UTC)

Hello,

I learned how to make my molecules from the helpful page laid out by Benjah-bmm27 of Wikipedia. Here is a link to his guide.

SubDural12 (talk) 03:28, 5 May 2011 (UTC)

Thank you very much :) --71.88.23.164 15:36, 5 May 2011 (UTC)

The factual accuracy of the chemical structure File:Lindanebns1.png is disputed

Dispute notification

The chemical structure File:Lindanebns1.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) 14:00, 18 May 2011 (UTC)

File:Monosodium_glutamate2.png

Dear SubDural12,

I came across your image of monosodium glutamate. I'd like to reproduce it in my forthcoming book, CONNECTOME. I realize you placed the image in the public domain, but I thought I would ask your permission anyway. Could you email me at seung@mit.edu?

Sebastian

Kainic acid images

I have marked File:Kainic acid spacefill.png and File:Kainic acid2.png with {{disputed chem}} because the chemical structures are incorrect. Can you please take a look and correct them? Thank you. Ed (Edgar181) 21:21, 29 August 2011 (UTC)

The factual accuracy of the chemical structure File:Simvastatin spacefill.png is disputed

Dispute notification

The chemical structure File:Simvastatin spacefill.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) 14:52, 6 May 2013 (UTC)

There are similar problems with File:Simvastatin2.png. Regards, Ed (Edgar181) 15:01, 6 May 2013 (UTC)

The factual accuracy of the chemical structure File:Monosodium glutamate2.png is disputed

Dispute notification

The chemical structure File:Monosodium glutamate2.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) 14:40, 22 February 2017 (UTC)

File:Monosodium glutamate2.png

File:Monosodium glutamate2.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) 05:30, 2 April 2017 (UTC)

File:Pyridine2.png

File:Pyridine2.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) 07:31, 21 November 2017 (UTC)

File:Amphetamine2.png

File:Amphetamine2.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) 07:39, 21 November 2017 (UTC)

File:Methamphetamine2.png

File:Methamphetamine2.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) 07:41, 21 November 2017 (UTC)