Theoretical designs for germaacetylene (RC≡GeR'): a new target for synthesis

The effect of substitution on the potential energy surfaces of RC≡GeR (R = F, H, OH, CH(3), SiH(3), Tbt, Ar*, SiMe(SitBu(3))(2) and SiiPrDis(2)) was explored using density functional theories (B3LYP/LANL2DZdp and B3PW91/6-31G(d)). Our theoretical studies indicate that all the triply bonded RC≡GeR species prefer to adopt trans-bent geometry, which is in agreement with the theoretical model (mode (B)). Additionally, we show that the stabilities of the RC≡GeR species bearing smaller substituents (R = F, H, OH, CH(3) and SiH(3)) decrease in the order R(2)C=Ge: > RC≡GeR > :C=GeR(2). On the other hand, the triply bonded RC≡GeR molecules with bulkier substituents (R = Tbt, Ar*, SiMe(SitBu(3))(2), SiiPrDis(2)) were found to possess the global minimum on the singlet potential energy surface and are both kinetically and thermodynamically stable. That is to say, both electronic and steric effects of bulky substituents play a crucial role in making triply bonded germaacetylenes (RC≡GeR) an interesting synthetic target.     

Distinctive attributes of β-lactam target proteins in Acinetobacter baumannii relevant to development of new antibiotics

Multi-drug-resistant forms of the Gram-negative pathogen Acinetobacter baumannii are an emerging threat to human health and further complicate the general problem of treating serious bacterial infections. Meeting this challenge requires an improved understanding of the relationships between the structures of major therapeutic targets in this organism and the activity levels exhibited against it by different antibiotics. Here we report the first crystal structures of A. baumannii penicillin-binding proteins (PBPs) covalently inactivated by four β-lactam antibiotics. We also relate the results to kinetic, biophysical, and computational data. The structure of the class A protein PBP1a was solved in apo form and for its covalent conjugates with benzyl penicillin, imipenem, aztreonam, and the siderophore-conjugated monocarbam MC-1. It included a novel domain genetically spliced into a surface loop of the transpeptidase domain that contains three conserved loops. Also reported here is the first high-resolution structure of the A. baumannii class B enzyme PBP3 in apo form. Comparison of this structure with that of MC-1-derivatized PBP3 of Pseudomonas aeruginosa identified differences between these orthologous proteins in A. baumannii and P. aeruginosa. Thermodynamic analyses indicated that desolvation effects in the PBP3 ligand-binding sites contributed significantly to the thermal stability of the enzyme-antibiotic covalent complexes. Across a significant range of values, they correlated well with results from studies of inactivation kinetics and the protein structures. The structural, biophysical, and computational data help rationalize differences in the functional performance of antibiotics against different protein targets and can be used to guide the design of future agents.     

Aerated milk protein emulsions — new microstructural aspects

The formation of stable aerated products based on milk protein emulsions, such as whipped creams, depends on (i) the physical properties of the emulsion before the whipping step; and (ii) how the air is incorporated and the created air bubbles are stabilised. The final texture of the product is determined by the arrangement of the microstructural entities and the interaction among them. Advances are being made mainly in the better understanding of the destabilisation of the oil–water interface of the emulsion, which is a key point in the formulation process. However, the connection to the ‘real product’ has still to be made. Further investigations, especially with regard to the foaming behaviour, have to be encouraged in order to predict and control the physical quality and stability of aerated milk protein emulsions.     

Phoxonic crystals—a new platform for chemical and biochemical sensors

A new sensor platform is based on so-called phoxonic crystals. Phoxonic crystals are structures designed for simultaneous control of photon and phonon propagation and interaction. They are characterized by a periodic spatial modulation of the dielectric constant as well as elastic properties on a common wavelength scale. Multiple scattering of photons and phonons results in a band gap where propagation of both waves is prohibited. The existence of photonic and phononic band gaps opens up opportunities for novel devices and functional materials. The usage of defect modes is an advantageous concept for measurement. The defect also acts as point of measurement. We show theoretically that the properties of the defect mode can be tailored to provide very high sensitivity to optical and acoustic properties of matter confined within a defect cavity or surrounding the defect or being adsorbed at the cavity surface. In this paper, we introduce the sensor platform and analyze the key features of the sensor transduction scheme. Experimental investigations using a macroscopic device support the theoretical findings.     

The falling ball viscometer— a new instrument for viscoelastic fluids

It is shown that the falling ball viscometer, a simple and inexpensive measuring system, can be used to determine the steady shear viscosity of viscoelastic fluids at low shear rates if appropriate analytical and experimental procedures are adopted. In addition, the relaxation time, a measure of the elasticity of these fluids, can be determined. These rheological properties are necessary for the analysis of the fluid mechanical and heat transfer behavior of viscoelastic fluids.     

Analytical Chemistry — a time for change?

A report of the RSC-Analytical Division Automated Methods Group Symposium, held in Ferndown, Dorset, U.K., 28–30 October 1987.     

Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK

We have used virtual screening to develop models for the binding of aryl substituted heterocycles to p38α MAPK. Virtual screening was conducted on a number of p38α MAPK crystal structures using a library of 46 known p38α MAPK inhibitors containing a heterocyclic core substituted by pyridine and fluorophenyl rings (structurally related to SB203580) and a set of decoy compounds. Multiple protonation states and tautomers of active and decoy compounds were considered. Each docking model was evaluated using receiver operating characteristic (ROC) curves and enrichment factors. The two best performing single crystal structures were found to be 1BL7 and 2EWA, with enrichment factors of 14.1 and 13.0 at 2 % of the virtual screen respectively. Ensembles of up to four receptors of similar conformations were generated, generally giving good or very good performances with high ROC AUCs and good enrichment. The 1BL7-2EWA ensemble was able to outperform each of its constituent receptors and gave high enrichment factors of 17.3, 12.0, 8.0 at 2, 5 and 10 % respectively, of the virtual screen. A ROC AUC of 0.94 was obtained for this ensemble. This method may be applied to other proteins where there are a large number of inhibitor classes with different binding site conformations.     

Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function

The intrinsic ability of protein structures to exhibit the geometric features required for molecular function in the absence of evolution is examined in the context of three systems: the reference set of real, single domain protein structures, a library of computationally generated, compact homopolypeptides, artificial structures with protein-like secondary structural elements, and quasi-spherical random proteins packed at the same density as proteins but lacking backbone secondary structure and hydrogen bonding. Without any evolutionary selection, the library of artificial structures has similar backbone hydrogen bonding, global shape, surface to volume ratio and statistically significant structural matches to real protein global structures. Moreover, these artificial structures have native like ligand binding cavities, and a tiny subset has interfacial geometries consistent with native-like protein-protein interactions and DNA binding. In contrast, the quasi-spherical random proteins, being devoid of secondary structure, have a lower surface to volume ratio and lack ligand binding pockets and intermolecular interaction interfaces. Surprisingly, these quasi-spherical random proteins exhibit protein like distributions of virtual bond angles and almost all have a statistically significant structural match to real protein structures. This implies that it is local chain stiffness, even without backbone hydrogen bonding, and compactness that give rise to the likely completeness of the library solved single domain protein structures. These studies also suggest that the packing of secondary structural elements generates the requisite geometry for intermolecular binding. Thus, backbone hydrogen bonding plays an important role not only in protein structure but also in protein function. Such ability to bind biological molecules is an inherent feature of protein structure; if combined with appropriate protein sequences, it could provide the non-zero background probability for low-level function that evolution requires for selection to occur.     

Thiazolylblue tetrazolium bromide — a new spectrophotometric reagent for determination of manganese

A method has been developed for the micro-determination of Mn(VII) by the selective extraction of the MnO₄ ^– anion with thiazolylblue tetrazolium bromide from acidic medium. The molar absorptivity of the complex is 1 × 10⁴lmol^–1cm^–1 at 250 nm and the system obeys Beer's law in the range 0.1–1.75 gml^–1 Mn(VII). The composition and stability of the complex are discussed. The characteristic values for the extraction equilibrium and the equilibrium in the aqueous phase are: extraction constantK _ex = 3.16 × 10⁴, distribution constantK _D = 21.85 and association constant =1.45 × 10³. Manganese(VII) was determined in soils and plants. The determination was carried out without preliminary separation of manganese.     

High-resolution monolithic columns—a new tool for effective and quick separation

This work describes a comparison of three types of commercial high-performance liquid chromatography silica monolithic columns with different inner diameters and generations of monolithic sorbent: a “classic” monolithic column, the first generation (Onyx? monolithic C₁₈, 100 mm?×?4.6 mm, Phenomenex); a “narrow” monolithic column for fast separation at lower flow rates (Chromolith® Performance RP-18e, 100 mm?×?3 mm, Merck); and a recently introduced “high-resolution” monolithic column, the next generation (Chromolith® HighResolution RP-18e, 100 mm?×?4.6 mm, Merck). Separation efficiency (number of theoretical plates, height equivalent to a theoretical plate and van Deemter curves), working pressure, the symmetry factor and resolution were critical aspects of the comparison in the case of the separation of ascorbic acid, paracetamol and caffeine. The separations were performed under isocratic conditions with a mobile phase consisting of 10:90 (v/v) acetonitrile–phosphoric acid (pH 2.80). Detailed comparison of the newest-generation monolithic column (Chromolith® HighResolution) with the previously introduced monolithic sorbents was performed and proved the advantages of the Chromolith® HighResolution column.

Terahertz spectroscopy: a powerful new tool for the chemical sciences?

Terahertz spectroscopy is only now beginning to make its transition from initial development by physicists and engineers to broader use by chemists, materials scientists and biologists, thanks to the increasing availability of commercial terahertz spectrometers. With the unique insights that terahertz spectroscopy can provide into intermolecular bonding and crystalline matter, it could prove to be an invaluable addition to the chemist's analytical toolset. This tutorial review aims to give an introduction to terahertz spectroscopy, its techniques, equipment, current applications and potential for the chemical sciences to a broad readership.     

Development of a direct ELISA based on carboxy-terminal of penicillin-binding protein BlaR for the detection of β-lactam antibiotics in foods

β-Lactam antibiotics, including penicillins and cephalosporins, are commonly used in veterinary medicine. Illegal use and abuse of β-lactams could cause allergy and selected bacterial resistance. BlaR-CTD, the carboxy-terminal of penicillin-recognizing protein BlaR from Bacillus licheniformis ATCC 14580, was utilized in this study to develop a receptor-based ELISA for detection and determination of β-lactam antibiotics in milk, beef, and chicken. This assay was based on directly competitive inhibition of binding of horseradish peroxidase-labeled ampicillin to the immobilized BlaR-CTD by β-lactams. The assay was developed as screening test with the option as semiquantitative assay, when the identity of a single type of residual β-lactam was known. The IC₅₀ values of 15 β-lactam antibiotics, including benzylpenicillin, ampicillin, amoxicillin, dicloxacillin, oxacillin, nafcillin, cefapirin, cefoperazone, cefalotin, cefazolin, cefquinome, ceftriaxone, cefotaxime, cefalexin, ceftiofur and its metabolite desfuroylceftiofur were evaluated and ranged from 0.18 to 170.81 μg L^?1. Simple sample extraction method was carried out with only phosphate-buffered saline, and the recoveries of selected β-lactam antibiotics in milk, beef, and chicken were in the range of 53.27 to 128.29 %, most ranging from 60 to 120 %. The inter-assay variability was below 30 %. Limits of detection in milk, beef, and chicken muscles with cefquinome matrix calibration were 2.10, 30.68, and 31.13 μg kg^?1, respectively. This study firstly established a rapid, simple, and accurate method for simultaneous detection of 15 β-lactams in edible tissues, among which 11 β-lactams controlled by European Union could be detected below maximum residue limits.

Computational clues for a new mechanism in the glycosylase activity of the human DNA repair protein hOGG1. A generalized paradigm for purine-repairing systems?

A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle responsible for the glycosylase activity of the human DNA repair protein hOGG1: enzyme activation, cleavage of the glycosidic bond, and expulsion of the damaged base. An unprecedented large quantum mechanics (QM) model system has been used, which includes a complete oxoG molecule, the deoxyribose ring bonded to the phosphate groups, and most of the surrounding residues that simulate the protein binding pocket. It has been found that Asp268 does not play any role in Lys249 activation and that the oxoG basis acts as a coenzyme, triggering nucleophile activation by Lys249 deprotonation. An SN2 nucleophilic attack by Lys249 on the anomeric carbon then follows. This is the rate-determining step of the process with an activation barrier of 16.7 kcal mol(-1) in good agreement with the experimental value of 17.1 kcal mol(-1). The expelled oxoG plays again as an enzyme cofactor at the end of the process by activating (via proton transfer) ribose ring opening and Schiff base formation. This study suggests a recurring catalytic strategy in the enzymatic cleavage of purine nucleoside where the activation of the leaving group by protonation of the nucleoside base (via an enzymatic general acid) triggers the cleavage of the glycosidic bond.     

The aromatic peroxygenase from Marasmius rutola—a new enzyme for biosensor applications

The aromatic peroxygenase (APO; EC 1.11.2.1) from the agraric basidomycete Marasmius rotula (MroAPO) immobilized at the chitosan-capped gold-nanoparticle-modified glassy carbon electrode displayed a pair of redox peaks with a midpoint potential of −278.5 mV vs. AgCl/AgCl (1 M KCl) for the Fe²⁺/Fe³⁺ redox couple of the heme-thiolate-containing protein. MroAPO oxidizes aromatic substrates such as aniline, p-aminophenol, hydroquinone, resorcinol, catechol, and paracetamol by means of hydrogen peroxide. The substrate spectrum overlaps with those of cytochrome P450s and plant peroxidases which are relevant in environmental analysis and drug monitoring. In M. rotula peroxygenase-based enzyme electrodes, the signal is generated by the reduction of electrode-active reaction products (e.g., p-benzoquinone and p-quinoneimine) with electro-enzymatic recycling of the analyte. In these enzyme electrodes, the signal reflects the conversion of all substrates thus representing an overall parameter in complex media. The performance of these sensors and their further development are discussed.     

4-cyanoimidazolate: a new pseudo-cyanide?

Because of its exobidentate nature, pK(a), and electronic properties, 4-cyanoimidazole has been examined as a ligand and as a pseudo-cyanide. The ligand reacts readily as an anion with both cobalt and nickel ions in solution to form coordination polymers. The magnetic susceptibility and thermal stability of these materials are reported. 4-Cyanoimidazolate forms a hexakis complex with nickel, to form the first observed hexakis imidazolate nickelate complex.     

Kojic acid—a new fragment for the preparation of bent‐core mesogens

Kojic acid was used to synthesize bent‐core mesogens. Antiferroelectric polar smectic mesophases, an oblique and a rectangular columnar mesophase were found. The mesophases were characterized by X‐ray scattering, electro‐optical measurements, polarizing microscopy and DSC. On the base of these measurements, models of the mesophases are proposed.     

Throughput and efficiency of a mass spectrometry-based screening assay for protein—Ligand binding detection

An H/D exchange- and MALDI mass spectrometry-based screening assay was applied to search for novel ligands that bind to cyclophilin A, a potential therapeutic and diagnostic target in lung cancer. The assay is based on stability of unpurified proteins from rates of H/D exchange (SUPREX), which exploits the H/D exchange properties of amide protons to measure the increase in a protein's thermodynamic stability upon ligand binding in solution. The current study evaluates the throughput and efficiency with which 880 potential ligands from the Prestwick Chemical Library (Illkirch, France) could be screened for binding to cyclophilin A. Screening was performed at a rate of 3 min/ligand using a conventional MALDI mass spectrometer. False positive and false negative rates, based on a set of control data, were as low as 0% and 9%, respectively. Based on the 880-member library screening, a false positive rate of 0% was observed when a two-tier selection strategy was implemented. Although novel ligands for cyclophilin A were not discovered, cyclosporin A, a known ligand to CypA and a blind control in the library, was identified as a hit. We also describe a new strategy to eliminate some of the complications related to back exchange that can arise in screening applications of SUPREX.     

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are different. By analyzing microseconds-long all-atom molecular dynamics simulations of a polypeptide, we find that a distance based on backbone dihedral angles performs very well in distinguishing structures that are kinetically correlated from those that are not, while the widely used C(α) root mean square distance performs more poorly. The root mean square difference between contact matrices turns out instead to be the metric providing the highest clustering coefficient, namely, according to this similarity measure, the neighbors of a structure are also, on average, neighbors among themselves. We also propose a combined distance measure which, for the system considered here, performs well both for distinguishing structures which are distant in time and for giving a consistent cluster analysis.