Communication: Density-functional theory for inhomogeneous hyperbranched polymeric fluids: polydisperse effect of degree of branching

We developed a new density-functional theory (DFT) for inhomogeneous hyperbranched polymers that is able to describe the polydisperse degree of branching quantitatively. The topological contributions of the polymer chains to the Helmholtz free energy take into account the effect of triple connections that are absent in previous DFT investigations. One key advantage of the new theory is that the computational cost shows only a linear relationship with the molecular weight (rather than an exponential relationship). The practical utility of the new DFT is illustrated by investigating colloidal stability in the presence of monodisperse and polydisperse hyperbranched polymers.     

Nucleic acid based biosensors: the desires of the user

The need for nucleic acid based diagnostic tests has increased enormously in the last few years. On the one hand, this has been stimulated by the discovery of new hereditary genetic disease loci following the completion of the Human Genome Project, but also by the presence of new rapidly spreading viral threats, such as that of the SARS epidemic, or even micro-organisms released for the purpose of biological warfare. As in many instances rapid diagnoses of specific target genetic loci is required, new strategies have to be developed, which will allow this to be achieved directly at the point-of-care setting. One of these avenues being explored is that of biosensors. In this review, we provide an overview of the current state of the art concerning the high-throughput analysis of nucleic acids, and address future requirements, which will hopefully be met by new biosensor-based developments.     

Febantel: looking for new polymorphs

The aim of this work was to search for new polymorphic forms of febantel, an anthelminthic drug of great present interest for the veterinary industry. Solvent-based recrystallization, thermal and mechanical treatments and spray drying were chosen to discover new solid forms. The solids obtained were physicochemically characterized by thermal techniques (DSC and TG), FTIR spectroscopy, laboratory and synchrotron X-ray powder diffraction and scanning electron microscopy. Our work leads to obtain a new solid form never described in the literature. In particular, the new polymorph was obtained by the anti-solvent method and the crystallization from isopropanol. The experimental conditions of crystallization favorable to the formation of the highest amount of the new solid phase were selected. The new phase shows a thermal, spectroscopic and diffractometric behavior unique. Furthermore, the preliminary structure investigation suggests two possible crystal systems: an orthorhombic or a monoclinic one, with really comparable lattice parameters and cell volume. Measurements put into evidence that the new phase is a metastable polymorph that is in monotropic relationship with the stable and known form.

     

Electrodialysis in a non-aqueous medium: production of sodium methoxide

A method is described for the production of an alkali alkoxide from an alcohol and a salt by way of electrodialysis. The principle involves the double decomposition of a salt and an alcohol. In effect, an alcohol is split into protons and alkoxide ions, the latter forming the alkoxide with the metal ions of the salt. This finding opens new venues of application and offers opportunities for new chemical processes.     

Selective complexation of N-alkylpyridinium salts: binding of NAD+ in water

A new class of receptor molecules is presented that is highly selective for N-alkylpyridinium ions and electron-poor aromatics. Its key feature is the combination of a well-preorganized molecular clip with an electron-rich inner cavity and strategically placed, flanking bis-phosphonate monoester anions. This shape and arrangement of binding sites attracts predominantly flat electron-poor aromatics in water, binds them mainly by pi-cation, pi-pi, CH-pi, and hydrophobic interactions, and leads to their highly efficient desolvation. NAD(+) and NADP, the important cofactors of many redox enzymes, are recognized by the new receptor molecule, which embraces the catalytically active nicotinamide site and the adenine unit. Even nucleosides such as adenosine are likewise drawn into the clip's cavity. Complex formation and structures were examined by one- and two-dimensional NMR spectroscopy, Job plot analyses, and isothermal titration microcalorimetric (ITC) measurements, as well as quantum chemical calculations of (1)H NMR shifts. The new receptor molecule is a promising tool for controlling enzymatic oxidation processes and for DNA chemistry.     

Pulsed laser polymerization: Analytical solutions of the chain length distribution revisited

A new solution for chain‐length distributions of “dead” polymer and their moments (obtained by solving the coupled system of non‐linear differential equations in full generality) is presented and compared to existing theoretical and numerical approaches. The new solution for chain‐length distributions (cld) (at least numerically) coincides with our earlier results (analytical solution as well as data computed by use of numerical models) which were obtained by starting with strict coupling of time and degree of polymerization followed by an a posteriori Poisson broadening. (As a consequence the new solution also coincides with a numerical treatment based on fluctuating propagation probabilities by introducing an a priori Poisson broadening.) In turn, for termination exclusively by disproportionation this earlier solution is fully equivalent to Aleksandrov's approach (after some modification of the latter expression). This holds true also for termination exclusively by combination if one corrects for errors in Aleksandrov's derivation. The new solution of the moments of the cld agrees with our former results, while Aleksandrov's expressions are shown to be worthless under the usual experimental conditions.     

An improvement of Davidson's iteration method: Applications to MRCI and MRCEPA calculations

Davidson's method is widely used for finding the lowest eigenvalues of large matrices. Recently, mathematicians have shown that Davidson's derivation could be improved. They have corrected the derivation yielding a new iteration method. In this article this new method is adapted for realistic MRCI and MRCEPA calculations. Results show that the new method converges significantly faster in H₂O and O₂ with moderately elongated bonds than Davidson's original method. The new method offers new insights into the rate of convergence of Davidson's original method. © 1996 by John Wiley & Sons, Inc.     

The gene-protein database of Escherichia coli: edition 4.

The gene-protein database of Escherichia coli has as its core an index that links each of the protein spots from a two-dimensional polyacrylamide gel to the gene that encodes the protein. Additional information about each protein and its gene is generated from two-dimensional gel analysis or collated from the literature to form the database. Earlier editions of the database have provided periodic updates of information. The current edition does this, but also introduces a new reference gel image produced by an electrophoresis system recently adopted in this laboratory. The new gel system was chosen because it offers an improved opportunity for other investigations to produce close replicas of the reference gel pattern, thereby allowing easier access to the information of the database and encouraging independent contribution to the database. The new gel format also is larger and hence more compatible with computer assisted image analysis, which has become essential for a project of this magnitude. This edition continues the use of the former reference gel images, but adds a reference image of an equilibrium gel of E. coli strain W3110 produced by the new standardized gel system. At this time, 55% of the protein spots annotated on the previous equilibrium reference gel for this organism have been located on the new reference image, and these identifications are included in the tables of the database.     

DelPhi Suite: New Developments and Review of Functionalities

Electrostatic potential, energies, and forces affect virtually any process in molecular biology, however, computing these quantities is a difficult task due to irregularly shaped macromolecules and the presence of water. Here, we report a new edition of the popular software package DelPhi along with describing its functionalities. The new DelPhi is a C++ object-oriented package supporting various levels of multiprocessing and memory distribution. It is demonstrated that multiprocessing results in significant improvement of computational time. Furthermore, for computations requiring large grid size (large macromolecular assemblages), the approach of memory distribution is shown to reduce the requirement of RAM and thus permitting large-scale modeling to be done on Linux clusters with moderate architecture. The new release comes with new features, whose functionalities and applications are described as well. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Cyclic peptide helices: a hybrid beta-hairpin/beta-helical supersecondary structure

This communication describes the design and characterization of a new peptide motif that is a hybrid of beta-hairpin and beta-helical structures. This motif was supported by CD and IR spectrocopies in nonpolar organic solvents and was confirmed by NMR spectroscopy and structure calculations using NMR-derived restraints. The beta-hairpin/beta-helical motif represents a potentially attractive new structural template for a variety of possible applications in biomolecular design, such as ligands for macromolecular targets and building blocks for new protein architectures.     

Synthesis of 1H-indazole: a combination of experimental and theoretical studies

A new practical synthesis of 1H-indazole is presented. A previous mechanism for the cyclization step is proved to be nonfeasible and a hydrogen bond propelled mechanism is proposed. The new mechanism is suitable for similar cyclization, and a new reaction is predicted.     

Nanostructuration of soft hydrogels: synthesis and characterization of saccharidic methacrylate gels

With the tremendous development of biosensors, there is a strong need in new biocompatible materials avoiding possible denaturing of biological species, which can be easily processed with already existing technologies. The scope of this study was to develop new hydrogels which could be nanostructured by common lithographic methods. Therefore, new methacrylate hydrogels are described, which include functionalized monomers bearing either neutral groups, such as saccharidic moieties, anionic, or cationic groups. The gels have been synthesized by redox or photochemical-initiated radical polymerization. Their porosity has been characterized by thermoporometry, AFM, and electronic microscopy. The kinetics of the photocross-linking has been analyzed by piezorheometry on some of the materials and has been shown to be compatible with technological process time range. Although the obtained hydrogels are soft, their nanostructuration into 500-nm patterns could be performed by nanoimprint photolithography process, and these patterns were observed to be stable for several months.     

Synthesis of heterocycles : Synthesis of 4H-1,4-benzothiazines

A new synthesis of fluorinated 4H-1,4-benzothiazines is being reported for the first time, obtained by condensing O-aminobenzenethiol with fluorinated β-diketones. An oxidative cyclisation mechanism, involving an intramolecular nucleophilic attack in an intermediate enamine system is suggested.     

Nucleophilic addition to electron-rich heteroaromatics: dearomatizing anionic cyclizations of pyrrolecarboxamides

[reaction: see text] Despite its electron-rich nature, a pyrrole ring is susceptible to intramolecular nucleophilic attack by organolithiums. The resulting dearomatizing anionic cyclization yields new 5- or 7-membered heterocyclic rings. Formation of a new 5-membered ring, by cyclization of an N-benzylpyrrolecarboxamide, is accompanied by ring opening of the original pyrrole to yield 3-aminovinylpyrrolinones. Formation of a new 7-membered ring, by cyclization of an N-allyl pyrrolecarboxamide, yields bicyclic pyrroloazepinones.     

Odds and Trends: Recent Developments in the Chemistry of Odorants

Fragrance chemistry is, together with the closely related area of flavor chemistry, one of the few domains, if not the only one, in which chemists can immediately experience structure–activity relationships. This review presents structure–odor correlations and olfactophore models for the main odor notes of perfumery: “fruity”, “marine”, “green”, “floral”, “spicy”, “woody”, “amber”, and “musky”. New trendsetters and so‐called captive odorants of these notes are introduced, and recent activities and highlights in fragrance chemistry are summarized. The design of odorants, their chemical synthesis, and their use in modern perfumery is discussed. Our selection is guided and illustrated by creative fragrances, and features new odorants which encompassed current trends in perfumery. New odorants for grapefruit and blackcurrant, for galbanum, and leafy top notes are presented. Compounds with fashionable marine, ozonic, and aquatic facets are treated, as well as new odorants for classical lily‐of‐the‐valley, rose, and jasmine accords. Compounds with sweet and spicy tonalities are also discussed, as are the most recent developments for woody notes such as sandalwood and vetiver. We conclude with musky and ambery odorants possessing uncommon or unusual structural features. Some odor trends and effects are illustrated by microencapsulated fragrance samples, and areas where there is need for the development of new synthetic materials and methodologies are pointed out. Thus, chemists are invited to explore fragrance chemistry and participate in the design and synthesis of new odorants. This review gives the latest state of the art of the subject.     

Analysis of CL-20 in environmental matrices: water and soil

Analytical techniques for the detection of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazatetracyclo(5.5.0.05,9.03,11)dodecane (CL-20) in water and soil are developed by adapting methods traditionally used for the analysis of nitroaromatics. CL-20 (a new explosives compound) is thermally labile, exhibits high polarity, and has low solubility in water. These constraints make the use of specialized sample handling, preparation, extraction, and analysis necessary. The ability to determine the concentrations of this new explosive compound in environmental matrices is helpful in understanding the environmental fate and effects of CL-20; understanding the physical, chemical, and biological fate of CL-20; and can be used in developing remediation technologies and determining their efficiency. The toxicity and mobility of new explosives in soil and groundwater are also of interest, and analytical techniques for quantitating CL-20 and its degradation products in soil and natural waters make these investigations possible.     

General Formalism for New Generation Geometrical Model: Application to the Thermodynamics of Liquid Mixtures

In our previous papers, a new geometric model has been proposed for calculating the thermodynamic properties of a multi-component system in terms of the properties of its three sub-binary systems. This new model can overcome the inherent defects of the traditional symmetrical and asymmetrical geometric models. Consequently, it is more reasonable theoretically and more reliable in practical applications. However, calculations using this new model involve a series of integration processes which make it complicated and affects its applications. Since a large number of real systems can be approximately fit through a Redlich–Kister polynomial, in this paper a new formalism is presented for the model, based on the binary Redlich–Kister type parameters. The advantage of this treatment is that the whole integration process is avoided by using algebraic operations, thereby simplifying the calculation.     

Medicinal chemistry in academia: molecular recognition with biological receptors

Why carry out medicinal chemistry at a university, when it means competing with the billion-dollar research efforts of the pharmaceutical industry? In academic research, the race to get a drug to market is not the prime motivation. Instead, university-based medicinal chemistry is driven by the search for new knowledge and the opportunity to educate a new generation of chemists. Furthermore, academia can complement commercial efforts by addressing diseases neglected by private industry.