User talk:SubDural12

Welcome!

Hello, SubDural12, and welcome to Wikipedia! Thank you for your contributions. I hope you like the place and decide to stay. Here are some pages that you might find helpful:

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I hope you enjoy editing here and being a Wikipedian! Please sign your messages on discussion pages using four tildes (~~~~); this will automatically insert your username and the date. If you need help, check out Wikipedia:Questions, ask me on my talk page, or ask your question on this page and then place {{help me}} before the question. Again, welcome! JFW | T@lk 10:13, 17 January 2011 (UTC)[reply]

Prednisone

Hi SubDural2, Thsnks for the gr8 prednisone molecule image at prednisone. Did you create it? If so, what program did you use? Welcome to WP. -JB

Hello JB,

Thank you for your commendation on my work with prednisone. I used a program called BKchem to design the ".mol" file, and then used Discovery Studio Visualizer 3.0 to create my rendition of the final product. I then transferred it to Adobe Photoshop CS5 to made the background transparent and resize the image.

I also have work on various other immunosuppresant/anti-inflammatory drugs featured in my main user page.

Also, please sign your messages on discussion pages using four tildes (~~~~). It is much easier, and it also inserts the time and date, along with a link to your main user page.

SubDural12 (talk) 00:04, 28 January 2011 (UTC)[reply]

Heme

Hi SubDural,

You recently added images to Heme a (diff) and Heme b (diff), which are beautifully rendered but chemically ridiculous.

I don't know how you came up with the structures (perhaps an error in translation between your BKchem .mol file and Discovery Studio Visualizer), but you should check your structures make sense before uploading them!

You'd be much better off drawing your molecules directly in 3D in DSV then minimising them. If you need help getting computed or experimentally determined structures, please ask at WT:CHEMISTRY, as many of us have access to data that is not freely available.

Keep up the good work,

Ben (talk) 00:56, 28 January 2011 (UTC)[reply]

Ben,

On the contrary, I do not think that something is wrong between the translation of the .mol file into DSV, but in the reading of BKchem of my SMILES.

This is one of the problems with BKchem and macromolecules. I can't get over the incredulity that this damn program brings me! (I guess I should be checking over my files, shouldn't I? You must think that I close my eyes before uploading a file)

I will remove the files from the public wikipedia page and re-upload, and then check again before posting. Thanks again for your vigilance. *face turns red*

EDIT: I think I fixed the images of [heme A], [heme A spacefill], [heme B], and [heme B spacefill]. I am surprised that I did not notice how the iron atom was not linear or square planar.

SubDural12 (talk) 02:27, 28 January 2011 (UTC)[reply]

Amino acids

Hi SubDural,

I noticed you've uploaded 3D models of the following amino acids:

As you've drawn them, all of these molecules contain neutral CO₂H and NH₂ groups at the same time. This is usually not the lowest energy state for these molecules to adopt, because RCO₂H groups are acidic and RNH₂ are basic. The two groups react with each other (formally an intramolecular reaction) to lower their energy. What you observe in solution (at neutral pH) and in crystal structures is RCO₂⁻ and RNH₃⁺ groups.

It is a difficult issue to resolve, because we usually want the non-zwitterionic neutral 2D structure in the chembox for simplicity, but for 3D structures this becomes more of an issue. To get the correct 3D structure, you either need to use computational chemistry to calculate what the structure would be if it didn't react with itself, or you determine the structure with x-ray crystallography or similar, and find that it's acutally a zwitterion.

See Talk:Glycine#Structure for further discussion of the fact that amino acids usually exist as zwitterions.

What you're uploading isn't wrong per se, but I thought you should be aware of this complexity. It is for this reason that I generally avoid making 3D structures for molecules likely to form zwitterions, because one structure doesn't tell the whole story and can be misleading.

Ben (talk) 12:05, 1 February 2011 (UTC)[reply]

Ben,

Unfortunately, I will not be able to correctly determine these structures; I guess I should pull down my images. My school is too penurious to spend prodigally on a nice journal. I have access to very few full texts, and these texts are generally - as demonstrated to you earlier - very aberrant and incredulous. If only I had a way to access good chemical journals...

SubDural12 (talk) 01:18, 2 February 2011 (UTC)[reply]

Oh, I think that's a bit of an overreaction. Your structures are OK, I just wanted to warn you in case you received queries.

Leave your images up. Someone may replace them eventually, or they may not.

Ben (talk) 18:22, 2 February 2011 (UTC)[reply]

Ben,

How do you always demonstrate delocalized electrons in your images?

SubDural12 (talk) 22:18, 3 February 2011 (UTC)[reply]

Depends what kind they are. For benzene rings I generally change the bonds from single or double to aromatic.

Ben (talk) 00:32, 4 February 2011 (UTC)[reply]

Space filling warfarin model

The space filling model of yours on the Warfarin page looks like it has at least one error in it. From what I can tell, it has two ring oxygens, as opposed to one ring oxygen and the extra-cyclic phenolic hydroxyl. Any chance you could double-check the structure and re-do it if necessary? Also, though not an error, it looks like you made the structure of R-warfarin, as opposed to the more biologically active S-warfarin. If you're remaking the structure, it may be worth swapping the chirality on that central carbon to the more biologically active form (since you can't do racemic representations in 3D models). Cheers. -- 140.142.20.229 (talk) 23:27, 22 March 2011 (UTC)[reply]

Thanks,

Fixed.

SubDural12 (talk) 00:05, 26 March 2011 (UTC)[reply]