bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metallocenter Biosynthesis & Assembly
Authors: Mulrooney Scott B. , Hausinger Robert P. 
Published: March 2006

AbstractMetalloproteins have been characterized intensively for decades, yet only recently has progress been made in characterizing the mechanisms of biological metallocenter biosynthesis and assembly. Here, we describe how cellular synthesis of metal sites makes use of several recurring themes, often with multiple themes combined into a single pathway. In the simplest situation, binding of a metal ion to a biological ligand occurs by reversible thermodynamic control. However, the prevalence of metallocenters deeply buried within macromolecules, the exceedingly low concentrations of free metal ions within cells, and the sophisticated structures of many metal‐containing active sites and cofactors provide evidence that alternative and more complex approaches also must exist. In some cases, metallochaperones are used to deliver the metal of interest to an apoprotein. In other cases the target protein undergoes posttranslational modification at the metal‐binding site, either prior to or after the metal is bound. Many metallocenters contain additional components that are added along with the metal ion or used to form a preassembled metal‐containing cofactor. Scaffolding proteins may be used to provide a framework for construction of the cofactor. Electron transfer reactions involving the metal, an added compound, or the protein ligand can participate in activation. Finally, molecular chaperones that bind to and alter the conformation of the target apoprotein may be utilized. In many cases, the function of the molecular chaperone is coupled to nucleotide triphosphate hydrolysis.
Metallochaperones & Metal Ion Homeostasis
Authors: Culotta Valeria C. 
Published: March 2006

Abstract
There exists a large array of proteins that rely on metal ions such as copper and manganese for function and these so‐called metalloproteins are housed in diverse locations throughout the cell. It is imperative that each metalloprotein connects with the proper metal ion and also at the right time. How does this meeting of protein and metal occur in a specific and regulated fashion? The problem seems paramount when one considers the potentially toxic nature of metals. With the harm that metals can impose on biomolecules, these ions are never allowed to roam freely in the reactive form and, as such, the bioavailability of metals within cells is very limited. To overcome this problem, eukaryote cells have evolved with specific ‘metal trafficking pathways’ or designated routes a metal ion can follow once inside the cell. On one hand, the bulk of the metal may be subject to a dead fate involving sequestration by metal detoxification systems. On the other hand, a fraction of the metal destined for metalloproteins enters a trafficking pathway that involves both membrane transporters and ‘metal chaperones’ that directly insert the metal into the target metalloprotein. The bulk of current knowledge on metal chaperones and metal trafficking pathways has emerged from studies on copper and to a lesser degree on manganese. The work described herein focuses on paradigms developed for copper and manganese, with possible implications for other essential metals as well.
Metalloprotein Design & Engineering
Authors: Lu Yi 
Published: March 2006

AbstractThis review covers recent advances in metalloprotein design, with focus on different approaches to the design. Impressive progress has been made in designing metal‐binding sites in peptides, de novo designed proteins, and native protein scaffolds. The approach can be rational or combinatorial. Under rational design, redesigning an existing metal‐binding site to a new site with dramatically different structure and function complements well the design of new metal‐binding sites by revealing the role of specific residues responsible for a particular structural or functional feature of the metal‐binding site of interest. To create a new metal‐binding site, several approaches have been used, including design based on structural homology, by inspection, using automated computer search algorithms, or combination of the above approaches. In addition, modular approach by transplanting a conserved structural unit from one protein into another has also been shown to be effective. Design through combinatorial and evolution methods has also been successful as it requires little prior knowledge of the protein structure. Finally, introducing unnatural amino acids or nonnative metal ions/prosthetic groups to expand the repertoires of metalloproteins have been demonstrated. Successful examples of each of the approaches are given; advantages and disadvantages of the approaches are discussed; the outlook for future research is also presented.
Multi‐Heme Cytochromes & Enzymes
Authors: Pereira Inês A. C. , Xavier António V. 
Published: March 2006

AbstractMultihemeccytochromes and enzymes are a diverse group of proteins having several hemesccovalently bound to the polypeptide chain that are either enzymes involved in redox chemistry or electron transfer proteins. Most known members of this group are associated with the respiratory chains of proteobacteria. These proteins are characterized by a low amino acid to heme ratio, bis‐histidinyl coordination (with a few exceptions), and low redox potentials of the hemes. The hemes are usually tightly packed in close contact, allowing very fast electron transfer. Despite the absence of overall sequence identity between proteins, the hemes are found in quite conserved structural motifs, which tend to be organized in diheme pairs that are either parallel or perpendicular to each other. From the structures available, two families can be recognized in terms of the heme structural arrangement: the cytochromec3family where the perpendicular motif is predominant, and the hydroxylamine oxidoreductase (HAO) family where the stacked parallel motif alternates with the perpendicular motifs. Other multiheme cytochromes for which the structure is not yet available may be part of novel structural families.
Semiconductor Nanocrystal Quantum Dots
Authors: Hollingsworth Jennifer A. 
Published: March 2006

AbstractSemiconductor quantum dots (QDs) bridge the gap between cluster molecules and bulk materials. The boundaries between molecular, QD, and bulk regimes are not well defined and are strongly material dependent. However, a range from ∼100 to ∼10 000 atoms per particle can be considered as a rough estimate of sizes for which the nanocrystal regime occurs. The lower limit of this range is determined by the stability of the bulk crystalline structure with respect to isomerization into molecular structures. The upper limit corresponds to sizes for which energy level spacings approach thermal energy, kT. In this nanosize regime, the semiconductor energy‐ or band gap is dependent upon the particle size. This phenomenon is known as thequantum‐size effect, and it allows band‐gap‐dependent material properties to be tuned with particle size. Specifically, semiconductor absorption and emission wavelengths can be controllably blueshifted from their bulk semiconductor values over hundreds of nanometers.Semiconductor quantum dots (QDs) have been prepared by a variety of ‘physical’ and ‘chemical’ methods. Here, we review the synthetic chemistry of QDs prepared by colloidal chemical routes. These QDs, known as nanocrystal quantum dots (NQDs), comprise an inorganic core overcoated with a layer of organic ligand molecules. The organic capping provides electronic and chemical passivation of surface dangling bonds, prevents uncontrolled growth and agglomeration of the nanoparticles, and allows NQDs to be chemically manipulated like large molecules with solubility and reactivity determined by the identity of the surface ligand. In contrast, with substrate‐bound epitaxial QDs prepared by physical deposition methods (e.g. molecular beam epitaxy and metal‐organic chemical vapor deposition), NQDs are ‘freestanding.’ In this discussion, we concentrate on the most successful synthesis methods, where success is determined by high crystallinity, adequate surface passivation, solubility in nonpolar or polar solvents, and good size monodispersity. Size monodispersity is critical as it permits the study and, ultimately, the use of materials‐size‐effects to define novel electronic, optical, and structural materials properties. Further, we examine many of the most significant contributions in the areas of NQD chemical surface modification (organic and inorganic), particle shape control, and phase control.
Organic Synthesis Using Metal‐Mediated Coupling Reactions
Authors: Goodson Felix E. , Cichowicz Melissa B. 
Published: March 2006

Abstract
This article provides an overview of the cross‐coupling protocols most commonly used in organic synthesis. Particular emphasis is placed upon topics likely to be of interest to the inorganic chemist, namely, history, catalyst development, and mechanistic studies. While not a comprehensive review, this treatment is intended to provide the reader with a summary of some successful catalyst design strategies, methodological improvements, and mechanistic insights that have been achieved over the past 10 years.
Porous Inorganic Materials
Authors: Wang Xiqing , Bu Xianhui , Feng Pingyun 
Published: March 2006

AbstractPorous inorganic materials cover a range of solids, both oxides and nonoxides, crystalline and amorphous, that have a pore size extending from about 3 Å to over 500 Å. Crystalline microporous materials such as zeolites have been known for over 200 years, and the research in the past decade has extended types of microporous materials from traditional oxides to chalcogenides and metal–organic frameworks. Efforts aimed toward developing new microporous materials that integrate uniform microporosity with other functionality have also led to promising results.Periodically ordered mesoporous materials are a recent addition to the family of ordered inorganic porous materials. They can be made in the presence of organized assemblies of organic molecules (e.g. amines, cationic, anionic, or nonionic surfactants) or polymers (e.g. amphiphilic block copolymers). Micellar solutions, lyotropic liquid crystals, and microemulsions can all serve as structure‐directing agents during the cocondensation of inorganic precursors with organic species. A number of synthetic pathways have been developed for the preparation of mesoporous solids in a variety of chemical compositions including silica, organosilica, transition metal oxides, chalcogenides, and even elemental forms such as carbon and platinum. Much progress has also been made in the control of macroscopic morphologies (e.g. films, fibers, monoliths, and spheres). The pore geometry is closely related to the nature of the organic assemblies and other synthetic parameters and can be controlled to a certain degree to allow the synthesis of mesoporous materials with the desirable architecture and properties.The past decade has also witnessed a rapid development in the synthesis of ordered macroporous materials and porous materials that are ordered at multiple‐length scales. Commonly used templates for the control of the macroscopic ordering include colloidal crystals such as latex or silica spheres and emulsion droplets. With the availability of a variety of inorganic porous materials, numerous applications are awaiting the exploration of materials researchers.
Self‐Assembled Inorganic Architectures
Authors: Bera Jitendra K. , Bacsa John , Dunbar Kim R. 
Published: March 2006

Abstract
The field of inorganic chemistry is witnessing an enormous growth period in the area of molecular self‐assembly. This review highlights key advances in this area with an emphasis on novel structures and the dynamic nature of inorganic self‐assembly reactions. Multidentate N‐heterocylic, cyanide, and carboxylate ligands are discussed in detail with respect to their use in the design of discrete structures, including molecular triangles, squares, pentagon, cubes, as well as polyhedra, oligomers, and polymers. Inorganic structures that employ metal–coordination and hydrogen bonds are also highlighted. The examples described herein illustrate the fact that the available binding sites and the topicity of the ligands along with the coordination requirements of metal ions are the key elements for building desired architectures. The role of intrinsic factors such as geometrical preferences of the metal ion as well as extrinsic factors such as the presence of a template in stabilizing a particular product are discussed. Recent progress in the rational design of functional materials vis‐à‐vis the manipulation of supramolecular chemistry is also covered in brief.
Hydrogen Bonding & Dihydrogen Bonding
Authors: Crabtree Robert H. 
Published: March 2006

AbstractThe review begins with the historical development of the area, notably Pauling's contribution. The current interest is in part related to the rise of supramolecular chemistry and molecular recognition, as well as the significance of hydrogen bonding in biology and biochemistry. Strong and weak cases are distinguished. A relationship with hypervalency is proposed, in which the bridging proton of a FHF anion is considered as hypervalent hydrogen. Dihydrogen bonding is considered the latest hydrogen bond type. Structural and spectroscopic aspects are discussed, together with applications. Hydrogen bonding in metal complexes is covered together with the distinction between hydrogen bonding and sigma complexation.
Carbon–Carbon & Carbon–Heteroatom Activation
Authors: Crabtree Robert H. 
Published: March 2006

AbstractActivation involves binding of the intact CC or CX bond to the metal followed by CC or CX bond cleavage. Both aspects are considered here. The activation of CC bonds is facilitated by an enforced close approach of the CC bond to the metal or by the presence of a strong driving force such as a strained ring starting material or aromatization during the reaction. The reactivity order is: sp–sp > sp2–sp2 > sp3–sp3. The activation of CX bonds occurs by a number of mechanistic pathways depending on the system. Halocarbon complexes of type RXM are often intermediates and can be isolated in favorable cases.
Main Group: Multiple Bonding
Authors: Robinson Gregory H. 
Published: March 2006

Abstract
This chapter summarizes the many quite remarkable discoveries that have been made in recent years regarding multiple bonding of the heavier main group elements. While the general concept of multiple bonding is well established and easily embraced in organic chemistry, this is not the case for much of organometallic chemistry. The criteria that are routinely employed to assign double and triple bond character in organic compounds, that is, bond distance and bond strength, are of little significance in many cases involving the heavier main group elements. For example, the EE (E = Sn or Pb) double bond is both longer and weaker than the corresponding EE single bond. This chapter will discuss such seminal discoveries as the syntheses of the first digallyne (GaGa), dibismuthene (BiBi), and disilyne (SiSi). Central to these breakthroughs is the incorporation of sterically demanding ligand systems, which both stabilize and inhibit decomposition pathways of the heavier main group atoms.
Copper Proteins with Type 2 Sites
Authors: McGuirl Michele A. , Dooley David M. 
Published: March 2006

AbstractThe copper enzymes covered in this article span a wide range in terms of both their structural and reactivity properties. Yet the copper centers in each share similar coordination geometries and have been designated ‘Type 2 (or II)’ copper proteins. Type 2 copper proteins lack the unique spectroscopic or magnetic signatures that typify the so‐called Type 1 and Type 3 copper proteins, and the unique tetranuclear cluster found in nitrous oxide reductase. Indeed, the basis for classifying proteins as Type 2 was that the EPR (Electron Paramagnetic Resonance) spectra of the oxidized (resting) forms of these proteins closely resembled the spectra of ‘normal’ tetragonal CuIIcomplexes, withg∥ > g⊥ > 2.00, andA∥ ≥ 120 G at X‐band. It was generally surmised that the coordination environments of the copper sites in such enzymes were unexceptional, with five‐ or six‐coordinate structures composed of N, O ligands. As is often the case in science, many fascinating and totally unexpected structural and chemical phenomena turned out to be concealed behind this deceptively ‘normal’ facade. Each of the Type 2 enzymes covered here (superoxide dismutase, amine oxidase, lysyl oxidase, galactose oxidase, dopamine‐β‐monooxygenase, peptidylglycine α‐hydroxylating monooxygenase, and quercetinase) displays unique active‐site properties. Elucidating and elaborating structure/function relationships for these enzymes has been greatly aided by the availability of high‐resolution crystal structures for one or more enzymes from each group. These have generally corroborated the fairly detailed structural models that were developed from extensive spectroscopic studies. At the same time, the 3D structures have revealed many surprising details of the active sites. Indeed, the roles of copper in these ‘normal’ Type 2 copper centers are more diverse than ever imagined.
Beryllium: Inorganic Chemistry
Authors: Keizer Timothy S. , McCleskey T. Mark 
Published: March 2006

Abstract
The speciation and molecular interactions of beryllium have remained relatively unexplored compared to most metals, despite its high toxicity and extensive use in industry. One reason for this fact is the difficulty in characterizing beryllium species in solution. Herein, the chemistry of beryllium, and its interaction with hydroxo, inorganic and organic ligands are discussed. The structure and formation of beryllium species are communicated with emphasis on the stability of species in solution.
Subvalent Compounds
Authors: Brothers Penelope J. 
Published: March 2006

Abstract
Subvalent compounds are those in which a main group element occurs in an oxidation state lower than its normal group oxidation state. Traditionally, these have been identified in solid‐state inorganic phases, but more recently there have been major advances in the preparation of stable, molecular compounds containing subvalent main group elements. This has occurred in some cases through the use of specially designed ligands able to stabilize low oxidation state species through electronic stabilization or steric protection using bulky substituents. Ingenious synthetic routes such as the preparation of solutions in organic solvents of metastable aluminum(I) and gallium(I) halides have allowed access to other novel species. Apart from a relatively small number of types of mononuclear complexes, most subvalent molecular compounds involve homoatomic element–element bonds in the form of rings, chains, and clusters. Many of these have unusual structural and electronic properties that challenge established, classical ideas of bonding and electronic structure. This discussion focuses on recent advances in the structure and chemistry of molecular subvalent compounds, with an emphasis on the groups 13 and 14 elements. In addition to mononuclear and simple homonuclear single‐bonded compounds, several classes of cluster compounds are examined, including electron‐precise, electron‐rich, and electron‐deficient clusters. The latter include the Zintl ions. A very new class of aluminum and gallium metalloid clusters containing metal–metal bonds unsupported by ligands represents species on the pathway to formation of the bulk metal. An area in which exciting developments have taken place in the last decade encompasses subvalent compounds that are heavier main group element analogs of alkenes and alkynes, and significant structural features and new bonding models for these are discussed.
Inorganic Ring Systems
Authors: Haiduc Ionel 
Published: March 2006

AbstractInorganic rings of various types can be formed as a result of the broad range of bond types available. Cyclic structures formed by self‐assembly of molecular building units (tectons) are discussed in terms of supramolecular chemistry concepts. The formation of covalent rings can be understood in terms of combining various fragments (synthons) in which the central atoms can display various oxidation states, coordination numbers, and geometries, leading to a broad structural diversity of cyclic structures for a given composition of the ring skeleton (as illustrated for P2N2and Si2N2rings).
Current Developments in Optical Data Storage with Organic Dyes
Authors: Mustroph Heinz , Stollenwerk Manfred , Bressau Volker 
Published: March 2006

AbstractThe main motivation for the development of digital data storage has been the improvement in play‐back quality and the increase in storage capacity. In 1982 Philips and Sony introduced the first technically and economically successful system based on this—the compact disc (CD) and a compatible player. A very broad diversity of optical data recording formats are available today, and a difference is drawn between prerecorded, recordable, and rewritable media. This Review gives an overview of the systems used, the main features of production, and then concentrates on the properties of the organic dyes that are used in recordable systems. Dyestuffs chemistry has gained the reputation of having become a mature field of activity. Is this prejudice or a justified swan song for dyestuffs chemistry? When applications in optical data storage are considered, it is evident that even today progresses such as CD‐R and DVD/R would not be feasible without functional dyes.
Helical twists of collagen model peptides
Authors: Okuyama Kenji , Wu Guanghan , Jiravanichanun Nattha , Hongo Chizuru , Noguchi Keiichi 
Published: March 2006

AbstractAverage helical twists were calculated by the method of Sugeta and Miyazawa (Biopolymers 1967, 5, 673–679) for all of the collagen model peptides analyzed to date. Calculation of the helical twists of all triplets in each peptide strand provided novel insights for several model peptides. In the (Pro‐Pro‐Gly)n (n = 9 and 10), the helical twists showed cyclic fluctuations between 40 and 65° with a 20 Å period, suggesting that their molecular conformations were close enough to the ideal 7/2‐helix to show the helical repeat of 20 Å. Rather small helical twists in the guest regions of IBP in complex and T3‐785 were attributed to the interaction with Integrin I domain and a relaxed conformation caused by three consecutive triplets lacking imino acid residues, respectively. Although most of the triplets used in this study were imino acid–rich triplets, helical twists were scattered in a wide range from 30 to 70° with an overall average of 52.6°. This distribution of helical twists indicated a strong preference for the 7/2‐helical conformation (51.4°) rather than the 10/3‐helical model (36°). © 2006 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 84: 421–432, 2006This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com