bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iron: Models of Proteins with Dinuclear Active SitesBased in part on the article Iron: Models of Proteins with Dinuclear Active Sites by Will E. Lynch & Donald M. Kurtz, Jr. which appeared in the
Encyclopedia of Inorganic Chemistry, First Edition
.
Authors: Chavez Ferman A. , Que Lawrence 
Published: December 2011

Abstract
The nonheme diiron enzymes are a class of metalloproteins that share a common function in the binding and activation of dioxygen. In recent years, interest in these enzymes has grown at a steady rate. The focus is both of a fundamental and applied nature. Understanding how these enzymes have evolved to perform synthetically challenging organic transformations under moderate conditions will provide insights into evolutionary processes and possibly help to develop techniques for engineering such active sites into proteins. These studies have led to the development of synthetic catalysts for these transformations through the ‘biomimetic’ approach. Through structural studies it has become clear that many of the metal binding sites in nonheme diiron enzymes possess carboxylate‐rich ligation, which is believed to be important in facilitating redox processes and structural rearrangements during catalysis. The use of model compounds to study these enzymes has many advantages that are not offered with other approaches. For example, a model for a proposed reactive intermediate may be stabilized at low temperature and studied. Synthetic compounds can also be selectively modified to examine the influence of a certain geometry, ligand set, or chemical environment on the properties and reactivity of the compound. In this article, several approaches are discussed toward the development of diiron model compounds. In one approach, multidentate ligands possessing two metal binding sites are examined. This approach has led to metal complexes with closely spaced iron centers, a key structural feature in these enzymes. In a second approach, mononuclear metal complexes supported by multidentate ligands are bridged by oxygen groups to generate the diiron core structure. A third approach focuses on dicarboxylate ligands that bridge the two iron centers. This approach allows for variation of the remaining terminal ligands. The fourth approach relies on steric interactions. Intramolecular ligand interactions are used to control the geometry of the diiron complex. To date, these four approaches have been very successful in generating many of the intermediates seen in the diiron enzyme catalytic cycles and a few have been shown to reproduce the catalytic activity to some extent. It is anticipated that many more insights will be garnered from model studies and that new chemistries will be discovered.
Iron Porphyrin Chemistry
Authors: Walker F. Ann , Simonis Ursula 
Published: December 2011

AbstractThis article reviews most aspects of the chemistry of iron porphyrins, from Fe(0) to Fe(V), including occurrence and roles of natural iron porphyrins (hemes) and their synthetic analogs, structures and electron configurations of iron porphyrins of all oxidation and spin states, π electron configuration of the porphyrin ring, synthesis of metal‐free porphyrins and other related macrocycles, insertion of iron into free‐base porphyrins and related macrocycles, the properties, reactions, uses and biological relevance of iron(0), ‐(I), ‐(II) porphyrins (the latter withS = 0, 1, and 2 spin state possibilities), of iron(II) porphyrin π‐cation radicals, of iron(III) porphyrins (withS = 1/2, 3/2, and 5/2 spin state possibilities), of iron(III) porphyrin and corrole π‐cation radicals, of iron(IV) porphyrins (including five‐ and six‐coordinate ferryl (FeO)2+, iron(IV) phenyl, carbene and hydrazine complexes, and the bis‐methoxide complex) and a comparison of iron(IV) porphyrins to iron(III) porphyrin π‐cation radicals, of iron(IV) porphyrin π‐cation radicals, and of the possible existence of iron(V) porphyrins. Included in the Fe(II) part are sections on addition of ligands to four‐coordinate iron(II) porphyrins, including equilibrium binding constants, photodissociation of ligands from PFeL2complexes, binding of small molecules (O2, CO, NO, HNO) to 5‐coordinate iron(II) porphyrins and design of porphyrin ligands that will mimic the active sites of heme proteins such as myoglobin and hemoglobin, the cytochromes P450 and nitric oxide synthases, and the nitrophorins and guanylyl cyclases. Included in the iron(III) part are sections on both 5‐ and 6‐coordinate high‐spin complexes and their similarities and differences, bridged or through‐space magnetically coupled complexes of high‐spin iron(III) porphyrins with other metal complexes as possible models for cytochrome oxidase and the assimilatory sulfite reductases, coupled oxidation of hemes by hydrogen peroxide or its equivalent, and the relationship of this reactivity to the reactions of heme oxygenase, iron(III) porphyrins as reduction catalysts, and photochemistry of iron(III) porphyrins, possible electron configurations of low‐spin iron(III) porphyrins, the phenomenon and possible electronic consequences of ruffling of the porphinato core in iron(III) porphyrins, the preferred orientation of planar axial ligands bound to low‐spin iron(III) porphyrins, NO complexes of iron(III) porphyrins, reduction potentials, equilibrium constants and rates of axial‐ligand addition and exchange, kinetics of axial‐ligand rotation and porphyrin ring inversion, kinetics of reduction and autoreduction of iron(III) porphyrins, electron self‐exchange between low‐spin iron(III) and iron(II) porphyrins, synthetic ferriheme proteins, and synthesis of five‐coordinate low‐spin iron(III) porphyrins having σ‐alkyl or σ‐aryl groups as axial ligands. The iron(IV) and iron(IV) cation radical sections discuss the high‐valent states of cytochromes P450 and related enzymes.
Iron Proteins for Storage & Transport & Their Synthetic Analogs
Authors: Lewin Allison , Le Brun Nick E. , Moore Geoffrey R. 
Published: December 2011

AbstractThis article reviews proteins involved in iron metabolism. Brief descriptions are given of the biological contexts for the proteins discussed but the main emphasis is on chemical and structural aspects of them.Iron is essential to almost all forms of life, but its low bioavailability and toxicity mean that they require sophisticated mechanisms to transport it. Mammals acquire heme and nonheme iron via proteins in the gut wall, and transport it around the body using serum transferrin, for ferric iron, and hemopexin, for heme. Microbes have an active iron uptake mechanism involving small iron chelators called siderophores, for example, ferrichrome inEscherichia coli. Ferrichrome enters the cell via FhuA, a β‐barrel in the outer membrane. The periplasmic protein FhuD then transfers it to the FhuBC complex in the cytoplasmic membrane. FhuB forms a channel through which the ferric siderophore passes using energy supplied by FhuC. Once inside the cytoplasm the iron is removed from the ligand, possibly via reduction by FhuF. Some pathogenic bacteria have a similar system for heme uptake, secreting hemophores such as HasA, which can remove heme from hemoglobin. Other pathogens have outer membrane receptors that remove ferric iron from transferrin and transport it into the periplasm, where it is bound by ferric binding proteins that closely resemble a single lobe of transferrin.Following its acquisition, iron needs to be stored safely. The most widespread form of iron storage is the ferritin superfamily, which includes ferritin, bacterioferritin, and Dps. Ferritin is found in bacteria, plants, and animals and is a large shell made up of 24 subunits within which up to 4,500 ferric ions can be stored as a ferrihydrite mineral core. Bacterioferritin is found in bacteria and is closely related to ferritin, but contains up to 12 heme groups bound between pairs of subunits, which may play a role in iron release or electron storage. The bacterial protein Dps is smaller than ferritin, with 12 subunits forming the protein shell, and can hold up to 500 ferric ions. All of these proteins contain dinuclear iron sites that catalyze the oxidation of ferrous iron. An alternative form of iron storage is frataxin, found in mitochondria. Although not related to ferritin, this protein has the ability to form large aggregates that can store up to 50 ferric ions per monomer in a mineral core resembling those of ferritins.
Iron–Sulfur Models of Protein Active SitesBased in part on the article Iron–Sulfur Models of Protein Active Sites by Akira Nakamura & Norikazu Ueyama which appeared in the
Encyclopedia of Inorganic Chemistry, First Edition
.
Authors: Collins David J. , Zhou Hong‐Cai 
Published: December 2011

Abstract

In pervasiveness of occurrence and multiplicity of function, iron–sulfur clusters rival biological prosthetic groups such as hemes and flavins. The development of iron–sulfur cluster chemistry paralleled the founding and maturation of the field of bioinorganic chemistry. Starting from the first spontaneous self‐assembly of the [Fe
4
S
4
(SR)
4
]
2−
cluster in 1972, and the identification of the protein‐bound Fe
4
S
4
in the same year, the study of iron–sulfur models of protein active sites has evolved into a unique field in which synthetic inorganic chemistry now resembles the total synthesis of natural products in organic chemistry. Some of the models had been built before the crystal structure of the protein was determined. Almost all the models successfully replicated the topology and the electronic properties of the protein active sites. In this article, the models will be discussed in the order of their complexity, from single iron rubredoxin models to Fe
2
S
2
, Fe
3
S
4
, Fe
4
S
4
, and Fe
8
S
7
model compounds. In each section, the chemical synthesis of the model compound will be discussed first, followed by structure comparison and contrast, electrochemical properties, and biochemical activities. Since the major function of iron–sulfur proteins is electron transfer, and the oxidation state of the iron atom determines its reactivity, electrochemical and Mössbauer data will be tabulated in detail. Some of the recent developments in site‐differentiated, peptide, and all‐ferrous Fe
4
S
4
clusters will be reviewed. Recent studies in modeling the topology of the P‐cluster of nitrogenase will also be covered. The challenge posed by iron–sulfur proteins has inspired new iron–sulfur cluster chemistry. No other metal–nonmetal combination has produced more structural types than the iron–sulfur system; the majority of them have yet to be found in biological systems. However, the modeling of the P‐cluster and the FeMoco center of nitrogenase have posed a daunting challenge to the analog chemists.
Iron–Sulfur Proteins
Authors: Johnson Michael K. , Smith Archer D. 
Published: December 2011

AbstractIron–sulfur proteins contain iron coordinated by at least one sulfur ligand and include proteins with mononuclear Fe centers with partial or complete cysteinyl sulfur ligation as well as proteins containing clusters of iron and inorganic sulfide. This review summarizes the structural, electronic, and redox properties of protein‐bound mononuclear FeS centers and FeS clusters containing [2Fe2S], [3Fe4S], and [4Fe4S] cores. In addition to the ubiquitous role in mediating biological electron transport, the roles of FeS centers have proliferated to include coupling of electron and proton transfer, substrate binding and activation, determining protein structure, regulation of gene expression and enzymatic activity, disulfide reduction, and iron, electron, or cluster storage. The diverse roles of FeS clusters are illustrated by discussion of specific systems: the mitochondrial and photosynthetic electron transport chains and a wide range of soluble redox enzymes and proteins; the active sites of nitrile hydratase, aconitase‐type (de)hydratases, superoxide reductase (SOR), radical‐SAM (S‐adenosylmethionine) enzymes, NiFe‐ and Fe‐hydrogenase, sulfite and nitrite reductase, nitrogenase, CO dehydrogenase, and acetyl‐CoA synthase; the structural FeS centers in DNA repair enzymes; the regulatory roles of FeS centers in the SoxR, fumarate–nitrate reduction (FNR), IscR/SufR, and iron‐regulatory protein (IRP) proteins and in selected enzymes; the two classes of FeS cluster containing disulfide reductases typified by ferredoxin–thioredoxin reductase (FTR) and heterodisulfide reductase (HDR); and the role of 8Fe ferredoxins and polyferredoxins in iron, electron, or cluster storage.
Iron Transport: Siderophores
Authors: Matzanke Berthold F. 
Published: December 2011

AbstractSiderophores (from the Greek: iron carrier) are low molecular mass (500–1500 Da) iron chelators that are synthesized in bacteria and fungi under conditions of iron deficiency. Siderophores exhibit extraordinarily high complex formation constants for ferric iron with β‐values ranging from 1020to approximately 1050. Fe2+‐siderophores are some 20 orders of magnitude less stable than their Fe3+counterparts. The d5 electronic configuration of Fe3+rules out any crystal field stabilization energy and makes ferric iron complexes relatively labile with respect to isomerization and ligand exchange. Siderophores display a selectivity for iron that is reflected in the corresponding complex stability constants that are higher with Fe3+than with Al3+, or with bivalent cations like Ca2+, Cu2+or Zn2+. Microorganisms excrete desferrisiderophores in order to scavenge iron from the environment. The competition for iron by siderophores, the mechanisms of siderophore uptake through microbial membranes, and the intracellular pathways of siderophore‐iron utilization strongly depend on thermodynamic, kinetic, and structural features of the ferric iron siderophore complexes.The structural features of siderophores are diverse. The ligating groups contain oxygen atoms of hydroxamate, catecholate, α‐hydroxy carboxylic and salicylic acids, or oxazoline and thiazoline nitrogen. Reduction potentials of ferric siderophore complexes vary between −700 and −150 mV. In particular at the low potential end below −450 mV, special biological strategies of reductive iron removal are required because these potentials are too negative for typical cellular reductases.The coordination and redox chemistry of siderophores is also reflected in the mechanisms of siderophore‐mediated iron uptake in microorganisms. A classic example is the intracellular removal of iron from enterobactin. The permeation of cell walls or bacterial membranes by siderophores is in most microbes a highly specific process requiring an array of up to eight proteins. The advent of modern molecular biology delivered a cornucopia of methods enabling high‐yield production of specific gene products relevant to siderophore synthesis and transport, analyses of structure‐function relationships (employing site directed mutagenesis), and detailed insights into the regulation of the corresponding processes.One siderophore, ferrioxamine B, serves as a detoxifier in iron overload diseases and in the treatment of β‐thalassemia. Siderophores and siderophore analogs also play a role in MRI and are employed as basic models for actinide chelators in order to remove these metals from the environment or from a contaminated body.
Ligand Field Theory & Spectra
Authors: Smith Derek W. 
Published: December 2011

Abstract

In any chemical environment – traditionally represented as a crystal field (CF), in which the donor atoms are represented by point charges – an
n
d subshell loses its fivefold degeneracy. The consequent splitting is described in detail for cubic (octahedral and tetrahedral) systems. The pure CF approach has serious shortcomings, but the effects of covalency can be accommodated without losing its simplicity altogether; this is often called
ligand field theory
(LFT). CF/LFT is important in the interpretation of the d–d spectra of complexes; the d–d states arising from cubic d

n

systems and their relative energies are analyzed, along with a discussion of the nephelauxetic effect. As examples of the analysis of d‐orbital splittings in noncubic complexes, chlorocuprates(II) and tetragonal tetraamminechromium(III) complexes are examined in detail, using the angular overlap and cellular ligand field models. Among applications of LFT, ligand field stabilization energy (LFSE) is useful in the rationalization of thermodynamic and kinetic observations. The Jahn–Teller effect is important in the structural chemistry of copper(II) especially.
Luminescence
Authors: Fouassier C. 
Published: December 2011

AbstractThis chapter is devoted to the luminescence of inorganic compounds. Luminescence characteristics are strongly host‐dependent. This is illustrated by various examples of the influence of covalency, crystal field, phonon energies, and structural features. The chapter is organized as follows.Section 2 describes the fundamentals of luminescence: probability of electronic transitions, shape of emission bands, quantum efficiency, energy transfer, and factors governing the position of the emitting level (nephelauxetic effect and crystal field splitting).Section 3 reviews the main families of luminescent ions: transition metal ions, lanthanide ions, and s2ions. The various types of electronic transitions responsible for the luminescence of transition and lanthanide ions are presented: nd → nd, (n + 1)s → nd, and charge transfer (CT) transitions for the former, 4f → 4f, 5d → 4f, and CT transitions for the latter. Data are given on the luminescence wavelength range, excited‐state lifetimes, thermal stability, and concentration quenching.Section 4 deals with donor‐acceptor transitions in ZnS.Section 5 presents the luminescence mechanisms for excitation through the host lattice. Vacuum ultraviolet (VUV), electron beam, X‐ray, and γ‐ray excitation are considered. The most efficient luminescent materials are given for the various types of excitation.Section 6 deals with electroluminescent materials.
Magnetic Oxides
Authors: Greedan John E. 
Published: December 2011

Abstract
An attempt has been made to survey the research activity in selected aspects of the field of magnetic oxides for the period ∼1993 to the present. Emphasis has been placed on oxides with the perovskite and related structures such as the Ruddlesden–Popper phases, A‐site and B‐site ordered perovskites, pillared perovskites, and materials with structures related to the hexagonal perovskites. As well, the field of geometrically frustrated magnetic materials is reviewed with emphasis on materials with the pyrochlore, spinel, and related structures. Phenomena exhibited by such compounds include colossal magneto‐resistance, charge and orbital ordering, half‐metallic ferromagnetism, low‐dimensional magnetism, spin glass, spin liquid, and spin ice ordering, among others.
Manganese: Inorganic & Coordination ChemistryBased in part on the article Manganese: Inorganic & Coordination Chemistry by Charles A. McAuliffe, Stephen M. Godfrey, & Michael Watkinson which appeared in theEncyclopedia of Inorganic Chemistry, First Edition.
Authors: Collomb Marie‐Noëlle , Deronzier Alain 
Published: December 2011

AbstractThis article covers the last 10 years of the inorganic and coordination chemistry of manganese at oxidation states (II), (III), (IV), (V), (VI), and (VII), as well as multinuclear compounds having oxidation states (II)–(IV) with both unitary and mixed valencies. The common ligands for manganese compounds involve the donor atoms nitrogen, oxygen, and the halogens while only few are known with other group V and group VI donors. One of the major areas of expansion has been the multinuclear complexes that are relevant to such diverse fields as metalloenzymes and single‐molecule magnets. Besides the small clusters, comprising two to four metal ions synthesized to model the structures and functions of manganese metalloenzymes, a lot of interest has been invested in larger clusters, not only for their biological relevance, but also for the development of materials with novel magnetic properties. Significant advances have been also been made in the chemistry of higher oxidation state manganese complexes (V), (VI), and (VII).
Manganese: The Oxygen‐Evolving Complex & ModelsBased in part on the article Manganese: Oxygen‐Evolving Complex & Models by Lars‐Erik Andréasson & Tore Vänngård which appeared in theEncyclopedia of Inorganic Chemistry, First Edition.
Authors: Charles Dismukes G. , van Willigen Rogier T. 
Published: December 2011

AbstractIn this article, we give an overview of nature's singular biological process for producing oxygen gas by the oxidation of water in photosynthetic organisms. The harnessing of light to accomplish the splitting of water was arguably nature's most successful experiment in biological innovation. It enabled global proliferation of oxygenic photosynthesis and created the biogeochemical cycles of oxygen and carbon on earth. We review the atomic structure of the metalloenzyme, the photosystem II water splitting complex (PSII‐WOC), as revealed by X‐ray diffraction and spectroscopic techniques. We describe: 1) The electronic structure of its inorganic core, Mn4Ca1OxCl1–2(HCO3)y, based upon spectroscopic and magnetic susceptibility measurements, 2) the organization of the protein subunits as revealed by X‐ray diffraction and the role of select amino acid residues as revealed by site‐directed mutagenesis, and 3) the kinetic sequence of steps during assembly of the inorganic core to the cofactor‐depleted apo‐protein and the functional consequences of substitution of the inorganic cofactors. We use these data together with physico‐chemical data describing the formation of light‐induced intermediates, the exchange rates between substrate and free water molecules, the stoichiometry of electron and proton release and the activation energies to discuss possible mechanisms for photosynthetic water splitting. The chemistry of photosynthetic water splitting is energetically demanding and mechanistically complex. The lessons learned from nature have guided chemists seeking to incorporate these design principles within catalysts suitable for abiotic water splitting. We end with a description of the few synthetic manganese complexes that have been found to produce oxygen gas from water and discuss the chemical mechanisms by which they appear to function.
Mechanisms of Reaction of Organometallic Complexes
Authors: Atwood Jim D. , Rosenberg Edward 
Published: December 2011

AbstractAn overview of the mechanistic features of organometallic reactions is presented. The primary mechanistic types discussed are ligand substitution, oxidative addition, reductive elimination, and electron transfer. Each reaction pathway is discussed within the context of the common electron counts encountered for most organometallic complexes. Examples of how these common reaction pathways extend to polynuclear complexes are also presented. Although reasonable generalizations with regard to overall reaction rates and stepwise mechanisms using the electron count formalism can be made, many recent reports point out that the details of ligand and metal center structure can override these general trends. A considerable amount of quantitative rate data is provided and computational methodologies for understanding the observed rates are discussed.