DNA and RNA binding properties of an arginine-based ‘Extended Chiral Box’ Peptide Nucleic Acid

Lys-based ‘chiral box’ Peptide Nucleic Acids (PNAs with three adjacent 2D-Lys-based chiral monomers) have shown unsurpassed specificity in DNA recognition. In this Letter, the binding performances of arginine-based chiral PNAs were evaluated for PNAs containing in the middle part of the strand either a 2D,5L-Arg monomer or three adjacent 2D-; 2D,5L-; 5L-Arg monomers (‘Extended Chiral Box’), a combination never studied before. The binding performances of the PNAs were studied by evaluating the melting temperatures of fullmatch and mismatch PNA-DNA and PNA-RNA hybrids and by studying their structure by circular dichroism (CD). The data indicated that the arginine side chains inserted in the PNA structure are perfectly equivalent to lysine side chains as far as oligonucleotide recognition is concerned. The insertion of an ‘Extended Chiral Box’ into PNA differently influences the binding properties to DNA and RNA: the additional side chains had no observable effect on binding affinity and selectivity toward DNA, whereas, seemed to slightly disturb the binding affinity to RNA but at the same time highly enhancing the recognition selectivity.     

Bypassing the lack of reactivity of endo-substituted norbornenes with the catalytic rectification–insertion mechanism

The catalytic 1,2-insertion polymerization of polar norbornenes (NBEs) leads to the formation of functional rigid macromolecules with exceptional thermal, optical and mechanical properties. However, this remarkable reaction is plagued by the low reactivity of the polar monomers, and most notably of those bearing a functional group in endo position. We have examined the polymerization mechanism of NBEs bearing one or two CO₂Me groups either in exo or endo position catalyzed by the so-called naked allyl Pd⁺ SbF₆^– catalyst (1). Although endo dimethyl ester of 5-norbornene-2,3-dicarboxylic acid (NBE(CO₂Me)₂) is polymerized by 1, two endo units are never inserted consecutively along the polymer chain. Indeed, 1 is a tandem catalyst which not only catalyzes the insertion of the monomer but also the isomerization of endo and exo isomers. Thus, the polymerization of endo monomers proceeds via a novel mechanism, coined rectification–insertion mechanism, whereby half of the endo monomers are rectified into exo ones prior insertion, leading to the formation of an alternating endo–exo copolymer using an endo only feedstock. With this mechanism, the lack of reactivity of endo norbornenes is bypassed, and the polymerization of predominantly endo polar NBEs bearing a variety of functionalities such as esters, imides, acids, aldehydes, alcohols, anhydrides, or alkyl bromides proceeds with catalyst loadings as low as 0.002 mol%.     

The ‘fully protected backbone’ approach as a versatile tool for a new solid-phase PNA synthesis strategy

The ‘fully protected backbone’ (FPB) strategy has been efficiently adapted to the solid-phase synthesis of homothymine, homocytosine and ‘mixed’ pyrimidine PNAs. This versatile and simple method avoids the preparation of PNA monomers and relies on easy available starting materials, highly efficient backbone elongations and effective nucleobase units condensations.     

Li2MnO3-based composite cathodes for lithium batteries: A novel synthesis approach and new structures

A new, simple technique has been demonstrated for fabricating high-capacity composite electrode structures. In this technique, Li₂MnO₃ is leached in acid in the presence of soluble transition metal ions and subsequently annealed between 450 and 850 °C. The technique can be used to prepare a wide variety of composite compounds, in particular, a new family of ‘layered–rocksalt’ xLi₂MnO₃·(1−x)MO (e.g., M = Ni and Co) structures and modifications thereof, as well as ‘layered–layered’ xLi₂MnO₃·(1−x)LiMO₂ (e.g., M = Mn, Ni, and Co) and ‘layered–spinel’ xLi₂MnO₃·(1−x)LiM₂O₄ (e.g., M = Mn and Ni). This novel approach also holds promise for 1) synthesizing materials that reduce the extent of internal phase transitions of composite cathode structures with a high manganese content, and 2) minimizing the extent to which cells need to be electrochemically activated to remove Li₂O, thereby reducing the extent of the irreversible capacity loss on the first charge/discharge cycle.     

Monitoring of NO2 in the ambient air with passive samplers before and after a road reconstruction event

Nitrogen dioxide (NO₂) concentrations were used to evaluate the air quality before and after the infrastructural change of an important traffic artery in Mortsel, Antwerp (Belgium). During the reconstruction works two pairs of traffic lanes were reduced to one in each direction. Two sampling campaigns were conducted: the first one before the works in 2003 and the second one in 2005, after the road works were finished. Sampling was performed on a weekly base with the use of passive diffusion tubes on the streets, and also indoors in nearby houses. The samples were analyzed by ion chromatography, from which data the NO₂ concentrations in air could be calculated. These results were compared with NO₂ values from the air monitoring station 42R801 of the Flemish Environment Agency in Borgerhout, Antwerp. On the base of different NO₂ concentrations, correlated well with the traffic density, sampling locations were classified into three groups as follows: 1) ‘heavily polluted’ (heavy traffic); 2) ‘moderately polluted’ (medium traffic); or 3) ‘less polluted’ (low traffic density). Sampling sites located further from the road works, enclosed to the group ‘less polluted’, showed the lowest NO₂ concentrations. The highest NO₂ level was found for the locations close to reconstruction works, which belonged to the group ‘heavily polluted’. The contribution of NO₂ was at the same level before and after the road works. During the first campaign it ranged from 30 ± 7 µg/m³ to 71 ± 11 µg/m³ and during the second sampling it was between 36 ± 17 µg/m³ and 73 ± 17 µg/m³. These modernization works had no impact on preventing the traffic-related pollutant as NO₂ and as a consequence no significant effect on the air quality in the studied region. It has been proven that the impact of traffic on the air quality is unmistakably high and simply reduction of the number of the traffic lanes, intended to discourage the traffic flow, had apparently no environmentally advantageous effect.     

Synthesis and structural characterization of copper(II) and vanadium(V) complexes of pyridyl/pyrimidyl–pyrazole derived Schiff base ligands – Metal specific adjustment of ligand binding mode

Two mononuclear copper(II) complexes [Cu(L₁)ClO₄] (1), [Cu(L₂)ClO₄] (3) and two mononuclear vanadium(V) complexes [{VO(L₁)(OCH₃)(CH₃OH)}{VO(L₁)(OCH₃)}] (2) and [VO(L₂) (OCH₃)(CH₃OH)] (4) have been synthesized using two Schiff base ligands HL₁ [N′-(2-hydroxybenzylidene)-5-methyl-1-(pyridin-2-yl)-1H-pyrazole-3-carbohydrazide] and HL₂ [1-(4,6-dimethylpyrimidin-2-yl)-N′-(2-hydroxybenzylidene)-5-methyl-1H-pyrazole-3-carbohydrazide]. These two similar ligands HL₁ and HL₂ in their ‘ketoimine’ form function as mononegative NNNO tetradentate ones towards the Cu(II) centre forming square planar part of the square pyramidal geometry. Where as the same ligands in their ‘imineol’ form behave as binegative ONO tridentate ones to form their V(V) analogues. In the asymmetric unit of 2, there are two independent V(V) complex molecules differing in their conformations as well as in coordination environment – octahedral V(V) in ‘unit A’ is hexa-coordinated while that in ‘unit B’ being penta-coordinated is square pyramidal. Vanadium atom in 4 is in octahedral geometry with NO₅ chromophore. The ligands HL₁ and HL₂ have been synthesized for the first time in our laboratory and characterized by X-ray crystallography and spectroscopy. The complexes (1, 2 and 4) are also characterized by X-ray crystallography, spectroscopic and electrochemical studies.     

Isolation and structural analysis of novel conformational isomers of the m-xylylene-bridged calix[6]arenes: the ‘partial cone’ and ‘inverted cone’ isomers

In the benzylation of a m-xylylene-bridged calix[6]arene tetrol, the first example of the ‘partial cone’ isomer of a calix[6]arene was obtained in addition to the corresponding cone and 1,2,3-alternate isomers, and its structure was established by X-ray crystallographic analysis. The synthesis and crystal structure of the ‘inverted cone’ isomer as well as its thermal conversion to the ‘normal cone’ isomer are also described.     

Ethynylation of pyrroles with 1-acyl-2-bromoacetylenes on alumina: a formal ‘inverse Sonogashira coupling’

Pyrroles are cross-coupled with 1-acyl-2-bromoacetylenes on the surface of Al₂O₃ at room temperature under solvent-free conditions to afford 2-(acylethynyl)pyrroles with 100% regioselectivity and in good yields, thus representing the first example of a palladium-, copper-, base-, and solvent-free (‘green’) ethynylation of pyrroles, which can be considered a formal ‘inverse Sonogashira coupling’. Given the interest in functionalized pyrroles and acetylenes, this new facile and environmentally friendly cross-coupling should be of significant interest for the role of acylhaloacetylenes in pyrrole and acetylene chemistry.     

Comparison of indices and multivariate models to non-destructively predict the fruit chlorophyll by means of visible spectrometry in apple fruit

Non-destructive, rapid, instrumental tools in fruit production are required for predicting the optimum harvest window and monitoring fruit quality during shelf life. The degree of chlorophyll degradation is a sensitive indicator for fruit maturation and ageing. Adequate indices for chlorophyll prediction by means of non-destructive spectral analysis have been studied in the fields of photosynthesis research and remote sensing developments. However, an evaluation of these indices and multivariate linear regression models does not exist so far for predicting the fruit chlorophyll content.Spectral transmittance recordings in the visible wavelength range were carried out on apple fruit Malus domestica Borkh. ‘Elstar’ (n=99) and ‘Jonagold’ (n=117). The fruit chlorophyll a content of ‘Elstar’ apples was measured wet-chemically and predicted by means of the specific indices: NDVI, Tr₆₉₈/Tr₇₆₀, red-edge, TrII on Tr′(λ), TrII, and RVSI with the correlation coefficients of determination R²=0.84, 0.81, 0.75, 0.81, 0.15, and 0.67, respectively. Partial least-squares (PLS) calibration models were built using calibrated spectra (630-730 nm), first derivative of spectra and second derivative of spectra yielding multivariate correlation coefficients of determination R²=0.81, 0.86, and 0.92, respectively. Similar results were found for ‘Jonagold’ apple fruit. Linear regression of indices and PLS calibration models were empirically tested on the chlorophyll a content of apple fruit measuring the same cultivars grown in a different seasons and growing locations. In the case of ‘Elstar’ apple fruit, correlation coefficients of fruit chlorophyll a content analysed wet-chemically as well as fruit maturation measured as calendar weeks were similar to those in the calibration experiment. Application of linear regression equations of indices and PLS models on spectra of ‘Jonagold’ apple fruit led to less accurate results for those methods, which use wavelengths above 720 nm as indicative range.     

Surface modification of chromatography adsorbents by low temperature low pressure plasma

In this study we show how low temperature glow discharge plasma can be used to prepare bi-layered chromatography adsorbents with non-adsorptive exteriors. The commercial strong anion exchange expanded bed chromatography matrix, Q HyperZ, was treated with plasmas in one of two general ways. Using a purpose-designed rotating reactor, plasmas were employed to either: (i) remove anion exchange ligands at or close to the exterior surface of Q HyperZ, and replace them with polar oxygen containing functions (‘plasma etching and oxidation’); or (ii) bury the same surface exposed ligands beneath thin polymer coatings (‘plasma polymerization coating’) using appropriate monomers (vinyl acetate, vinyl pyrrolidone, safrole) and argon as the carrier gas. X-ray photoelectron spectroscopy analysis (first ∼10 nm depth) of Q HyperZ before and after the various plasma treatments confirmed that substantial changes to the elemental composition of Q HyperZ's exterior had been inflicted in all cases. The atomic percent changes in carbon, nitrogen, oxygen, yttrium and zirconium observed after being exposed to air plasma etching were entirely consistent with: the removal of pendant Q (trimethylammonium) functions; increased exposure of the underlying yttrium-stabilised zirconia shell; and introduction of hydroxyl and carbonyl functions. Following plasma polymerization treatments (with all three monomers tested), the increased atomic percent levels of carbon and parallel drops in nitrogen, yttrium and zirconium provided clear evidence that thin polymer coats had been created at the exteriors of Q HyperZ adsorbent particles. No changes in adsorbent size and surface morphology, nor any evidence of plasma-induced damage could be discerned from scanning electron micrographs, light micrographs and measurements of particle size distributions following 3 h exposure to air (220 V; 35.8 W L⁻¹) or ‘vinyl acetate/argon’ (170 V; 16.5 W L⁻¹) plasmas. Losses in bulk chloride exchange capacity before and after exposure to plasmas enabled effective modification depths within hydrated Q HyperZ adsorbent particles to be calculated as 0.2–1.2 μm, depending on the conditions applied. The depth of plasma induced alteration was strongly influenced by the power input and size of the treated batch, i.e. dropping the power or increasing the batch size resulted in reduced plasma penetration and therefore shallower modification. The selectivity of ‘surface vs. core’ modification imparted to Q HyperZ by the various plasma treatments was evaluated in static and dynamic binding studies employing appropriate probes, i.e. plasmid DNA, sonicated calf thymus DNA and bovine serum albumin. In static binding studies performed with adsorbents that had been exposed to plasmas at the 5 g scale (25 g L⁻¹ of plasma reactor), the highest ‘surface/core’ modification selectivity was observed for Q HyperZ that had been subjected to 3 h of air plasma etching at 220 V (35.8 W L⁻¹). This treatment removed ∼53% of ‘surface’ DNA binding at the expense of a 9.3% loss in ‘core’ protein binding. Even more impressive results were obtained in dynamic expanded bed adsorption studies conducted with Q HyperZ adsorbents that had been treated with air (220 V, 3 h) and ‘vinyl acetate/argon’ (170 V, 3 h) plasmas at 10.5 g scale (52.5 g L⁻¹ of plasma reactor). Following both plasma treatments: the 10% breakthrough capacities of the modified Q HyperZ adsorbents towards ‘surface’ binding DNA probes dropped very significantly (30–85%); the DNA induced inter-particle cross-linking and contraction of expanded beds observed during application of sonicated DNA on native Q HyperZ was completely eradicated; but the ‘core’ protein binding performance remained unchanged cf. that of the native Q HyperZ starting material.     

Synthesis of a cytisine/epibatidine hybrid: a radical approach

With the aim of developing a new ligand of neuronal nicotinic receptors (nAChRs), ionic, and radical routes to the synthesis of a cytisine/epibatidine hybrid were studied. The key step of the convergent synthesis was an unprecedented intramolecular coupling between a primary radical and a pyridine heterocycle. The target compound ‘6,11-diaza’ was formed with its ‘4,11-diaza’ regioisomer (‘6,11″/’4,11″: 70/30). Both compounds exhibited a nanomolar affinity at the α₄β₂ nAChR subtype, slightly better for the unexpected regioisomer [K_i (nM) target compound and its regioisomer: 3.5 and 0.5 nM, respectively].     

Potentiometric determination of the 'formal' hydrolysis ratio of aluminium species in aqueous solutions

The ‘formal’ hydrolysis ratio (h = C(OH⁻)_added/C(Al)_total) of hydrolysed aluminium-ions is an important parameter required for the exhaustive and quantitative speciation-fractionation of aluminium in aqueous solutions. This paper describes a potentiometric method for determination of the formal hydrolysis ratio based on an automated alkaline titration procedure. The method uses the point of precipitation of aluminium hydroxide as a reference (h = 3.0) in order to calculate the initial formal hydrolysis ratio of hydrolysed aluminium-ion solutions. Several solutions of pure hydrolytic species including aluminium monomers (AlCl₃), Al₁₃ polynuclear cluster ([Al₁₃O₄(OH)₂₄(H₂O)₁₂]⁷⁺), Al₃₀ polynuclear cluster ([Al₃₀O₈(OH)₅₆(H₂O)₂₆]¹⁸⁺) and a suspension of nanoparticulate aluminium hydroxide have been used as ‘reference standards’ to validate the proposed potentiometric method. Other important variables in the potentiometric determination of the hydrolysis ratio have also been optimised including the concentration of aluminium and the type and strength of alkali (Trizma-base, NH₃, NaHCO₃, Na₂CO₃ and KOH). The results of the potentiometric analysis have been cross-verified by quantitative ²⁷Al solution nuclear magnetic resonance (²⁷Al NMR) measurements. The ‘formal’ hydrolysis ratio of a commercial basic aluminium chloride has been measured as an example of a practical application of the developed technique.     

Microchip device for rapid screening and fingerprint identification of phenolic pollutants

A new microchip protocol has been developed for rapid measurements of the ‘total’ content of phenolic compounds, as well as for a detailed fingerprint identification of the ‘individual’ ones. The protocol involves the use of a microchip flow-injection analysis for fast screening and early detection of phenols and switching to the separation (fingerprint) mode once such compounds are detected. This is readily accomplished by exchanging the run buffers in the separation channel. While operating with an acidic run buffer (pH 5) offers high speed flow-injection measurements of the ‘total’ phenolic content, on chip switching to a basic buffer (pH 8) leads to ionization of the phenolic compounds and to their effective separation and detection. Under optimum conditions, assay rates of about 120 and 18 samples/h can be realized for the ‘total’ and ‘individual’ measurements, respectively. The effect of the buffer pH, switching (washing) time, applied voltages and other relevant variables, is described. The concept is illustrated in connection to amperometric detection and is attractive for a wide range of environmental-monitoring applications.     

Synthesis and photosensitized oxygenation of cyclopropylidenecyclobutenes

Cyclopropylidenecyclobutenes and -cyclobutanes were conveniently prepared using the Petasis titanocene approach. The cyclobutenes were unreactive to singlet oxygen, reacting sluggishly via a photoinitiated free radical autooxidative epoxidation process, to yield the corresponding spiroketones. By contrast, cyclopropylidenecyclobutanes react rapidly with ¹O₂, via an ‘ene’ process, initially generating a cyclopropyl hydroperoxide, which proceeds to products via Hock cleavage. The inertness of cyclopropylidenecyclobutenes to a ¹O₂ ‘ene’ reaction mode may be attributed to the fact that it would require the formation of the relatively high energy cyclobutadiene moiety.     

Highly efficient and versatile chemoselective addition of amines to epoxides in water catalyzed by erbium(III) triflate

Er(OTf)₃ is proposed as a highly efficient and reusable catalyst for the opening of epoxides in water with aliphatic as well as aromatic amines leading to the synthesis of β-amino alcohols. The aqueous conditions employed in the present method will make it ‘environmentally friendly’ and potentially useful for industrial applications.     

Polynuclear manganese grids and clusters—A magnetic perspective

High nuclearity paramagnetic, spin-coupled transition metal clusters and grids are fascinating chemists and physicists partly because of their structural beauty, and the challenge of creating them, but also because of their novel physical properties. Magnetic interactions between the spin centers are a primary focus. This review will examine a selection of Mn(II) polynuclear grids and clusters, with nuclearities in the range Mn₄ to Mn₉. Theoretical treatments of the magnetic properties are discussed, and approaches to solving the exchange problem for ‘large’ spin systems related to computational difficulties. A freely available software package (MAGMUN4.1) is presented as a means of dealing simply with spin-coupled clusters in general, and symmetry reduction methods are discussed briefly as a means of dealing with ‘large’ spin systems.     

Beneficial effect of water as second solvent in ionic liquid biphasic catalytic hydrogenations

When reactions take place in ionic liquids, a solvent is normally used to extract the products after reaction. It is reported here how the presence of the solvent during the reaction already can seriously improve the catalytic performance. Above all, employing water as the added solvent enhanced the catalytic activities significantly, ascribed to the creation of a well mixed ‘emulsion-like’ system. The reductions of methyl 2-acetamidoacrylate with Rh-EtDuPHOS and of 2-cyclohexen-1-one with Wilkinson’s catalyst in bmimPF₆ were thus successfully performed in the presence of water. The complexes were easily recycled and Rh-EtDuPHOS was even no longer air sensitive.     

Chemometric classification of gunshot residues based on energy dispersive X-ray microanalysis and inductively coupled plasma analysis with mass-spectrometric detection

A gunshot residue sample that was collected from an object or a suspected person is automatically searched for gunshot residue relevant particles. Particle data (such as size, morphology, position on the sample for manual relocation, etc.) as well as the corresponding X-ray spectra and images are stored. According to these data, particles are classified by the analysis-software into different groups: ‘gunshot residue characteristic’, ‘consistent with gunshot residue’ and environmental particles, respectively. Potential gunshot residue particles are manually checked and – if necessary – confirmed by the operating forensic scientist.     

Regioselective synthesis of spiro-cyclopropanated 1-aminopyrrol-2-ones by Bi(OTf)3-catalyzed one-pot ‘Mukaiyama-Michael addition/cyclization/ring-contraction’ reactions of 1,2-bis(trimethylsilyloxy)cyclobutene with 1,2-diaza-1,3-butadienes

Unknown spiro-cyclopropanated 1-aminopyrrol-2-ones are regioselectively prepared in high yields by Bi(OTf)₃-catalyzed one-pot ‘Mukaiyama-Michael addition/cyclization/ring-contraction’ reactions of 1,2-bis(trimethylsilyloxy)cyclobutene with 1,2-diaza-1,3-butadienes at room temperature.     

Synthesis and biological evaluation of anthranilamide-based non-peptide mimetics of ω-conotoxin GVIA

Non-peptide mimetics based on an anthranilamide ‘scaffold’ possessing fragments that mimic Lys2, Tyr13 and Arg17 in ω-conotoxin GVIA have been prepared. Compounds were assayed for binding to the voltage-gated calcium channels Ca_v2.2 (‘N-type’) and Ca_v2.1 (‘P/Q-type’) in rat brain. The primary synthetic target, 2-(6-amino-hexanoylamino)-5-(3-guanidino-propoxy)-N-[4-(4-hydroxyphenoxy)-phenyl]-benzamide (2a), exhibited low μM binding to Ca_v2.2 and was more than 30-fold selective for Ca_v2.2 over Ca_v2.1.