Showing papers in "ChemInform in 2006"

Why Gold Nanoparticles Are More Precious than Pretty Gold: Noble Metal Surface Plasmon Resonance and Its Enhancement of the Radiative and Nonradiative Properties of Nanocrystals of Different Shapes

Abstract: This tutorial review presents an introduction to the field of noble metal nanoparticles and their current applications. The origin of the surface plasmon resonance and synthesis procedures are described. A number of applications are presented that take advantage of the electromagnetic field enhancement of the radiative properties of noble metal nanoparticles resulting from the surface plasmon oscillations.

Sources, Fate and Transport of Perfluorocarboxylates

Abstract: This review describes the sources, fate, and transport of perfluorocarboxylates (PFCAs) in the environment, with a specific focus on perfluorooctanoate (PFO). The global historical industry-wide emissions of total PFCAs from direct (manufacture, use, consumer products) and indirect (PFCA impurities and/or precursors) sources were estimated to be 3200−7300 tonnes. It was estimated that the majority (∼80%) of PFCAs have been released to the environment from fluoropolymer manufacture and use. Although indirect sources were estimated to be much less important than direct sources, there were larger uncertainties associated with the calculations for indirect sources. The physical−chemical properties of PFO (negligible vapor pressure, high solubility in water, and moderate sorption to solids) suggested that PFO would accumulate in surface waters. Estimated mass inventories of PFO in various environmental compartments confirmed that surface waters, especially oceans, contain the majority of PFO. The only environm...

Synthesis of Transportation Fuels from Biomass: Chemistry, Catalysts, and Engineering

Abstract: 1.0. Introduction 4044 2.0. Biomass Chemistry and Growth Rates 4047 2.1. Lignocellulose and Starch-Based Plants 4047 2.2. Triglyceride-Producing Plants 4049 2.3. Algae 4050 2.4. Terpenes and Rubber-Producing Plants 4052 3.0. Biomass Gasification 4052 3.1. Gasification Chemistry 4052 3.2. Gasification Reactors 4054 3.3. Supercritical Gasification 4054 3.4. Solar Gasification 4055 3.5. Gas Conditioning 4055 4.0. Syn-Gas Utilization 4056 4.1. Hydrogen Production by Water−Gas Shift Reaction 4056

Fragmentation Pathways of Protonated Peptides

Abstract: The fragmentation pathways of protonated peptides are reviewed in the present paper paying special attention to classification of the known fragmentation channels into a simple hierarchy defined according to the chemistry involved. It is shown that the 'mobile proton' model of peptide fragmentation can be used to understand the MS/MS spectra of protonated peptides only in a qualitative manner rationalizing differences observed for low-energy collision induced dissociation of peptide ions having or lacking a mobile proton. To overcome this limitation, a deeper understanding of the dissociation chemistry of protonated peptides is needed. To this end use of the 'pathways in competition' (PIC) model that involves a detailed energetic and kinetic characterization of the major peptide fragmentation pathways (PFPs) is proposed. The known PFPs are described in detail including all the pre-dissociation, dissociation, and post-dissociation events. It is our hope that studies to further extend PIC will lead to semi-quantative understanding of the MS/MS spectra of protonated peptides which could be used to develop refined bioinformatics algorithms for MS/MS based proteomics. Experimental and computational data on the fragmentation of protonated peptides are reevaluated from the point of view of the PIC model considering the mechanism, energetics, and kinetics of the major PFPs. Evidence proving semi-quantitative predictability of some of the ion intensity relationships (IIRs) of the MS/MS spectra of protonated peptides is presented.

Ruthenium-Catalyzed Cycloaddition of Alkynes and Organic Azides.

Abstract: Cp*RuCl(PPh3)2 is an effective catalyst for the regioselective "fusion" of organic azides and terminal alkynes, producing 1,5-disubstituted 1,2,3-triazoles. Internal alkynes also participate in this catalysis, resulting in fully substituted 1,2,3-triazoles.

Introduction to Half‐Metallic Heusler Alloys: Electronic Structure and Magnetic Properties

Abstract: Intermetallic Heusler alloys are amongst the most attractive half-metallic systems due to the high Curie temperatures and the structural similarity to the binary semiconductors. In this review we present an overview of the basic electronic and magnetic properties of both Heusler families: the so-called half-Heusler alloys like NiMnSb and the the full-Heusler alloys like Co2MnGe. Ab-initio results suggest that both the electronic and magnetic properties in these compounds are intrinsically related to the appearance of the minority-spin gap. The total spin magnetic moment Mt scales linearly with the number of the valence electrons Zt, such that Mt = Zt − 24 for the full-Heusler and Mt = Zt − 18 for the half-Heusler alloys, thus opening the way to engineer new half-metallic alloys with the desired magnetic properties.

Reducing Implant-Related Infections: Active Release Strategies

Abstract: Despite sterilization and aseptic procedures, bacterial infection remains a major impediment to the utility of medical implants including catheters, artificial prosthetics, and subcutaneous sensors. Indwelling devices are responsible for over half of all nosocomial infections, with an estimate of 1 million cases per year (2004) in the United States alone. Device-associated infections are the result of bacterial adhesion and subsequent biofilm formation at the implantation site. Although useful for relieving associated systemic infections, conventional antibiotic therapies remain ineffective against biofilms. Unfortunately, the lack of a suitable treatment often leaves extraction of the contaminated device as the only viable option for eliminating the biofilm. Much research has focused on developing polymers that resist bacterial adhesion for use as medical device coatings. This tutorial review focuses on coatings that release antimicrobial agents (i.e., active release strategies) for reducing the incidence of implant-associated infection. Following a brief introduction to bacteria, biofilms, and infection, the development and study of coatings that slowly release antimicrobial agents such as antibiotics, silver ions, antibodies, and nitric oxide are covered. The success and limitations of these strategies are highlighted.

Protein Posttranslational Modifications: The Chemistry of Proteome Diversifications

Abstract: The diversity of distinct covalent forms of proteins (the proteome) greatly exceeds the number of proteins predicted by DNA coding capacities owing to directed posttranslational modifications. Enzymes dedicated to such protein modifications include 500 human protein kinases, 150 protein phosphatases, and 500 proteases. The major types of protein covalent modifications, such as phosphorylation, acetylation, glycosylation, methylation, and ubiquitylation, can be classified according to the type of amino acid side chain modified, the category of the modifying enzyme, and the extent of reversibility. Chemical events such as protein splicing, green fluorescent protein maturation, and proteasome autoactivations also represent posttranslational modifications. An understanding of the scope and pattern of the many posttranslational modifications in eukaryotic cells provides insight into the function and dynamics of proteome compositions.

Solid‐State Kinetic Models: Basics and Mathematical Fundamentals

Abstract: Many solid-state kinetic models have been developed in the past century. Some models were based on mechanistic grounds while others lacked theoretical justification and some were theoretically incorrect. Models currently used in solid-state kinetic studies are classified according to their mechanistic basis as nucleation, geometrical contraction, diffusion, and reaction order. This work summarizes commonly employed models and presents their mathematical development.

Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins

Abstract: The term molecular mechanics (MM) refers to the use of simple potential-energy functions (e.g., harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular mechanics approaches are widely applied in molecular structure refinement, molecular dynamics (MD) simulations, Monte Carlo (MC) simulations, and ligand-docking simulations. Typically, molecular mechanics models consist of spherical atoms connected by springs which represent bonds. Internal forces experienced in the model structure are described using simple mathematical functions. For example, Hooke’s law is commonly used to describe bonded interactions, and the nonbonded atoms might be treated as inelastic hard spheres or may interact according to a Lennard-Jones potential. Using these simple models, a molecular dynamics simulation numerically solves Newton’s equations of motion, thus allowing structural fluctuations to be observed with respect to time. Dynamic simulation methods are widely used to obtain information on the time evolution of conformations of proteins and other biological macromolecules1–4 and also kinetic and thermodynamic information. Simulations can provide fine detail concerning the motions of individual particles as a function of time. They can be utilized to quantify the properties of a system at a precision and on a time scale that is otherwise inaccessible, and simulation is, therefore, a valuable tool in extending our understanding of model systems. Theoretical consideration of a system additionally allows one to investigate the specific contributions to a property through “computational alchemy”,5 that is, modifying the simulation in a way that is nonphysical but nonetheless allows a model’s characteristics to be probed. One particular example is the artificial conversion of the energy function from that representing one system to that of another during a simulation. This is an important technique in free-energy calculations.6 Thus, molecular dynamics simulations, along with a range of complementary computational approaches, have become valuable tools for investigating the basis of protein structure and function. This review offers an outline of the origin of molecular dynamics simulation for protein systems and how it has developed into a robust and trusted tool. This review then covers more recent advances in theory and an illustrative selection of practical studies in which it played a central role. The range of studies in which MD has played a considerable or pivotal role is immense, and this review cannot do justice to them; MD simulations of biomedical importance were recently reviewed.4 Particular emphasis will be placed on the study of dynamic aspects of protein recognition, an area where molecular dynamics has scope to provide broad and far-ranging insights. This review concludes with a brief discussion of the future potential offered to advancement of the biological and biochemical sciences and the remaining issues that must be overcome to allow the full extent of this potential to be realized. 1.1. Historical Background MD methods were originally conceived within the theoretical physics community during the 1950s. In 1957, Alder and Wainwright7 performed the earliest MD simulation using the so-called hard-sphere model, in which the atoms interacted only through perfect collisions. Rahman8 subsequently applied a smooth, continuous potential to mimic real atomic interactions. During the 1970s, as computers became more widespread, MD simulations were developed for more complex systems, culminating in 1976 with the first simulation of a protein9,10 using an empirical energy function constructed using physics-based first-principles assumptions. MD simulations are now widely and routinely applied and especially popular in the fields of materials science11,12 and biophysics. As will be discussed later in this review, a variety of experimental conditions may be simulated with modern theories and algorithms. The initial simulations only considered single molecules in vacuo. Over time, more realistic or at least biologically relevant simulations could be performed. This trend is continuing today. The initial protein MD simulation, of the small bovine pancreatic trypsin inhibitor (BPTI), covered only 9.2 ps of simulation time. Modern simulations routinely have so-called equilibration periods much longer than that, and production simulations of tens of nanoseconds are routine, with the first microsecond MD simulation being reported in 1998.13 In addition, the original BPTI simulation included only about 500 atoms rather than the 104-106 atoms that are common today. While much of this advancement results from an immense increase in availability of computing power, major theoretical and methodological developments also contribute significantly. The number of publications regarding MD theory and application of MD to biological systems is growing at an extraordinary pace. A single review cannot do justice to the recent applications of MD. Using data from ISI Web of Science, the authors estimate that during 2005 at least 800 articles will be published that discuss molecular dynamics and proteins. The historical counts are shown in Figure 1. Open in a separate window Figure 1 Articles matching ISI Web of Science query “TS=(protein) AND TS=(molecular dynamics)”.

Polymer Therapeutics: Concepts and Applications

Abstract: Polymer therapeutics encompass polymer-protein conjugates, drug-polymer conjugates, and supramolecular drug-delivery systems. Numerous polymer-protein conjugates with improved stability and pharmacokinetic properties have been developed, for example, by anchoring enzymes or biologically relevant proteins to polyethylene glycol components (PEGylation). Several polymer-protein conjugates have received market approval, for example the PEGylated form of adenosine deaminase. Coupling low-molecular-weight anticancer drugs to high-molecular-weight polymers through a cleavable linker is an effective method for improving the therapeutic index of clinically established agents, and the first candidates have been evaluated in clinical trials, including, N-(2-hydroxypropyl)methacrylamide conjugates of doxorubicin, camptothecin, paclitaxel, and platinum(II) complexes. Another class of polymer therapeutics are drug-delivery systems based on well-defined multivalent and dendritic polymers. These include polyanionic polymers for the inhibition of virus attachment, polycationic complexes with DNA or RNA (polyplexes), and dendritic core-shell architectures for the encapsulation of drugs. In this Review an overview of polymer therapeutics is presented with a focus on concepts and examples that characterize the salient features of the drug-delivery systems.

Electrodes with High Power and High Capacity for Rechargeable Lithium Batteries.

Abstract: New applications such as hybrid electric vehicles and power backup require rechargeable batteries that combine high energy density with high charge and discharge rate capability. Using ab initio computational modeling, we identified useful strategies to design higher rate battery electrodes and tested them on lithium nickel manganese oxide [Li(Ni 0.5 Mn 0.5 )O 2 ], a safe, inexpensive material that has been thought to have poor intrinsic rate capability. By modifying its crystal structure, we obtained unexpectedly high rate-capability, considerably better than lithium cobalt oxide (LiCoO 2 ), the current battery electrode material of choice.

Acetylcholinesterase Inhibitors from Plants and Fungi

Abstract: This review describes 183 compounds obtained from plants and fungi which have been shown to inhibit acetylcholinesterase. The mechanism of action of cholinesterase, together with the binding sites, and, where this is known, the mode of action of inhibitors is described. The relative activities of the different compounds are recorded. The strongest inhibitors are generally alkaloids although some meroterpenoids from fungi have also been found to be active and display better selectivity.

Shape-Controlled Synthesis of Metal Nanostructures: The Case of Silver

Abstract: The concept of shape-controlled synthesis is discussed by investigating the growth mechanisms for silver nanocubes, nanowires, and nanospheres produced through a polymer-mediated polyol process. Experimental parameters, such as the concentration of AgNO(3) (the precursor to silver), the molar ratio between poly(vinylpyrrolidone) (PVP, the capping agent) and AgNO(3), and the strength of chemical interaction between PVP and various crystallographic planes of silver, were found to determine the crystallinity of seeds (e.g., single crystal versus decahedral multiply twinned particles). In turn, the crystallinity of a seed and the extent of the PVP coverage on the seed were both instrumental in controlling the morphology of final product. The ability to generate silver nanostructures with well-defined morphologies provides a great opportunity to experimentally and systematically study the relationship between their properties and geometric shapes.

Ganoderma — A Therapeutic Fungal Biofactory

Abstract: Ganoderma is a basidiomycete white rot fungus which has been used for medicinal purposes for centuries particularly in China, Japan and Korea. A great deal of work has been carried out on Ganoderma lucidum. The common names for preparations include Lingzhi, Munnertake, Sachitake, Reishi and Youngzhi. This review collates the publications detailing activities and compounds by representative species whilst considering the most valid claims of effectiveness. The biological activities reported of preparations from Ganoderma are remarkable and given most emphasis herein as distinct from structure/activity information. The metabolites consist of mainly polysaccharides and terpenoids. Many are activities against the major diseases of our time and so the present review is of great importance. The list of effects is huge ranging from anti-cancer to relieving blockages of the bladder. However, the reports have not all been tested scientifically with the convincing evidence is reserved for assays of pure compounds. It is a prime example of an ancient remedy being of great relevance to the modern era. There does appear to be an assumption that the therapeutic effects attributed to the fungus have been proven. The next step is to produce some effective medicines which may be hampered by problems of mass production.

Dissolution of Cellulose with Ionic Liquids and Its Application: A Mini‐Review

Abstract: Dissolution of cellulose with ionic liquids allows the comprehensive utilization of cellulose by combining two major green chemistry principles: using environmentally preferable solvents and bio-renewable feed-stocks. In this paper, the dissolution of cellulose with ionic liquids and its application were reviewed. Cellulose can be dissolved, without derivation, in some hydrophilic ionic liquids, such as 1-butyl-3-methylimidazolium chloride (BMIMCl) and 1-allyl-3-methylimidazolium chloride (AMIMCl). Microwave heating significantly accelerates the dissolution process. Cellulose can be easily regenerated from its ionic liquid solutions by addition of water, ethanol or acetone. After its regeneration, the ionic liquids can be recovered and reused. Fractionation of lignocellulosic materials and preparation of cellulose derivatives and composites are two of its typical applications. Although some basic studies, such as economical syntheses of ionic liquids and studies of ionic liquid toxicology, are still much needed, commercialization of these processes has made great progress in recent years.

Mollusk Shell Formation: A Source of New Concepts for Understanding Biomineralization Processes

Abstract: The biological approach to forming crystals is proving to be most surprising. Mollusks build their shells by using a hydrophobic silk gel, very acidic aspartic acid rich proteins, and apparently also an amorphous precursor phase from which the crystals form. All this takes place in a highly structured chitinous framework. Here we present ideas on how these disparate components work together to produce the highly structured pearly nacreous layer of the mollusk shell.

CuI‐Catalyzed Alkyne—Azide “Click” Cycloadditions from a Mechanistic and Synthetic Perspective

Abstract: CuI-catalyzed alkyne–azide cycloaddition provides 1,4-disubstituted 1,2,3-triazoles with such efficiency and scope that the transformation has been described as “click” chemistry. An overview of the mechanism of this remarkable reaction is presented as a means to explain the myriad of experimental results, particularly the various methods of catalyst generation, solvent and substrate effects, and choice of base or ligand. Both solution-phase and solid-phase results are comprehensively examined. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)

Polymers of Intrinsic Microporosity (PIMs): Organic Materials for Membrane Separations, Heterogeneous Catalysis and Hydrogen Storage

Abstract: This tutorial review describes recent research directed towards the synthesis of polymer-based organic microporous materials termed Polymers of Intrinsic Microporosity (PIMs). PIMs can be prepared either as insoluble networks or soluble polymers with both types giving solids that exhibit analogous behaviour to that of conventional microporous materials such as activated carbons. Soluble PIMs may be processed into thin films for use as highly selective gas separation membranes. Preliminary results also demonstrate the potential of PIMs for heterogeneous catalysis and hydrogen storage.

Gas Response Control Through Structural and Chemical Modification of Metal Oxide Films: State of the Art and Approaches

Abstract: In this review the structural and physical–chemical properties of nanoscaled metal oxide films (SnO2 and In2O3), aimed for solid state chemical sensors were analyzed. It has been shown that structural factor even for nanoscaled materials is complicated conception. One has to consider not only size, but also such a parameters as crystallite shape; nanoscopic structure; crystallographic orientation of nanocrystallites planes, forming gas sensing surface; film agglomeration; phase composition; surface architecture. The methods suitable for control of these structural and physical–chemical parameters have been discussed. Results, mainly obtained during study of both SnO2 and In2O3 thin films deposited by spray pyrolysis have been used for showing an opportunity of structural engineering of metal oxides for optimization of gas sensing characteristics.

Giant Electrocaloric Effect in Thin‐Film PbZr0.95Ti0.05O3.

Abstract: An applied electric field can reversibly change the temperature of an electrocaloric material under adiabatic conditions, and the effect is strongest near phase transitions. We demonstrate a giant electrocaloric effect (0.48 kelvin per volt) in 350-nanometer PbZr 0.95 Ti 0.05 O 3 films near the ferroelectric Curie temperature of 222°C. A large electrocaloric effect may find application in electrical refrigeration.