Thursday, November 5, 2009

Finally: Leaving the Shorthand Notation for Heme Species Behind--It's Freedom, "Everse-Style"

Finally. This [Everse, 1998: (http://www.ncbi.nlm.nih.gov/pubmed/9626592)] is an article that addresses some of the significant problems with the notation used to represent heme compounds. The notation just doesn't make any sense, in many cases. Everse (1998) also confirms, when viewed alongside the other articles I have, my suspicion that the Fe=O bond has two electrons. Some of my older mechanisms need to be corrected, because I show homolytic cleavage of a pi or d(pi)-p(pi) bond (the "pi double bond") in some instances. The mechanisms are valid, but it's necessary to not show all of the electron transfer occurring at once. But the diagram showing one electron in the pi*(xz) antibonding molecular orbital, in the previous posting, is accurate. There's another electron in the pi*(yz) antibonding molecular orbital, and those are the only electrons in the bond. It's not a double bond, and Everse (1998) refers to it as a biradical pi-bonding interaction. Or one could call it a d(pi)-p(pi) interaction. But the whole thing with [Fe(IV)O]2+ doesn't make any sense, and I think the whole thing with the [Fe(III)-OH(-)]+ is a convention left over from the whole "crystal field theory" concept of dsp3 and d2sp3 orbitals, etc. In that type of theoretical framework, the ligand "O" is treated as if it's "O2-" or something. It doesn't even have that electronic strucure, though, and Everse (1998) reiterates the point that the oxygen in Fe=O has an oxene (atomic oxygen) electron configuration and has six valence electrons. I also finally found a great article that analyzes the electronic structure of a ferric heme species (t-butoxo-iron(III)-heme) [Lehnert et al., 2001: (http://www.ncbi.nlm.nih.gov/pubmed/11516278)], and that article, as other articles have shown, shows that some ferric heme species do contain sigma bonds. But ferryl heme has no sigma bonding electrons in the molecular orbitals that are included in the ferryl (Fe(IV)=O) moiety of heme.

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