Showing papers in "Topics in Current Chemistry in 2011"

Charge transport in organic semiconductors.

Abstract: Modern optoelectronic devices, such as light-emitting diodes, field-effect transistors and organic solar cells require well controlled motion of charges for their efficient operation. The understanding of the processes that determine charge transport is therefore of paramount importance for designing materials with improved structure-property relationships. Before discussing different regimes of charge transport in organic semiconductors, we present a brief introduction into the conceptual framework in which we interpret the relevant photophysical processes. That is, we compare a molecular picture of electronic excitations against the Su-Schrieffer-Heeger semiconductor band model. After a brief description of experimental techniques needed to measure charge mobilities, we then elaborate on the parameters controlling charge transport in technologically relevant materials. Thus, we consider the influences of electronic coupling between molecular units, disorder, polaronic effects and space charge. A particular focus is given to the recent progress made in understanding charge transport on short time scales and short length scales. The mechanism for charge injection is briefly addressed towards the end of this chapter.

Micromixing Within Microfluidic Devices

Abstract: Micromixing is a crucial process within microfluidic systems such as micro total analysis systems (μTAS). A state-of-art review on microstructured mixing devices and their mixing phenomena is given. The review first presents an overview of the characteristics of fluidic behavior at the microscale and their implications in microfluidic mixing processes. According to the two basic principles exploited to induce mixing at the microscale, micromixers are generally classified as being passive or active. Passive mixers solely rely on pumping energy, whereas active mixers rely on an external energy source to achieve mixing. Typical types of passive micromixers are discussed, including T- or Y-shaped, parallel lamination, sequential, focusing enhanced mixers, and droplet micromixers. Examples of active mixers using external forces such as pressure field, electrokinetic, dielectrophoretic, electrowetting, magneto-hydrodynamic, and ultrasound to assist mixing are presented. Finally, the advantages and disadvantages of mixing in a microfluidic environment are discussed.

Introduction to Fragment-Based Drug Discovery

Abstract: Fragment-based drug discovery (FBDD) has emerged in the past decade as a powerful tool for discovering drug leads. The approach first identifies starting points: very small molecules (fragments) that are about half the size of typical drugs. These fragments are then expanded or linked together to generate drug leads. Although the origins of the technique date back some 30 years, it was only in the mid-1990s that experimental techniques became sufficiently sensitive and rapid for the concept to be become practical. Since that time, the field has exploded: FBDD has played a role in discovery of at least 18 drugs that have entered the clinic, and practitioners of FBDD can be found throughout the world in both academia and industry. Literally dozens of reviews have been published on various aspects of FBDD or on the field as a whole, as have three books (Jahnke and Erlanson, Fragment-based approaches in drug discovery, 2006; Zartler and Shapiro, Fragment-based drug discovery: a practical approach, 2008; Kuo, Fragment based drug design: tools, practical approaches, and examples, 2011). However, this chapter will assume that the reader is approaching the field with little prior knowledge. It will introduce some of the key concepts, set the stage for the chapters to follow, and demonstrate how X-ray crystallography plays a central role in fragment identification and advancement.

Synthesis of Pyrrole and Carbazole Alkaloids

Abstract: An overview of recent transition metal-catalyzed syntheses of pyrroles and carbazoles is presented The focus is on methods which have been applied to the preparation of biologically active naturally occurring pyrrole and carbazole alkaloids For pyrroles, special attention is paid to silver(I)-catalyzed cyclization reactions For carbazoles, iron(0)-mediated and palladium(0/II)-catalyzed cyclization reactions are highlighted and their broad range of applications is discussed

Nanoparticles in liquid crystals and liquid crystalline nanoparticles.

Abstract: Combinations of liquid crystals and materials with unique features as well as properties at the nanoscale are reviewed. Particular attention is paid to recent developments, i.e., since 2007, in areas ranging from liquid crystal-nanoparticle dispersions to nanomaterials forming liquid crystalline phases after surface modification with mesogenic or promesogenic moieties. Experimental and synthetic approaches are summarized, design strategies compared, and potential as well as existing applications discussed. Finally, a critical outlook into the future of this fascinating field of liquid crystal research is provided.

Synthesis of polypeptides by ring-opening polymerization of α-amino acid N-carboxyanhydrides.

Abstract: This chapter summarizes methods for the synthesis of polypeptides by ring-opening polymerization. Traditional and recently improved methods used to polymerize α-amino acid N-carboxyanhydrides (NCAs) for the synthesis of homopolypeptides are described. Use of these methods and strategies for the preparation of block copolypeptides and side-chain-functionalized polypeptides are also presented, as well as an analysis of the synthetic scope of different approaches. Finally, issues relating to obtaining highly functional polypeptides in pure form are detailed.

Molecularly imprinted polymers.

Abstract: Molecular imprinting is a process that allows for the synthesis of artificial receptors for a given target molecule based on synthetic polymers. The target molecule acts as a template around which interacting and cross-linking monomers are arranged and co-polymerized to form a cast-like shell. In essence, a molecular memory is imprinted in the polymer, which is now capable of selectively binding the target. Molecularly imprinted polymers (MIPs) thus possess the most important feature of biological antibodies - specific molecular recognition. They can thus be used in applications where selective binding events are of importance, such as immunoassays, affinity separation, biosensors, and directed synthesis and catalysis. Since its beginnings in the 1970s, the technique of molecular imprinting has greatly diversified during the last decade both from a materials point of view and from an application point of view. Still, there is much room for further improvement. The key challenges, in particular the binding site homogeneity and water compatibility of MIPs, and the possibility of synthesizing MIPs specific for proteins, are actively addressed by research groups over the World. Other important points are the conception of composite materials based on MIPs, in order to include additional interesting properties into the material, and the synthesis of very small and quasi-soluble MIPs, close in size to proteins.

Peptide-Based and Polypeptide-Based Hydrogels for Drug Delivery and Tissue Engineering

Abstract: Bio-inspired materials chemistry is an interdisciplinary field in which biological functions and structures are used as inspirations to construct a wide variety of new synthetic materials and devices. Peptide sequences that provide structural, mechanical, chemical, or biological function can be borrowed from nature and fused into synthetic poly(amino acid) chains without replicating the entire natural biomolecular sequence. Supramolecular self-assembly of such rationally designed peptidic sequences is emerging as a promising route to novel biofunctional materials. This chapter highlights recent progress in bio-inspired peptide and polypeptide hydrogels that have potential biomedical and pharmaceutical applications. The focus is on synthetic or biosynthetic poly(amino acid) hydrogels based on α-helical coiled-coils, β-sheets, dipeptides, peptide amphiphiles, elastin-like peptides, and on hybrids of organic polypeptides or polymers functionalized with peptides.

The Use of Residual Dipolar Coupling in Studying Proteins by NMR

Abstract: The development of residual dipolar coupling (RDC) in protein NMR spectroscopy, over a decade ago, has become a useful and almost routine tool for accurate protein solution structure determination. RDCs provide orientation information of magnetic dipole–dipole interaction vectors within a common reference frame. Its measurement requires a nonisotropic orientation, through a direct or indirect magnetic field alignment, of the protein in solution. There has been recent progress in the developments of alignment methods to allow the measurement of RDC and of methods to analyze the resulting data. In this chapter we briefly go through the mathematical expressions for the RDC and common descriptions of the alignment tensor, which may be represented using either Saupe order or the principal order matrix. Then we review the latest developments in alignment media. In particular we looked at the lipid-compatible media that allow the measurement of RDCs for membrane proteins. Other methods including conservative surface residue mutation have been invented to obtain up to five orthogonal alignment tensors that provide a potential for de novo structure and dynamics study using RDCs exclusively. We then discuss approximations assumed in RDC interpretations and different views on dynamics uncovered from the RDC method. In addition to routine usage of RDCs in refining a single structure, novel applications such as ensemble refinement against RDCs have been implemented to represent protein structure and dynamics in solution. The RDC application also extends to the study of protein–substrate interaction as well as to solving quaternary structure of oligomer in equilibrium with a monomer, opening an avenue for RDCs in high-order protein structure determination.

Constitutional dynamic chemistry: bridge from supramolecular chemistry to adaptive chemistry.

Abstract: Supramolecular chemistry aims at implementing highly complex chemical systems from molecular components held together by non-covalent intermolecular forces and effecting molecular recognition, catalysis and transport processes. A further step consists in the investigation of chemical systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels.

Real-world predictions from ab initio molecular dynamics simulations.

Abstract: In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.

Photocatalytic reduction of CO₂: from molecules to semiconductors.

Abstract: We are facing three serious problems related to fossil resources, i.e., shortage of energy, shortage of carbon resources, and the global worming problem. Development of practical systems for converting CO₂ to useful chemicals using solar light, i.e., photocatalytic CO₂ reduction systems, should be one of the best solutions for these problems. In this article, we review photocatalytic CO₂ reduction systems, which are classified in two categories: (1) homogeneous reaction systems mainly using transition metal complexes, and (2) heterogeneous systems mainly using inorganic semiconductor as a light absorber.

Drug Delivery by Water-Soluble Organometallic Cages

Abstract: Until recently, organometallic derivatives were generally viewed as moisture- and air-sensitive compounds, and consequently very challenging to synthesise and very demanding in terms of laboratory requirements (Schlenk techniques, dried solvent, glove box). However, an increasing number of stable, water-soluble organometallic compounds are now available, and organometallic chemistry in aqueous phase is a flourishing area of research. As such, coordination-driven self-assemblies using organometallic building blocks are compatible with water, thus opening new perspectives in bio-organometallic chemistry.

Genetics of Prion Disease

Abstract: Prion diseases or transmissible spongiform encephalopathies (TSEs) are neurodegenerative disorders of humans and animals for which there are no effective treatments or cure. They include Creutzfeldt-Jakob disease (CJD) in humans and sheep scrapie, bovine spongiform encephalopathy (BSE) and chronic wasting disease (CWD) in cervids. The prion protein (PrP) is central to the disease process. An abnormal form of PrP is generally considered to be the sole or principal component of the infectious agent and a multimeric isomer (PrPSc) is deposited in affected brains. Inherited prion diseases are caused by over 30 mutations in the prion protein gene (PRNP) and common polymorphisms can have a considerable affect on susceptibility and phenotype. Susceptibility and incubation time are also partly determined by other (non-PRNP) genetic modifiers. Understanding how these other genes modify prion diseases may lead to insights into biological mechanisms. Several approaches including human genome wide association studies (GWAS), mouse mapping and differential expression studies are now revealing some of these genes which include RARB (retinoic acid receptor beta), the E3 ubiquitin ligase HECTD2 and SPRN (Shadoo, shadow of prion protein gene).

Powder Diffraction Crystallography of Molecular Solids

Abstract: Many important crystalline solids cannot be prepared as single crystals of suitable size and quality for structural characterization by conventional single-crystal X-ray diffraction techniques and can instead be prepared only as microcrystalline powders. However, recent advances in techniques for determining crystal structures directly from powder X-ray diffraction data have created a unique opportunity for establishing structural properties of such materials. This chapter surveys the applications of powder X-ray diffraction across various aspects of structural and materials chemistry, focusing mainly on the opportunities that have emerged in recent years for carrying out complete crystal structure determination from powder X-ray diffraction data and giving particular emphasis to the case of molecular crystal structures. The current scope and future potential of powder X-ray diffraction as a strategy for crystal structure determination are discussed, and examples of applications across several disciplines of materials chemistry are presented.

Fluorinated liquid crystals: design of soft nanostructures and increased complexity of self-assembly by perfluorinated segments.

Abstract: The effects of perfluorinated and semiperfluorinated hydrocarbon units on the self-assembly of rod-like, disc-like, polycatenar, taper- and star-shaped, dendritic, and bent-core liquid crystalline (LC) materials is reviewed. The influence of fluorinated segments is analyzed on the basis of their contributions to the cohesive energy density, molecular shape, conformational flexibility, micro-segregation, space filling, and interface curvature. Though the focus is on recent progress in the last decade, previous main contributions, general aspects of perfluorinated organic molecules, and the basics of LC self-assembly are also briefly discussed to provide a complete overall picture. The main focus is on structure-property-relations and the use of micro-segregation to tailor mesophase morphologies. Especially polyphilic molecules with perfluorinated segments provide new modes of LC self-assembly, leading to ordered fluids with periodic multi-compartment structures and enhanced complexity compared to previously known systems.

Targeting protein-protein interactions and fragment-based drug discovery.

Abstract: Protein-protein interactions (PPI) are integral to the majority of biological functions. Targeting these interactions with small molecule inhibitors is of increased interest both in academia as well as in the pharmaceutical industry, both for therapeutic purposes and in the search for chemical tools for basic science. Although the number of well-characterised examples is still relatively modest, it is becoming apparent that many different kinds of interactions can be inhibited using drug-like small molecules. Compared to active site targeting, PPI inhibition suffers from the particular problem of more exposed and less defined binding sites, and this imposes significant experimental challenges to the development of PPI inhibitors. PPI interfaces are large, up to thousands of square angstroms, and there is still debate as to what part of the interface one should target. We will review recent developments in the field of PPI inhibition, with emphasis on fragment-based methods, and discuss various factors one should take into account when developing small molecule inhibitors targeted at PPI interfaces.

Synthesis of Morphine Alkaloids and Derivatives

Abstract: This review summarizes recent developments in the total synthesis of morphine alkaloids and some of the semisynthetic derivatives. The literature is covered for the period of 5 years after the publication of the last review in 2005. The syntheses that appeared in this period are covered in detail and are placed in the context of all syntheses of opiate alkaloids since the original one published by Gates in 1952. The introduction covers the historical aspects of total synthesis of these alkaloids. The synthesis of some of the medicinally useful derivatives is reviewed in the last section along with some of the methodology required for their preparation.

Lycopodium alkaloids: isolation and asymmetric synthesis.

Abstract: Lycopodium alkaloids have attracted the attention of many natural product chemists and synthetic organic chemists due to their important biological activities and unique skeletal characteristics. In this review we describe isolation and asymmetric syntheses of several new alkaloids such as lycoposerramines-C, -V, -W, and cernuine, and show that asymmetric total synthesis played a key role in elucidating the structures of these complex natural products.

Spontaneous achiral symmetry breaking in liquid crystalline phases.

Abstract: It is well known that spontaneous deracemization or spontaneous chiral resolution occasionally occurs when racemic molecules are crystallized. However, it is not easy to believe such phenomenon will occur when forming liquid crystal phases. Spontaneous chiral domain formation is introduced, when molecules form particular liquid crystal phases. Such molecules possess no chiral carbon but may have axial chirality. However, the potential barrier between two chiral states is low enough to allow mutual transformation even at room temperature. Therefore the systems are essentially not racemic but nonchiral or achiral. First, enhanced chirality by doping chiral nematic liquid crystals with nonchiral molecules is described. Emphasis is made on ester molecules for their anomalous behavior. Second, spontaneous chiral resolution is discussed. Three examples with rod-, bent-, and disk-shaped molecules are shown to give such phenomena. Particular attention will be paid to controlling enantiomeric excess (ee). Actually, almost 100% ee was obtained by applying some external chiral stimuli. This is very noteworthy in the sense that we can create chiral molecules (chiral field) without using any chiral species.

Prion protein and its conformational conversion: a structural perspective.

Abstract: The key molecular event in the pathogenesis of prion diseases is the conformational conversion of a cellular prion protein, PrP(C), into a misfolded form, PrP(Sc). In contrast to PrP(C) that is monomeric and α-helical, PrP(Sc) is oligomeric in nature and rich in β-sheet structure. According to the "protein-only" model, PrP(Sc) itself represents the infectious prion agent responsible for transmissibility of prion disorders. While this model is supported by rapidly growing experimental data, detailed mechanistic and structural aspects of prion protein conversion remain enigmatic. In this chapter we describe recent advances in understanding biophysical and biochemical aspects of prion diseases, with a special focus on structural underpinnings of prion protein conversion, the structural basis of prion strains, and generation of prion infectivity in vitro from bacterially-expressed recombinant PrP.

Fragment screening using X-ray crystallography.

Abstract: The fragment-based approach is now well established as an important component of modern drug discovery. A key part in establishing its position as a viable technique has been the development of a range of biophysical methodologies with sufficient sensitivity to detect the binding of very weakly binding molecules. X-ray crystallography was one of the first techniques demonstrated to be capable of detecting such weak binding, but historically its potential for screening was under-appreciated and impractical due to its relatively low throughput. In this chapter we discuss the various benefits associated with fragment-screening by X-ray crystallography, and describe the technical developments we have implemented to allow its routine use in drug discovery. We emphasize how this approach has allowed a much greater exploitation of crystallography than has traditionally been the case within the pharmaceutical industry, with the rapid and timely provision of structural information having maximum impact on project direction.

Site-Directed Spin Labeling of Membrane Proteins

Abstract: EPR spectroscopy of site-directed spin labeled membrane proteins is at present a common and valuable biophysical tool to study structural details and conformational transitions under conditions relevant to function. EPR is considered a complementary approach to X-ray crystallography and NMR because it provides detailed information on (1) side chain dynamics with an exquisite sensitivity for flexible regions, (2) polarity and water accessibility profiles across the membrane bilayer, and (3) distances between two spin labeled side chains during protein functioning. Despite the drawback of requiring site-directed mutagenesis for each new piece of information to be collected, EPR can be applied to any complex membrane protein system, independently of its size. This chapter describes the state of the art in the application of site-directed spin labeling (SDSL) EPR to membrane proteins, with specific focus on the different types of information which can be obtained with continuous wave and pulsed techniques.

Chronic Wasting Disease

Abstract: Chronic wasting disease (CWD) is a prion disease of free-ranging and farmed ungulates (deer, elk, and moose) in North America and South Korea. First described by the late E.S. Williams and colleagues in northern Colorado and southern Wyoming in the 1970s, CWD has increased tremendously both in numerical and geographical distribution, reaching prevalence rates as high as 50% in free-ranging and >90% in captive deer herds in certain areas of USA and Canada. CWD is certainly the most contagious prion infection, with significant horizontal transmission of infectious prions by, e.g., urine, feces, and saliva. Dissemination and persistence of infectivity in the environment combined with the appearance in wild-living and migrating animals make CWD presently uncontrollable, and pose extreme challenges to wild-life disease management. Whereas CWD is extremely transmissible among cervids, its trans-species transmission seems to be restricted, although the possible involvement of rodent and carnivore species in environmental transmission has not been fully evaluated. Whether or not CWD has zoonotic potential as had Bovine spongiform encephalopathy (BSE) has yet to be answered. Of note, variant Creutzfeldt–Jakob disease (vCJD) was only detected because clinical presentation and age of patients were significantly different from classical CJD. Along with further understanding of the molecular biology and pathology of CWD, its transmissibility and species restrictions and development of methods for preclinical diagnosis and intervention will be crucial for effective containment of this highly contagious prion disease.

Molecular logic gates and luminescent sensors based on photoinduced electron transfer.

Abstract: The competition between Photoinduced electron transfer (PET) and other de-excitation pathways such as fluorescence and phosphorescence can be controlled within designed molecular structures. Depending on the particular design, the resulting optical output is thus a function of various inputs such as ion concentration and excitation light dose. Once digitized into binary code, these input-output patterns can be interpreted according to Boolean logic. The single-input logic types of YES and NOT cover simple sensors and the double- (or higher-) input logic types represent other gates such as AND and OR. The logic-based arithmetic processors such as half-adders and half-subtractors are also featured. Naturally, a principal application of the more complex gates is in multi-sensing contexts.

Cycloisomerization of 1,n-Enynes Via Carbophilic Activation

Abstract: Metal-catalyzed cycloisomerization of 1,n-enynes has appeared as a highly attractive methodology for the synthesis of original carbo- and heterocycles. This chapter intends to propose an overview of the recent and seminal advances in 1,n-enynes cycloisomerization reactions in the presence of carbophilic transition metals. The recent mechanistic insights, the enantioselective versions, and the applications in total synthesis are highlighted.

Selective Fluoroalkylation of Organic Compounds by Tackling the "Negative Fluorine Effect"

Abstract: The presence of fluorine on a carbanion center will dramatically influence the nucleophilic alkylation reactions. Based on our own experience, we noticed that the fluorine substitution on the carbanionic carbon poses a negative effect in many nucleophilic fluoroalkylation reactions [we propose this effect as “negative fluorine effect (NFE)”]. Two factors were believed to contribute to the NFE: (1) thermal instability of fluorinated carbanions caused by α-elimination (self-decomposition) and (2) the intrinsic nucleophilicity of fluorinated carbanion influenced by the fluorine atoms (such as hard/soft nature of the fluorinated carbanions). By tackling the NFE, our research group has attempted to design nucleophilic fluoroalkylation reactions with fluorinated sulfones and related reagents. These results were summarized as four methods to modulate the fluoroalkylation reactions: (1) changing the number of fluorine atoms, (2) slightly changing the neighboring groups, (3) changing the metal counterion, including using carbon-metal covalent bond to tune the reactivity, and (4) enhancing the generation of carbene species.

Indole Prenylation in Alkaloid Synthesis

Abstract: Important biologically active indole alkaloids are decorated with prenyl (3,3-dimethylallyl) and tert-prenyl (1,1-dimethylallyl) groups. Covering the literature until the end of 2010, this review article comprehensively summarises and discusses the currently available technologies of prenylation and tert-prenylation of indoles, which have been applied in natural products total syntheses or could be applied there in the near future. We focus on those procedures which introduce the C5 units in one step, organised according to the indole position to be functionalised. Key strategies include electrophilic and nucleophilic prenylation and tert-prenylation, prenyl and tert-prenyl rearrangements, transition metal-mediated reactions and enzymatic methods.

Radicals in Transition Metal Catalyzed Reactions? Transition Metal Catalyzed Radical Reactions? – A Fruitful Interplay Anyway

Abstract: This review summarizes the current status of radical-based transition metal catalyzed reactions in organic chemistry. The underlying features of radical generation from transition metal complexes and radical reactivity in the framework of transition metal catalysis are discussed. The available arsenal to detect radicals in transition metal catalyzed transformations is presented. Available strategies to combine radical intermediates with transition metal catalysis are outlined. In the main part the currently known synthetic methodology of transition metal catalyzed reactions proceeding via radical intermediates is discussed. This part covers catalytic radical reactions involving group 4 to group 7 elements.

Solid-state (19)F-NMR of peptides in native membranes.

Abstract: To understand how membrane-active peptides (MAPs) function in vivo, it is essential to obtain structural information about them in their membrane-bound state. Most biophysical approaches rely on the use of bilayers prepared from synthetic phospholipids, i.e. artificial model membranes. A particularly successful structural method is solid-state NMR, which makes use of macroscopically oriented lipid bilayers to study selectively isotope-labelled peptides. Native biomembranes, however, have a far more complex lipid composition and a significant non-lipidic content (protein and carbohydrate). Model membranes, therefore, are not really adequate to address questions concerning for example the selectivity of these membranolytic peptides against prokaryotic vs eukaryotic cells, their varying activities against different bacterial strains, or other related biological issues.