Synthesis of an isostere of an O-linked glycopeptide

[reaction: see text] A route for the synthesis of an electrophilic, carbocyclic galactose equivalent from D-galactose is described. The strategy utilizes ring-closing metathesis with Grubbs's second-generation catalyst as the key step. The galactose-derived electrophile reacted in an S(N)2 fashion with N-Boc-cysteine methyl ester to provide an alpha-galactosylserine isostere. The method was extended to the synthesis of a glycopeptide isostere.     

Multicut-HDMR with an application to an ionospheric model

A new High Dimensional Model Representation (HDMR) tool, Multicut-HDMR, is introduced and applied to an ionospheric electron density model. HDMR is a general set of quantitative model assessment and analysis tools for improving the efficiency of deducing high-dimensional input-output system behavior. HDMR describes an output [f(x)] in terms of its input variables (x = [x(1), x(2), em leader, x(n)]) via a series of finite, hierarchical, correlated function expansions. Various forms of HDMR are constructed for different purposes such as modeling laboratory or field data, or reproducing a complicated mathematical model. The Cut-HDMR technique, which expresses f(x) with respect to a specified reference point x in the input space, is appropriate when the input space is sampled in an orderly fashion. However, if the desired domain of the input space is too large, the HDMR function expansion may not converge, and Cut-HDMR will be unable to accurately approximate f(x). The new Multicut-HDMR technique addresses this problem through the use of multiple reference points in the input space.     

Activating an enzyme by an engineered coiled coil switch

We designed a de novo protein based on a circular permutant of RNaseT1, in which the enzymatic activity can be manipulated by engineered peptide binding. The circular permutant of RNaseT1 was obtained by tethering the original C- and N-termini with a GPAG linker and cleaving the molecule between Glu82 and Asn83. This mutant lacked enzymatic activity, due to the destabilization of entire protein structure. We previously reported the construction of ABC-type heterotrimeric coiled coil peptides, in which the A- and B-type peptides cannot form the folded trimeric structure without the C-type peptide. The introduction of the A- and B-type coiled coil peptides to the C- and N-termini of the circular permutant of RNaseT1, respectively, and the subsequent addition of the C-type coiled coil peptide enabled the RNaseT1 domain to refold properly, thus, restoring the enzymatic activity. The formation of the trimeric coiled coil structure should bring the cleaved sites of RNaseT1 close enough to refold the RNaseT1 domain spontaneously.     

The Thermal Rearrangement of an NHC-Ligated 3-Benzoborepin to an NHC-Boranorcaradiene

An N-heterocyclic-carbene-ligated 3-benzoborepin with a bridged structure has been synthesized by double radical trans-hydroboration of benzo[3,4]cycloundec-3-ene-1,5-diyne with an N-heterocyclic carbene borane. The thermal reaction of the NHC-ligated borepin at 150 °C gives an isolable NHC-boranorcaradiene. Experiments and density functional theory calculations support a mechanism whereby the borepin initially rearranges to a boranorcaradiene by a thermal 6π-electrocyclic reaction. This is followed by 1,5-boron shift to give a rearranged boranorcaradiene. This shift occurs with stereoinversion at boron through a transition state with open-shell diradical character. This is the first example of the isolation of a boranorcaradiene from a thermal reaction of a borepin.     

Pi-dimer of an aniline dimer: an ESR-UV-vis spectroelectrochemical study

It is shown for the first time that the most important intermediate formed during aniline polymerization, the p-aminodiphenylamine, forms a pi-dimer under oxidation at room temperature in acidified organic solvents that are used in electropolymerization. N-Phenylquinonediimine, which is generally assumed to be formed under oxidation, is only formed in basic solutions and in ionic liquids. Most of the mechanistic studies reported so far take the formation of N-phenylquinonediimine under consideration, although it is not consistent with the UV-vis spectra measured during oxidation of p-aminodiphenylamine. The formation of a pi-dimer is very well consistent with the electronic spectra of the oxidation product. In this way the pi-dimer is very important for the interpretation of the UV-vis spectra of higher oligomers and polyaniline as well. Furthermore, it offers a new interpretation of the redox behavior of p-aminodiphenylamine as found by cyclic voltammetry and has to be considered in the mechanism of the electrochemical polyaniline formation.     

Synthesis and DNA triplex formation of an oligonucleotide containing an urocanamide

An urocanamide nucleoside designed and previously tested as its protected ribose derivative in aprotic solvents for binding a cytosine-guanine (CG) Watson-Crick base pair was successfully incorporated into a triplex forming oligonucleotide. Binding affinity and specificity of this nonnatural nucleoside were studied in a triple helix with duplex targets containing all four possible Watson-Crick base pairs opposite the nucleoside analog in the third strand. UV melting experiments indicate the formation of a well-defined triplex with specific binding of the urocanamide analog to a CG inversion of the homopurine-homopyrimidine target. However, binding affinities in the triplex are weak and much lower when compared to the canonical base triads.     

Converting an Esterase into an Epoxide Hydrolase

Entering the fold : A common structural motif in hydrolytic enzymes is the α,β‐hydrolase fold. The interconversion of one enzyme into another by introduction of mechanistically important residues is not enough; only substitution of a loop allows epoxide hydrolase activity in the esterase scaffold to be formed (see picture; structure comparison of epoxide hydrolases (green) with the esterase (orange)). The result is an enantioselective chimeric enzyme.

     

Integration of an electrochemical-based biolithography technique into an AFM system

An ordinary atomic force microscopy (AFM) was functionalized and applied to electrochemically draw micropatterns of biomolecules. To fabricate an electrochemical AFM probe having an electrode at the tip, a metal-coated AFM probe was first insulated with Parylene C, and then the apex of the tip was ground mechanically to expose the electrode. The effective electrode diameter was estimated to be ca. 500 nm. The electrode probe was positioned close to a heparin-coated antibiofouling substrate and used to locally generate hypobromous acid from a dilute Br⁻ solution to render the substrate surface protein-adhesive. In situ topographical imaging after the electrochemical treatment suggested the heparin layer became detached to allow the adsorption of proteins, in this case fibronectin. The diameter of the drawn fibronectin pattern was 2 μm, which is one order of magnitude smaller than we achieved previously using a microdisk electrode (tip diameter 10 μm). Figure AFM configuration integrated with the electrochemical-based surface modification and resultant micropatterns of fluorescence-labeled fibronectin Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Hypercoulometric effect in an electron capture detector polarized with an additional voltage

Summary This paper reports measurements of the current characteristics and of the signal corresponding to a constant concentration of Freon F-11 for an electron-capture detector, supplied with a pulse voltage with a changeable pulse duration, amplitude and repetition time. It was found that an additional voltage applied to the detector cathode increased the detector signal by about 50% and that the maximal signal was observed at 5 V. The influence of the polarized voltage on the electron caputure efficiency coefficient (p) measured with two detectors in series was demonstrated and the reliability of the sample mass calculation by means of (p) is discussed.     

Optical characteristics of an afterglow extracted from an inductively coupled plasma

An inductively coupled plasma is extracted into a quartz vacuum chamber through an orifice to observe optical characteristics of the extracted afterglow. The Mach disk, the barrel shock and the zone of silence, which are familiar in supersonic molecular beam experiments with neutral gases, are clearly observed. Axial profiles of the emission of various lines are measured with a photodiode array spectrometer. Intensities of ionic lines as well as atomic lines are stronger at the Mach disk than in the zone of silence. The location of the Mach disk with varying chamber presure is in conformity with an experimental equation obtained in supersonic molecular beam experiments.     

Amperometric biosensors employing an insoluble oxidant as an interference-removing agent

A strong oxidant membrane is introduced to amperometric biosensors in order to solve the problem associated with interference from readily oxidizable species. The proposed biosensors are in planar format, and are composed of four components, i.e. a base amperometric transducer, an enzyme layer, a protecting membrane, and an oxidant membrane. In this sensor format, interfering species are removed by an oxidation reaction during their diffusion through the oxidant membrane. The oxidant membrane is introduced by dispensing a mixture of an oxidant and a polymer matrix as dissolved in an organic solvent, and thus, could be easily adapted to mass fabrication of miniature biosensors. In this work, several different reagents are examined as oxidants: BaO₂, CeO₂, MnO₂ and PbO₂. Of these, PbO₂ is shown to yield biosensors with the best performance, in terms of reducing interfering signals. Two different matrix systems are devised for use in formulating oxidant membranes: hydrophilic polyurethane (HPU) and cellulose acetate incorporating poly(ethylene glycol) (CA/PEG). While the CA/PEG-type sensor displays better sensitivity and faster response behavior, the HPU-type is shown to exhibit more pronounced interference-removing ability. The analytical utility of the proposed oxidant membrane is demonstrated by fabricating amperometric glucose and creatinine sensors as the model biosensor systems, and by investigating their response characteristics.     

Evaluation of an inductively-coupled plasma with an extended-sleeve torch as an atomization cell for laser-excited fluorescence spectrometry

An inductively-coupled plasma (ICP) with an extended-sleeve torch has been evaluated as an atomization cell for laser-excited fluorescence spectrometry. Limits of detection for 20 lines are given. The detection power is almost equivalent to that obtained by excitation with a hollow-cathode lamp. Interelement effects and spectral interferences are discussed.     

Adsorption study of an industrial dye by an organic clay

In this study, the adsorption of an industrial dye Supranol Yellow 4GL onto Cetyltrimethylammonium-bentonite (CTAB-bentonite) is investigated. The organobentonite is synthesised by exchanging cetyltrimethylammonium cations (CTAB) with inorganic ions on the surface of bentonite. The adsorption of Supranol Yellow 4GL onto organobentonite is found to be maximum when the concentration of CTAB exchanged is 100% according to the cation exchange capacity of the clay (CEC). The modification of organobentonite is examined using XRD and FTIR techniques. The effect of the process parameters such as: contact time, adsorbate concentration, adsorbent dose, pH and temperature are reported. Nearly 1200 seconds of contact time are found to be sufficient for the adsorption to reach equilibrium. The pseudo second order model is used to describe the kinetic data, and the rate constant is therefore evaluated. The dye adsorption to organobentonite is characterized by monolayer isotherm and caused by adsorption with relatively strong uptake. The Langmuir and Freundlich models adsorption are applied to describe the isotherm equilibrium and to determine its constants. The Langmuir and Freundlich models agree well with the experimental data with a adsorption capacity of 0.5 g of dye per g of organobentonite. A better fixation was obtained at acidic pH. The effect of temperature on the adsorption of dye has been also studied and the thermodynamic parameters ΔH, ΔS, ΔG, were determined. Organobentonite is found to be effective for removing Supranol Yellow 4GL dye from wastewater.     

Collective reaction behavior of an oscillating system coupled with an excitable reaction

The collective reaction behavior of limit cycles coupled to a nonoscillatory forcing is investigated experimentally and computationally. The coupled chemical system is constructed by adding 1,4-cyclohexanedione (CHD), a species which is capable of forming an oscillator with acidic bromate, into the cerium-catalyzed Belousov-Zhabotinsky reaction. Two levels of coupling exist in the system: (1) through autocatalytic reactions with bromine dioxide radicals and (2) via reactions with oxidized metal catalysts. Experiments illustrate that there is an optimum [1,4-CHD]/[cerium] ratio for inducing complex oscillations, whereas in the 1,4-CHD and malonic acid concentration phase plane two resonant ratios are observed for the onset of complex behavior. In addition, bromate, the oxidant for both suboscillators, also exhibits subtle influences on the complexity of the collective reaction behavior. The experimental observations are qualitatively reproduced with the Field-Koros-Noyes mechanism, modified to account for the coupling reactions with the 1,4-CHD-bromate system.     

Sonoelectroanalysis – an overview

The coupling of power-ultrasound with well established but under-exploited electrochemical stripping voltammetry has led to the emergence of a powerful new analytical technique – sonoelectroanalysis. Where classical electroanalytical techniques were plagued with electrode-fouling and/or sensitivity limitations, the introduction of ultrasound into the system has given great increases in analytical efficiency and substrate applicability, predominantly through enhanced mass transport and electrode surface activation. This revitalised analytical technology has been applied to a range of modern analytical problems, allowing sensitive determination of a wide number of analytes from a variety of otherwise hostile matrices, including copper in beer and blood, lead in wine, petrol and river bed sediment, vanadium in aqueous media, nitrite in egg and manganese in instant tea granules. This paper gives an overview of these recent advances.     

Intracellular Photophysics of an Osmium Complex bearing an Oligothiophene Extended Ligand

This contribution describes the excited-state properties of an Osmium-complex when taken up into human cells. The complex 1 [Os(bpy)₂(IP-4T)](PF₆)₂ with bpy=2,2′-bipyridine and IP-4T=2-{5′-[3′,4′-diethyl-(2,2′-bithien-5-yl)]-3,4-diethyl-2,2′-bithiophene}imidazo[4,5-f][1,10]phenanthroline) can be discussed as a candidate for photodynamic therapy in the biological red/NIR window. The complex is taken up by MCF7 cells and localizes rather homogeneously within in the cytoplasm. To detail the sub-ns photophysics of 1 , comparative transient absorption measurements were carried out in different solvents to derive a model of the photoinduced processes. Key to rationalize the excited-state relaxation is a long-lived ³ILCT state associated with the oligothiophene chain. This model was then tested with the complex internalized into MCF7 cells, since the intracellular environment has long been suspected to take big influence on the excited state properties. In our study of 1 in cells, we were able to show that, though the overall model remained the same, the excited-state dynamics are affected strongly by the intracellular environment. Our study represents the first in depth correlation towards ex-vivo and in vivo ultrafast spectroscopy for a possible photodrug.     

Ion transmission in an electrospray ionization-mass spectrometry interface using an S-lens

We present the design and performance of an in-house built electrospray ionization-mass spectrometry (ESI-MS) interface equipped with an S-lens ion guide. The ion source was designed specifically for our ion beam experiments to investigate the chemical reactivity and deposition of the clusters and nanoparticles. It includes standard ESI-MS interface components, such as nanoelectrospray, ion transfer capillary, and the S-lens. A custom design enables systematic optimization of all relevant factors influencing ion formation and transfer through the interface. By varying the ESI voltage and flow rate, we determined the optimal operating conditions for selected silica emitters. A comparison of the pulled silica emitters with different tip inner diameters reveals that the total ion current is highest for the largest tip, whereas a tip with the smallest diameter exhibited the highest transmission efficiency through the ESI-MS interface. Ion transmission through the transfer capillary is strongly limited by its length, but the loss of ions can be reduced by increasing the capillary voltage and temperature. The S-lens was characterized over a wide range of RF frequencies and amplitudes. Maximum ion current was detected at RF amplitudes greater than 50 V peak-to-peak (p/p) and frequencies above 750 kHz, with a stable ion transmission region of about 20%. A factor of 2.6 increase in total ion current is observed for 650 kHz as RF amplitudes reach 400 V p/p. Higher RF amplitudes also focus the ions into a narrow beam, which mitigates their losses when passing through the ion guide.     

Cyclometallierungsreaktionen an o-Hydroxy-diarylazoverbindungen

Cyclometallation reactions of o-Hydroxy-diarylazocompounds The metallation of o-hydroxy-diarylazoligands with Pt(II)- or Pd (II)-salts leads not only to the classical complexes of type 3 but also to coordination compounds of type 2 , containing a metal-carbon bond. The latter coordinate carbon monoxide, which can be inserted into the metal-carbon bond, thus leading after reductive elemination of the metal to heterocyclic products.     

Complex rate constant for an electrochemical system involving an adsorbed intermediate

Two different methods of obtaining the impedance of a system involving an electrochemical reaction with an adsorbed intermediate are compared. The earlier method combines in parallel an impedance derived separately for the overall reaction with that for the rest of the system. It is appropriate for a fully supported electrolyte system but seems much less applicable to the unsupported situation. In contrast, the method derived and discussed herein involves complex reaction rate constants which may be directly incorporated in expressions for the total system impedance. This method may, therefore, be applied to either supported or unsupported situations. Several specific cases of the general complex rate constant results are discussed, particularly, various frequency dependencies possible. The overall small-signal impedance may be inductive in some parts of the frequency range and the low frequency limiting differential resistance negative, zero, or positive under various conditions.     

PNA forms an i-motif

A C-rich PNA hexanucleotide, p(C5T), has been shown to form an i-motif by nanoelectrospray ionization mass spectrometry coupled with H/D exchange, to have thermal stability comparable with its DNA analogue, but to exist over a much narrower pH range.