Showing papers in "ChemInform in 2005"

ZINC — A Free Database of Commercially Available Compounds for Virtual Screening.

Abstract: A critical barrier to entry into structure-based virtual screening is the lack of a suitable, easy to access database of purchasable compounds. We have therefore prepared a library of 727,842 molecules, each with 3D structure, using catalogs of compounds from vendors (the size of this library continues to grow). The molecules have been assigned biologically relevant protonation states and are annotated with properties such as molecular weight, calculated LogP, and number of rotatable bonds. Each molecule in the library contains vendor and purchasing information and is ready for docking using a number of popular docking programs. Within certain limits, the molecules are prepared in multiple protonation states and multiple tautomeric forms. In one format, multiple conformations are available for the molecules. This database is available for free download (http://zinc.docking.org) in several common file formats including SMILES, mol2, 3D SDF, and DOCK flexibase format. A Web-based query tool incorporating a molecular drawing interface enables the database to be searched and browsed and subsets to be created. Users can process their own molecules by uploading them to a server. Our hope is that this database will bring virtual screening libraries to a wide community of structural biologists and medicinal chemists.

Spin Crossover— An Overall Perspective

Abstract: In this chapter an outline is presented of the principal features of electronic spin crossover. The development of the subject is traced and the various modes of manifestation of spin transitions are presented. The role of cooperativity in influencing solid state behaviour is considered and the various strategies to strengthen it are addressed along with the chemical and physical perturbations which affect crossover behaviour. The role of intermediate spin states is discussed together with spin crossover in five-coordinate systems. The various techniques applied to monitoring a transition are presented briefly. An introduction to theoretical treatments is given and likely areas for future developments are suggested. Relevant review articles in the field are listed and reference to later chapters in the series is given where appropriate.

Revival of the Magnetoelectric Effect

Abstract: Recent research activities on the linear magnetoelectric (ME) effect?induction of magnetization by an electric field or of polarization by a magnetic field?are reviewed. Beginning with a brief summary of the history of the ME effect since its prediction in 1894, the paper focuses on the present revival of the effect. Two major sources for 'large' ME effects are identified. (i) In composite materials the ME effect is generated as a product property of a magnetostrictive and a piezoelectric compound. A linear ME polarization is induced by a weak ac magnetic field oscillating in the presence of a strong dc bias field. The ME effect is large if the ME coefficient coupling the magnetic and electric fields is large. Experiments on sintered granular composites and on laminated layers of the constituents as well as theories on the interaction between the constituents are described. In the vicinity of electromechanical resonances a ME voltage coefficient of up to 90?V?cm?1?Oe?1 is achieved, which exceeds the ME response of single-phase compounds by 3?5 orders of magnitude. Microwave devices, sensors, transducers and heterogeneous read/write devices are among the suggested technical implementations of the composite ME effect. (ii) In multiferroics the internal magnetic and/or electric fields are enhanced by the presence of multiple long-range ordering. The ME effect is strong enough to trigger magnetic or electrical phase transitions. ME effects in multiferroics are thus 'large' if the corresponding contribution to the free energy is large. Clamped ME switching of electrical and magnetic domains, ferroelectric reorientation induced by applied magnetic fields and induction of ferromagnetic ordering in applied electric fields were observed. Mechanisms favouring multiferroicity are summarized, and multiferroics in reduced dimensions are discussed. In addition to composites and multiferroics, novel and exotic manifestations of ME behaviour are investigated. This includes (i) optical second harmonic generation as a tool to study magnetic, electrical and ME properties in one setup and with access to domain structures; (ii) ME effects in colossal magnetoresistive manganites, superconductors and phosphates of the LiMPO4 type; (iii) the concept of the toroidal moment as manifestation of a ME dipole moment; (iv) pronounced ME effects in photonic crystals with a possibility of electromagnetic unidirectionality. The review concludes with a summary and an outlook to the future development of magnetoelectrics research.

Beyond Oil and Gas: The Methanol Economy

Abstract: Chapter 1: Introduction. Chapter 2: Coal in the Industrial Revolution, and Beyond. Chapter 3: History of Oil and Natural Gas. Oil Extraction and Exploration. Natural Gas. Chapter 4: Fossil Fuel Resources and Uses. Coal. Oil. Tar Sands. Oil Shale. Natural Gas. Coalbed Methane. Tight Sands and Shales. Methane Hydrates. Outlook. Chapter 5: Diminishing Oil and Gas Reserves. Chapter 6: The Continuing Need for Hydrocarbons and their Products. Fractional Distillation. Thermal Cracking. Chapter 7: Fossil Fuels and Climate Change. Mitigation. Chapter 8: Renewable Energy Sources and Atomic Energy. Hydropower. Geothermal Energy. Wind Energy. Solar Energy: Photovoltaic and Thermal. Electricity from Photovoltaic Conversion. Solar Thermal Power for Electricity Production. Electric Power from Saline Solar Ponds. Solar Thermal Energy for Heating. Economic Limitations of Solar Energy. Biomass Energy. Electricity from Biomass. Liquid Biofuels. Ocean Energy: Thermal, Tidal, and Wave Power. Tidal Energy. Waves. Ocean Thermal Energy. Nuclear Energy. Energy from Nuclear Fission Reactions. Breeder Reactors. The Need for Nuclear Power. Economics. Safety. Radiation Hazards. Nuclear Byproducts and Waste. Emissions. Nuclear Power: An Energy Source for the Future. Nuclear Fusion. Future Outlook. Chapter 9: The Hydrogen Economy and its Limitations. The Discovery and Properties of Hydrogen. The Development of Hydrogen Energy. The Production and Uses of Hydrogen. Hydrogen from Fossil Fuels. Hydrogen from Biomass. Photobiological Water Cleavage. Water Electrolysis. Hydrogen Production Using Nuclear Energy. The Challenge of Hydrogen Storage. Liquid Hydrogen. Compressed Hydrogen. Metal Hydrides and Solid Absorbents. Other Means of Hydrogen Storage. Hydrogen: Centralized or Decentralized Distribution? Safety of Hydrogen. Hydrogen in Transportation. Fuel Cells. History. Fuel Cell Efficiency. Hydrogen-Based Fuel Cells. PEM Fuel Cells for Transportation. Regenerative Fuel Cells. Outlook. Chapter 10: The "Methanol Economy": General Aspects. Chapter 11: Methanol as a Fuel and Energy Carrier. Properties and Historical Background. Present Uses of Methanol. Use of Methanol and Dimethyl Ether as Transportation Fuels. Alcohol as a Transportation Fuel in the Past. Methanol as Fuel in Internal Combustion Engines (ICE). Methanol and Dimethyl Ether as Diesel Fuels Substitute in Compression Ignition Engines. Biodiesel Fuel. Advanced Methanol-Powered Vehicles. Hydrogen for Fuel Cells from Methanol Reforming. Direct Methanol Fuel Cell (DMFC). Fuel Cells Based on Other Fuels and Biofuel Cells. Regenerative Fuel Cell. Methanol for Static Power and Heat Generation. Methanol Storage and Distribution. Methanol Price. Methanol Safety. Emissions from Methanol-Powered Vehicles. Methanol and the Environment. Methanol and Issues of Climate Change. Chapter 12: Production of Methanol from Syn-Gas to Carbon Dioxide. Methanol from Fossil Fuels. Production via Syn-Gas. Syn-Gas from Natural Gas. Methane Steam Reforming. Partial Oxidation of Methane. Autothermal Reforming and Combination of Steam Reforming and Partial Oxidation. Syn-Gas from CO2 Reforming. Syn-Gas from Petroleum and Higher Hydrocarbons. Syn-Gas from Coal. Economics of Syn-Gas Generation. Methanol through Methyl Formate. Methanol from Methane Without Syn-Gas. Selective Oxidation of Methane to Methanol. Catalytic Gas-Phase Oxidation of Methane. Liquid-Phase Oxidation of Methane to Methanol. Methanol Production through Mono-Halogenated Methanes. Microbial or Photochemical Conversion of Methane to Methanol. Methanol from Biomass. Methanol from Biogas. Aquaculture. Water Plants. Algae. Methanol from Carbon Dioxide. Carbon Dioxide from Industrial Flue Gases. Carbon Dioxide from the Atmosphere. Chapter 13: Methanol-Based Chemicals, Synthetic Hydrocarbons and Materials. Methanol-Based Chemical Products and Materials. Methanol Conversion to Olefins and Synthetic Hydrocarbons. Methanol to Olefin (MTO) Process. Methanol to Gasoline (MTG) Process. Methanol-Based Proteins. Outlook. Chapter 14: Future Perspectives. The "Methanol Economy" and its Advantages. Further Reading and Information. References. Index.

Charge‐Transfer and Energy‐Transfer Processes in π‐Conjugated Oligomers and Polymers: A Molecular Picture

Abstract: Inorganic semiconductor devices such as transistors have been instrumental in shaping the development of our society of information and communication. Recently, the electronics and photonics technologies have opened their materials base to organics, in particular π-conjugated oligomers and polymers. The goal with organics-based devices is not necessarily to attain or exceed the level of performance of inorganic semiconductor technologies (silicon is still the best at the many things that it does) but to benefit from a unique set of characteristics combining the electrical properties of (semi)conductors with the properties typical of plastics, that is, low cost, versatility of chemical synthesis, ease of processing, and flexibility. Interest in conjugated polymers picked up significantly after the 1976 discovery that they can be made highly electrically conducting following a redox chemical treatment.1 This discovery led to the 2000 Nobel Prize in Chemistry awarded to Alan Heeger, Alan MacDiarmid, and Hideki Shirakawa. By the mid-eighties, many research teams in both academia and industry were investigating π-conjugated oligomers and polymers for their nonlinear optical properties or their semiconducting properties, paving the way to the emergence of the fields of plastic electronics and photonics.2 The technological developments in plastic electronics and photonics have been required to gain a much better fundamental understanding of the nature of electronic excitations, charge carriers, and transport phenomena in ordered and disordered π-conjugated materials. Our aim in this contribution is to review a number of these issues and to highlight the fascinating chemistry and physics of these materials and the strong connection that exists in this field between basic and applied research. A major breakthrough in the field of organic electronics is the 1987 report by Tang and VanSlyke at Kodak of the first electroluminescent device based on a π-conjugated molecular material, tris(8-hydroxyquinoline) aluminum (Alq3). Shortly thereafter, Friend and his group at Cambridge discovered electroluminescence (EL) in a conjugated polymer, poly(paraphenylenevinylene) (PPV), thereby opening the way for the fabrication of polymer light-emitting diodes (LEDs).4 Typically, an organic LED is built5 by successively depositing the following materials on a transparent substrate: a transparent electrode made of a high work function compound, usually indium-tin oxide; one or several organic layers that in the case of molecular materials are generally deposited by vacuum sublimation6 or in the case of polymers are generally deposited by spin coating or ink-jet print* To whom correspondence should be addressed. Tel: 1-404-385-4986. Fax: 1-404-894-7452. E-mail: jean-luc.bredas@ chemistry.gatech.edu. † Georgia Institute of Technology. ‡ University of Mons-Hainaut. 4971 Chem. Rev. 2004, 104, 4971−5003

Bioreactor Performance in Anaerobic Digestion of Fruit and Vegetable Wastes

Abstract: This work reviews the potential of anaerobic digestion for material recovery and energy production from fruit and vegetable wastes (FVW). These wastes contain 8–18% total solids (TS), with a total volatile solids (VS) content of 86–92%. The organic fraction includes about 75% easy biodegradable matter (sugars and hemicellulose), 9% cellulose and 5% lignin. Anaerobic digestion of FVW was studied under different operating conditions using different types of bioreactors. It permits the conversion of 70–95% of organic matter to methane, with a volumetric organic loading rate (OLR) o f 1–6.8 g versatile solids (VS)/l day. A major limitation of anaerobic digestion of FVW is a rapid acidification of these wastes decreasing the pH in the reactor, and a larger volatile fatty acids production (VFA), which stress and inhibit the activity of methanogenic bacteria. Continuous two-phase systems appear as more highly efficient technologies for anaerobic digestion of FVW. Their greatest advantage lies in the buffering of the organic loading rate taking place in the first stage, allowing a more constant feeding rate of the methanogenic second stage. Using a two-stage system involving a thermophilic liquefaction reactor and a mesophilic anaerobic filter, over 95% volatile solids were converted to methane at a volumetric loading rate of 5.65 g VS/l d. The average methane production yield was about 420 l/kg added VS.

Integrated Nanoparticle—Biomolecule Hybrid Systems: Synthesis, Properties, and Applications

Abstract: Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

The Organic Chemistry of Sugars

Abstract: A DISCUSSION OF CARBOHYDRATE CHEMISTRY An Historical Overview R.J. Ferrier Introduction to Carbohydrates J. Kuszmann Protective Group Strategies S. Oscarson Glycosylation Methods P. Fugedi Oligosaccharide Synthesis P. Fugedi FROM SUGARS TO SUGAR-LIKE STRUCTURES TO NON-SUGARS Functionalization of Sugars D.E. Levy Strategies Towards C-Glycosides D.E. Levy From Sugars to Carba-Sugars M. Sollogoub and P. Sinay Sugars with Endocyclic Heteroatoms Other than Oxygen P. Greimel, J. Spreitz, F.K. Sprenger, A.E. Stutz, and T.M. Wrodnigg SUGARS AS TOOLS, CHIRAL POOL STARTING MATERIALS AND FORMIDABLE SYNTHETIC TARGETS Sugars as Chiral Auxiliaries N. Pleuss, G. Zech, B. Furman, and H. Kunz Sugars as Chiral Starting Materials in Enantiospecific Synthesis Y. Chapleur and F. Chretien Synthesis of Carbohydrate Containing Complex Natural Compounds K. Toshima Total Asymmetric Synthesis of Monosaccharides and Analogs P. Vogel ADDITIONAL TOPICS Combinatorial Carbohydrate Chemistry P. Arya and B. VNBS Sarma Glycopeptides M. Mogemark, J. Kihlberg Carbohydrate Mimetics in Drug Discovery O. Schwardt, H.C. Kolb, and B. Ernst

Biogenic Amines in Food

Abstract: Recent trends in food security are promoting an increasing search for trace compounds that can affect human health. Biogenic amines, the so-called natural amines with physiological significance, belong to this group of substances. Their amounts are usually increased during controlled or spontaneous microbial fermentation of food or in the course of food spoilage. Several methods exist for isolation, identifying, and determination of biogenic amines in food.

Atroposelective Synthesis of Axially Chiral Biaryl Compounds

Abstract: A rotationally hindered and thus stereogenic biaryl axis is the structurally and stereochemically decisive element of a steadily growing number of natural products, chiral auxiliaries, and catalysts. Thus, it is not surprising that significant advances have been made in the asymmetric synthesis of axially chiral biaryl compounds over the past decade. In addition to the classic approach (direct stereoselective aryl-aryl coupling), innovative concepts have been developed in which the asymmetric information is introduced into a preformed, but achiral-that is, symmetric or configurationally labile-biaryl compound, or in which an aryl--C single bond is stereoselectively transformed into an axis. This Review classifies these strategies according to their underlying concepts and critically evaluates their scope and limitations with reference to selected model reactions and applications. Furthermore, the preconditions required for the existence of axial chirality in biaryl compounds are discussed.

Synthesis, Properties, and Applications of Iron Nanoparticles

Abstract: Iron, the most ubiquitous of the transition metals and the fourth most plentiful element in the Earth's crust, is the structural backbone of our modern infrastructure. It is therefore ironic that as a nanoparticle, iron has been somewhat neglected in favor of its own oxides, as well as other metals such as cobalt, nickel, gold, and platinum. This is unfortunate, but understandable. Iron's reactivity is important in macroscopic applications (particularly rusting), but is a dominant concern at the nanoscale. Finely divided iron has long been known to be pyrophoric, which is a major reason that iron nanoparticles have not been more fully studied to date. This extreme reactivity has traditionally made iron nanoparticles difficult to study and inconvenient for practical applications. Iron however has a great deal to offer at the nanoscale, including very potent magnetic and catalytic properties. Recent work has begun to take advantage of iron's potential, and work in this field appears to be blossoming.

Ab Initio Quantum Simulation in Solid State Chemistry

Abstract: Molecular quantum chemistry and quantum mechanical simulation of solids have followed substantially independent paths and strategies for many years, with almost no reciprocal influence. In the implementation of computational schemes and formalisms, they started from different elementary models: either the hydrogen or helium atom like, for example, the parameterization of a correlation functional based on accurate He atom calculations by Colle and Salvetti, or the electron gas, which is the reference system of the local density approximation (LDA) to density functional theory (DFT). Moreover, if we compare the simplest real crystals, like lithium metal or sodium chloride, with the smallest molecule, H2, the much greater complexity of the solid system is

Living Radical Polymerization by the RAFT Process

Abstract: This paper presents a review of living radical polymerization achieved with thiocarbonylthio compounds [ZC(=S)SR] by a mechanism of reversible addition–fragmentation chain transfer (RAFT). Since we first introduced the technique in 1998, the number of papers and patents on the RAFT process has increased exponentially as the technique has proved to be one of the most versatile for the provision of polymers of well defined architecture. The factors influencing the effectiveness of RAFT agents and outcome of RAFT polymerization are detailed. With this insight, guidelines are presented on how to conduct RAFT and choose RAFT agents to achieve particular structures. A survey is provided of the current scope and applications of the RAFT process in the synthesis of well defined homo-, gradient, diblock, triblock, and star polymers, as well as more complex architectures including microgels and polymer brushes.

Copper Oxide Nanocrystals.

Abstract: It is well-known that inorganic nanocrystals are a benchmark model for nanotechnology, given that the tunability of optical properties and the stabilization of specific phases are uniquely possible at the nanoscale. Copper (I) oxide (Cu(2)O) is a metal oxide semiconductor with promising applications in solar energy conversion and catalysis. To understand the Cu/Cu(2)O/CuO system at the nanoscale, we have developed a method for preparing highly uniform monodisperse nanocrystals of Cu(2)O. The procedure also serves to demonstrate our development of a generalized method for the synthesis of transition metal oxide nanocrystals. Cu nanocrystals are initially formed and subsequently oxidized to form highly crystalline Cu(2)O. The volume change during phase transformation can induce crystal twinning. Absorption in the visible region of the spectrum gave evidence for the presence of a thin, epitaxial layer of CuO, which is blue-shifted, and appears to increase in energy as a function of decreasing particle size. XPS confirmed the thin layer of CuO, calculated to have a thickness of approximately 5 A. We note that the copper (I) oxide phase is surprisingly well-stabilized at this length scale.

The Cucurbit[n]uril Family

Abstract: In 1981, the macrocyclic methylene-bridged glycoluril hexamer (CB[6]) was dubbed "cucurbituril" by Mock and co-workers because of its resemblance to the most prominent member of the cucurbitaceae family of plants--the pumpkin. In the intervening years, the fundamental binding properties of CB[6]-high affinity, highly selective, and constrictive binding interactions--have been delineated by the pioneering work of the research groups of Mock, Kim, and Buschmann, and has led to their applications in waste-water remediation, as artificial enzymes, and as molecular switches. More recently, the cucurbit[n]uril family has grown to include homologues (CB[5]-CB[10]), derivatives, congeners, and analogues whose sizes span and exceed the range available with the alpha-, beta-, and gamma-cyclodextrins. Their shapes, solubility, and chemical functionality may now be tailored by synthetic chemistry to play a central role in molecular recognition, self-assembly, and nanotechnology. This Review focuses on the synthesis, recognition properties, and applications of these unique macrocycles.

Bose—Einstein Condensation of Excitons in Bilayer Electron Systems

Abstract: An exciton is the particle-like entity that forms when an electron is bound to a positively charged 'hole'. An ordered electronic state in which excitons condense into a single quantum state was proposed as a theoretical possibility many years ago. We review recent studies of semiconductor bilayer systems that provide clear evidence for this phenomenon and explain why exciton condensation in the quantum Hall regime, where these experiments were performed, is as likely to occur in electron–electron bilayers as in electron–hole bilayers. In current quantum Hall excitonic condensates, disorder induces mobile vortices that flow in response to a supercurrent and limit the extremely large bilayer counterflow conductivity.

Gas‐Phase Radical Chemistry in the Troposphere

Abstract: Atmospheric free radicals are low concentration, relatively fast reacting species whose influence is felt throughout the atmosphere. Reactive radicals have a key role in maintaining a balanced atmospheric composition through their central function in controlling the oxidative capacity of the atmosphere. In this tutorial review, the chemistry of three main groups of atmospheric radicals HOx, NOx and XOx (X = Cl, Br, I) are examined in terms of their sources, interconversions and sinks. Key examples of the chemistry are given for each group of radicals in their atmospheric context.