Base-Pairing Properties of Double-Headed Nucleotides

Nucleotides that contain two nucleobases (double-headed nucleotides) have the potential to condense the information of two separate nucleotides into one. This presupposes that both bases must successfully pair with a cognate strand. Here, double-headed nucleotides that feature cytosine, guanine, thymine, adenine, hypoxanthine, and diaminopurine linked to the C2′-position of an arabinose scaffold were developed and examined in full detail. These monomeric units were efficiently prepared by convergent synthesis and incorporated into DNA oligonucleotides by means of the automated phosphoramidite method. Their pairing efficiency was assessed by UV-based melting-temperature analysis in several contexts and extensive molecular dynamics studies. Altogether, the results show that these double-headed nucleotides have a well-defined structure and invariably behave as functional dinucleotide mimics in DNA duplexes.     

SIMS of organic layers with unknown matrix parameters: Locating the interface in dual beam argon gas cluster depth profiles

Four simple methods are evaluated to determine their accuracies for establishing the interface location in secondary ion mass spectrometry intensity depth profiles of organic layers where matrix effects have not been measured. Accurate location requires the separate measurement of each ion's matrix factor. This is often not possible, and so estimates using matrix-less methods are required. Six pure organic material interfaces are measured using many secondary ions to compare their locations from the four methods with those from full evaluation with matrix terms. For different secondary ions, matrix effects cause the apparent interface positions to vary over 20 nm. The shifts in the intensity profiles on going from a layer of P into a layer of Q are in the opposite direction to that for going from Q into P, so doubling layer thickness errors. The four methods are as follows: M1, use of the median interface position in the intensity profiles for the five lightest ions for 15 ≤ m/z ≤ 150; M2, extrapolation of the position for each ion to m/z = 0 for ions with m/z ≤ 150; M3, as M2 but for m/z ≤ 300; and M4, the extreme positions for all m/z ≤ 100. Comparison with the location using matrix terms shows their ranking, from best to worst, to be M4, M3, M1, and M2 with average errors of 10%, 12%, 14%, and 17%, respectively, of the profile interface full widths at half maximum. Use of pseudo-molecular ions is very much poorer, exceeding 50%, and should be avoided.     

Comparison of two cold atmospheric pressure plasma jet configurations in argon

The present study compares the operation of two cold atmospheric plasma jet (CAPJ) configurations: needle-to-cylinder electrode configuration (CAPJ I) and single high-voltage cylinder electrode around the quartz tube (CAPJ II). The CAPJs were operated in argon flowing through a quartz capillary with 0.5-mm inner diameter into the ambient air, and the plasma was generated by sinusoidal kHz frequency AC power supplies. The main emphasis of the study was on the mechanism of the initiation of ionization waves for these two configurations. For both CAPJs, there appeared several ionization waves during one half-period of the applied voltage waveform, and the number of ionization waves increased at higher voltage amplitudes. However, we discovered marked differences in the initiation of the ionization waves for two different CAPJ configuration. The applied voltage controlled the initiation of consecutive ionization waves, which propagated from the grounded electrode towards the tube orifice in CAPJ I. In the case of CAPJ II, certain time had to pass for the initiation of a new ionization wave, and subsequent ionization waves within the same half-period started at the tube orifice. In addition to the differences in the initiation of the ionization waves, we observed that the CAPJ I was ignited and sustained at lower voltages, while CAPJ II produced a longer plasma jet. The observed advantages and deficiencies of investigated CAPJ configurations point out their potential in different applications.     

Methane as a Selectivity Booster in the Arc‐Discharge Synthesis of Endohedral Fullerenes: Selective Synthesis of the Single‐Molecule Magnet Dy2TiC@C80 and Its Congener Dy2TiC2@C80

The use of methane as a reactive gas dramatically increases the selectivity of the arc‐discharge synthesis of M‐Ti‐carbide clusterfullerenes (M=Y, Nd, Gd, Dy, Er, Lu). Optimization of the process parameters allows the synthesis of Dy₂TiC@C₈₀‐I and its facile isolation in a single chromatographic step. A new type of cluster with an endohedral acetylide unit, M₂TiC₂@C₈₀, is discovered along with the second isomer of M₂TiC@C₈₀. Dy₂TiC@C₈₀‐(I,II) and Dy₂TiC₂@C₈₀‐I are shown to be single‐molecule magnets (SMM), but the presence of the second carbon atom in the cluster Dy₂TiC₂@C₈₀ leads to substantially poorer SMM properties.     

A Metabolomic Approach to Beer Characterization

The consumers’ interest towards beer consumption has been on the rise during the past decade: new approaches and ingredients get tested, expanding the traditional recipe for brewing beer. As a consequence, the field of “beeromics” has also been constantly growing, as well as the demand for quick and exhaustive analytical methods. In this study, we propose a combination of nuclear magnetic resonance (NMR) spectroscopy and chemometrics to characterize beer. ¹H-NMR spectra were collected and then analyzed using chemometric tools. An interval-based approach was applied to extract chemical features from the spectra to build a dataset of resolved relative concentrations. One aim of this work was to compare the results obtained using the full spectrum and the resolved approach: with a reasonable amount of time needed to obtain the resolved dataset, we show that the resolved information is comparable with the full spectrum information, but interpretability is greatly improved.     

A two-point calibration method for quantifying organic binary mixtures using secondary ion mass spectrometry in the presence of matrix effects

Quantification of the composition of binary mixtures in secondary ion mass spectrometry (SIMS) is required in the analyses of technological materials from organic electronics to drug delivery systems. In some instances, it is found that there is a linear dependence between the composition, expressed as a ratio of component volumes, and the secondary ion intensities, expressed as a ratio of intensities of ions from each component. However, this ideal relationship fails in the presence of matrix effects and linearity is observed only over small compositional ranges, particularly in the dilute limits. In this paper, we assess an empirical method, which introduces a power law dependence between the intensity ratio and the volume fraction ratio. A previously published physical model of the organic matrix effect is employed to test the limits of the method and a mixed system of 3,3′-bis(9-carbazolyl) biphenyl and tris(2-phenylpyridinato)iridium (III) is used to demonstrate the method. This paper introduces a two-point calibration, which determines both the exponent in the power law and the sensitivity factor for the conversion of ion intensity ratio into volume fraction ratio. We demonstrate that this provides significantly improved accuracy, compared with a one-point calibration, over a wide compositional range in SIMS quantification and with a weak dependence on matrix effects. Because the method enables the use of clearly identifiable secondary ions for quantitative purposes and mitigates commonly observed matrix effects in organic materials, the two-point calibration method could be of significant benefit to SIMS analysts.     

Non-linear dynamic phenomena in the behaviour of a railway wheelset model

A dicone moving on a pair of cylindrical rails can be considered as a simplified model of a railway wheelset. Taking into account the non-linear friction laws of rolling contact, the equations of motion for this non-linear mechanical system result in a set of differential-algebraic equations. Previous simulations performed with the differential-algebraic solver DASSL, [2], and experiments, [7], indicated non-linear phenomena such as limit-cycles, bifurcations as well as chaotic behaviour. In this paper the non-linear phenomena are investigated in more detail with the aid of special in-house software and the path-following algorithm PATH [10]. We apply Poincaré sections and Poincaré maps to describe the structure of periodic, quasiperiodic and chaotic motions. The analyses show that part of the chaotic behaviour of the non-linear system can be fully understood as a non-linear iterative process. The resulting stretching and folding processes are illustrated by series of Poincaré sections.     

Summary of ISO/TC 201 Standard: ISO 22415—Surface chemical analysis—Secondary ion mass spectrometry—Method for determining yield volume in argon cluster sputter depth profiling of organic materials

The International Standard ISO 22415 provides methods to measure sputtering yield volumes of organic test materials using argon cluster ions. The test materials should consist of thin films of known thicknesses between 50 and 1000 nm. The format of the test materials, the measurement of sputtering ion dose, sputtered depth, and reporting requirements for sputtering yield volumes are described.