I added a caption to the screen snapshot of that diagram of compound II, for this posting, as discussed below. My main point with those postings was that I didn't like the way the whole process with this work (http://hardcorephysiologyfun.blogspot.com/2009/12/multiple-revisions-of-old-paper-of-mine.html) went. I did the first two last summer and then made some more revisions again, within the last two weeks or so. But it got so that the focus on the content with that type of thing seemed to not matter, really. So it's like I couldn't communicate freely on this blog, and the amount of work or the degree of validity of the things I'd worked on seemed to be of little consequence. Anyway, the work on heme has been going well, and it tends to be the case that it takes time to be able to shorten and condense things that I've recently tried to get up to speed on. I can write about something but still sort of require time to digest the material and be able to separate the wheat from the chaff. When I learn new things in an area, I tend to write long things and then be able to shorten them. The content on heme is still too long and has been for the last month or so, but I'm sure I'll be able to finish shortening it, here, etc. My main reason for getting into the electron configuration content was to see how I could draw and keep track of structural diagrams of reactions involving heme. It's like the bookkeeping of electron transfers between inorganic and organic elements, in organometallic compounds, is sort of shrouded in mystery still, more from the standpoint of the theoretical framework of chemistry than the experimental data that's reported in chemistry journals, but it's been interesting to sort of scratch the surface of. All the diagrams might have a sort of rock-and-roll quality to them, but the chemistry is just really complex. I still don't have a good understanding of what the different factors are, besides the apparently-slow, proton-coupled electron transfer reactions that can drive radical migration within a protein, but it's like amino acid residues are being protonated and deprotonated dynamically, due to small pH gradients or something like that, and that helps to dictate, as a slow process of "equilibration," the progression of this continuous and rapid electron tunneling that nonetheless is able to slowly progress toward equilibrium and allow for the existence of long-lived tyrosyl radicals. The main, "big-picture" things I've gotten (things that may or may not be relevant or things to include) are that free perferryl heme can, according to at least four or five articles, exist and that the iron(IV) Fe=O moiety of heme with a protein radical is, itself, inclusive of the radical, perferryl heme. Iron(IV)-heme with a protein radical that's mobile is perferryl heme, and so is iron(IV)-heme with a pi-cation radical on the porphyrin ring. But iron(IV)-heme with a closed-shell, nonradical porphyrin ring and no protein radical is ferryl heme, and, even though the diagramming may tend to suggest that the Fe=O moieties are the same in ferryl and perferryl heme, ferryl heme's Fe=O moiety is less oxidized than the Fe=O moiety in either of those states of perferryl heme. And when the amino acid residue harboring the mobile radical is reduced by a reductant, the oxidation state of the Fe=O oxygen changes, and the whole path and potential path of the mobile radical, within the protein (the whole protein, in effect), acts like an extension of the porphyrin ring. There's a change in the electron configuration or distribution that's translated through one or more of the axial ligands of the protein-bound heme. That's one thing that took awhile to recognize (see de Montellano, 1987, cited in past postings, and other articles). It gets so it wasn't really possible for me to discuss the topic in a way that made sense to me and that would make sense to others, in the absence of that information. In some cases, there are descriptions of "ferryl heme" with a protein radical present, but that overall heme-bound protein is, itself, perferryl heme, given that the radical is delocalized across its entire path, in effect. That's my understanding of the way it works, and the oxene-type electron configuration of perferryl heme isn't the same as the one in ferryl heme. Anyway, I've done most of the content on here, related to heme, to allow me to be able to talk about things in a way that makes sense to me, etc.
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