Talk:Porphyrin

Wiki Education Foundation-supported course assignment

This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Saimsiddiqui. Peer reviewers: Saimsiddiqui.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 06:59, 17 January 2022 (UTC)

Introduction

Less jargon in the summary/introduction! As a good rule of thumb, if there are six links to different technical terms just in the introduction, then the introduction is too complex.

(I know the comment above is from 8 years ago but) Disagree. Basic encyclopedic links such as heterocyclic, macrocycle, pi electron or aromaticity/aromatic are just there to help reading; for the purpose of depressing obsessiveness maybe they should be ignored, but after all, these directory links are part of the nature of an online encyclopedia -- and Wikipedia (English) so far is very serious, there should not be any weasel contents like some cosmetic or nutrition ads ranting. SzMithrandir (talk) 21:10, 16 June 2014 (UTC)

Rats

Not sure where this should be on the page:

Porphyrin is excreted by rats when they are fighting infections in the form of red-brown fluid from the eyes, nose or ears. This is often mistaken for a nosebleed. Discworldian 17:07, 30 November 2006 (UTC)

Geological context

It seems that porphyrin residues have been detected in shales dating back to the Cambrian era, but most of the pubs I could dredge with Google are subducted into subscription-only dark zones.

• Messel oil shale
• Treibs hypothesis (aka Treibs scheme)

From The Treibs hypothesis: An evaluation based on structural studies -- Keely 1999

The Treibs hypothesis linking sedimentary 13,15-ethanoporphyrins to an origin from chlorophylls requires the natural occurrence of a suite of intermediates on the proposed degradative pathway.^The hypothesis was suggested over 50 years ago, yet despite the now extensive literature on the structural characterization of sedimentary porphyrins, few of the putative intermediates have been isolated and identified.

From Porphyrins from Messel oil shale (Eocene, Germany): Structure elucidation, geochemical and biological significance, and distribution as a function of depth -- Ocampo 1992 (emp. mine)

The extraction and isolation procedures of twenty nickel porphyrins (seven alkylporphyrins, thirteen carboxylic acids) from lacustrine Messel shale ... are described. Ten porphyrins could be specifically correlated with biological precursors: algal chlorophyll c (4), bacteriochlorophylls d (3) and heme (3), while the remaining ones may arise from several chlorophylls. The structures of these fossil pigments mostly confirm the classical "Treibs scheme," including the origin of some porphyrins from nonchlorophyll sources.

From a Google link synopsis for a broken link:

Features of porphyrin compounds in Cambrian oil shales from Yakutiya, Siberia ... Vanadyl porphyrins were isolated from Yakutiya oil shale bitumens and also ...

MaxEnt 18:08, 29 June 2007 (UTC)

Conjugated

The lead sentence states that macrocycles are "therefore highly conjugated" and I don't even know which discipline resolves this term. Electrochemistry? Linguistics? Sexual reproduction? MaxEnt 17:29, 29 June 2007 (UTC)

I wikilinked it to the relevant page. DMacks 18:12, 29 June 2007

The table does not mention of X linked sideroblastic anemia. ALthough it is not a porphyria it is caused by mutations in the ALA synthase gene found on chromosome X.

Involved in photosynthesis?

"I need help with a biology essay question. How is a porphyrin ring related to the production/use of oxygen, ATP production, and oxidation/reduction reactions that occur in photosynthesis? Any one have the answer? Please contact me at [phone# removed]. Thank you so much. :)" -Anonymous. —Preceding unsigned comment added by 72.130.76.3 (talk) 05:45, 20 October 2009 (UTC)

I assume your grade is based on what you can do--if I give the answer, you will have to give me your grade points and keep a zero for yourself. There are whole articles about each of those topics (and I assume it's also in your textbook and class notes), including specific structures, examples, etc. All you have to do is actually read it and learn. DMacks (talk) 05:51, 20 October 2009 (UTC)

Diagram Confusion

The diagram detailing porphyrin biosynthesis shows the sidechains of URO-III and subsequent metabolites in a non-standard order.

The usual convention is that they are displayed (clockwise) as AP AP AP PA, and this is the order shown in the Wikipedia article on Uro-III and in the diagram of Heme at the head of this article. This diagram shows the order as PA PA PA AP (ie, the view from "behind" the molecule). It's not wrong, but it is somewhat confusing.

It's a beautiful diagram, and if I had access to a good molecular graphics package I'd "fix" (ie change) it, but I don't.

MrNerdy -- how do you feel about changing it.

RossBoswell (talk) 02:49, 21 November 2011 (UTC)

I assume we're talking about File:Heme-Synthesis-Chemical-Details-NEW.svg? Also the UPG II-synthase step, the reaction arrow notes "–HO₂", but the key cyclization reaction appears to be loss of H on the left-hand pyrrole and OH on the right-hand hydroxymethylpyrrole. If that's something other than a net "–H₂O", is there a missing other input or redox agent in the reaction? And the Porphyrin#Biosynthesis description above it says that HMB is cyclized by a "hydrolysis" reaction, but if anything it appears to be dehydration rather than addition of water? I'll ping McNerdy (creator of the image) on commons too, in case he does not follow this talk-page. DMacks (talk) 06:33, 21 November 2011 (UTC)

Hopefully McNerdy will still have this file and will respond. If so, I wonder if in addition to the errors you noted that he make other changes. Some notes are illegible. Vinyl groups are depicted in nonstandard format. The decarboxylations to give vinyl groups look fishy. Possibly the disease-related notes should be omitted.--Smokefoot (talk) 06:40, 21 November 2011 (UTC)

The "HO2" error is caused by wrong rendering of the SVG thumbnail, still thinking how to fix it. If you open the file itself, you'll see that everything is OK. I can mirror the formulas if you think it's useful, but the main goal for me was to make them look alike on one diagram! I don't really feel like removing disease data, because it could be useful for medical students. I'll review the diagram a bit later... --Mrnerdy (talk) 13:34, 23 November 2011 (UTC)

I discovered Inkscape and used it to edit the diagram in the way we've discussed. Another contributor [Clindberg] has fixed some rendering problems including the "HO2" error. You'll find the current version at

http://commons.wikimedia.org/wiki/File:Heme-Synthesis-Chemical-Details-Mirror.svg

As far as I can see it's largely correct but there is a remaining rendering problem in the thumbnail -- the subscript "3" is missing from "NH3" at PBG -> HMB. I haven't edited the page to use it, but if the consensus is that it's an improvement then someone might like to do that. -- RossBoswell (talk) 19:03, 20 January 2012 (UTC)

Diagram

In the first diagram of Biosynthesis, the ALA dehydrogenase should be ALA dehydratase (as in the second diagram). Maybe this enzyme has two names, but if not it should be checked.--Miguelferig (talk) 18:45, 25 December 2012 (UTC)

Possible Copyright Infringement?

Some of the text in this article is near identical to:

https://www.boundless.com/microbiology/textbooks/boundless-microbiology-textbook/microbial-metabolism-5/amino-acid-and-nucleotide-biosynthesis-54/biosynthesis-of-tetrapyrroles-351-1067/

Copying of the boundless.com text is allowed, but only with attribution.

The text is:

"Porphyrins are heterocyclic macrocycles composed of four modified pyrrole subunits interconnected at their α carbon atoms via methine bridges (=CH-). Porphyrins are aromatic, obeying Hückel's rule for aromaticity, possessing 4n+2 π electrons (n=4 for the shortest cyclic path) delocalized over the macrocycle. Thus, porphyrin macrocycles are highly conjugated systems. As a consequence, they typically have very intense absorption bands in the visible region and may be deeply colored. (The name porphyrin comes from a Greek word for purple. ) The macrocycle has 26 pi electrons in total. The parent porphyrin is porphine, and substituted porphines are called porphyrins. Porphine is the simplest porphyrin, an aromatic organic compound.

Porphyrins are the conjugate acids of ligands that bind metals to form complexes. The metal ion usually has a charge of 2+ or 3+. A schematic equation for these syntheses is:

H2porphyrin + [MLn]2+ → M(porphyrinate)Ln-4 + 4 L + 2 H+

where M=metal ion and L=a ligand

A porphyrin without a metal ion in its cavity is a free base. Some iron-containing porphyrins are called hemes. Heme-containing proteins, or hemoproteins, are found extensively in nature. Hemoglobin and myoglobin are two O2-binding proteins that contain iron porphyrins. Various cytochromes are also hemoproteins. Several other heterocycles are related to porphyrins. These include corrins, chlorins, bacteriochlorophylls and corphins. Chlorins (2,3-dihydroporphyrin) are more reduced, contain more hydrogen than porphyrins, and feature a pyrroline subunit. This structure occurs in a chlorophyll molecule. Replacement of two of the four pyrrolic subunits with pyrrolinic subunits results in either a bacteriochlorin (as found in some photosynthetic bacteria) or an isobacteriochlorin, depending on the relative positions of the reduced rings. Some porphyrin derivatives follow Hückel's rule, but most do not."

Source: Boundless. “Biosynthesis of Tetrapyrroles.” Boundless Microbiology. Boundless, 21 Jul. 2015. Retrieved 30 Dec. 2015 from https://www.boundless.com/microbiology/textbooks/boundless-microbiology-textbook/microbial-metabolism-5/amino-acid-and-nucleotide-biosynthesis-54/biosynthesis-of-tetrapyrroles-351-1067/

I also noted some of the same text here: http://www.itsmagicmaltese.com/photo3_9.html

Who is plagiarising whom? Marchino61 (talk) 10:28, 30 December 2015 (UTC)

According to the "sources" section on the Boundless page you linked, "Boundless vets and curates high-quality, openly licensed content from around the Internet. This particular resource used the following sources:" and then gives a list of multiple Wikipedia articles including this one. That's in keeping with Boundless (company). The other site is surely just unlicensed copypaste from us. DMacks (talk) 09:38, 2 January 2016 (UTC)

Removed statement

This removed statement seemed a little narrow and distracting for a broad article: "Various analyses indicate that not all atoms of the ring are involved equally in the conjugation or that the molecule's overall nature is substantially based on several smaller conjugated systems."--Smokefoot (talk) 15:41, 30 October 2017 (UTC)

I think I included that? But anyway, I support its inclusion because it's helps disprove the common textbook-level trope of "26 is a 4n+2 therefore the porphyrin ring is aromatic". DMacks (talk) 14:34, 31 October 2017 (UTC)

OK, my bad judgement. There does seem to be a lot of emphasis on aromaticity of porphyrins. I am no theoretician, but it seems a stretch to claim that rings of rings meet the criterion for aromaticity. But aromaticity a complicated term mixed with an aura and folklore, I wonder.--Smokefoot (talk) 15:52, 31 October 2017 (UTC)

References

Chemical Abstracts report: 16525 references in the last 5 years

Checking Chemical Abstracts reveals that 79,637 reports etc have appeared, >16000 in the past 5 years. About 8 reports per day. --Smokefoot (talk) 11:45, 18 July 2019 (UTC)

Theoretical interest in aromaticity

Rahulsoman (talk) 19:03, 20 August 2020 (UTC) In general Porphyrins are macrocyclic molecules that shows aromaticity and follows Hückel's 4n + 2 rule, interestingly upon core modification these porphyrinoid macrocycles can show variable aromaticity. Many scientists got attracted to porphyrinoids because of this variable aromatic behavior, Annulene chemist Emanuel Vogel synthesised first porphyrin isomer. This 18pi Hückel aromatic porphyrin isomer is named as porphycene. Later scientists have synthesized various antiaromatic, Mobious aromatic and non aromatic porphyrinoid macrocycles.

spectroscopic properties

porphyrin spectroscopy is a thing, much studied, but not much mentioned here. Relates to Soret peaks/bands. - Rod57 (talk) 09:25, 20 November 2020 (UTC)

Compress or replace applications sections

Porphyrins are essential to life, are beautiful literally, and their chemistry is lovely. But they have no applications. Here are the section headers for "Applications"

• Photodynamic therapy [condense and move to optical properties]

"Porphyrins have been evaluated in the context of photodynamic therapy ..." several refs

• Toxicology [move to heme]

"Heme biosynthesis is used as biomarker in environmental toxicology studies .." one ref

• Biological applications [remove]

"Porphyrins have been investigated as possible anti-inflammatory agents..." a few refs

• Synthetic applications [condense and move to reactions]

"Complexes of cobalt(II) porphyrins have been extensively utilized as catalysts in organic synthesis.... couple of refs

• Biomimetic catalysis [condense and move to reactions]

".. widely studied as catalysts for the oxidation of organic compounds...."

• Molecular electronics and sensors [condense and move to reactions]

Porphyrin-based compounds are of interest as possible components of molecular electronics ... several refs

• Supramolecular chemistry [condense and move to properties]

Porphyrins are often used to construct structures in supramolecular chemistry... three refs

• Theoretical interest in aromaticity [remove]

"Porphyrinoid macrocycles can show variable aromaticity..." two refs

Most of these sections could be replaced with a short section on "reactions" and "optical properties" (including Soret bands) as indicated above. --Smokefoot (talk) 18:51, 21 March 2023 (UTC)