Australian Synchrotron User Meeting 2014

Synchrotron users and experts from Australia, New Zealand, and further afield congregated in November for the Australian Synchrotron User Meeting 2014. Around 200 members of the synchrotron community attended the highly anticipated meeting held, in conjunction with the New User Symposium, at the Australian Synchrotron's National Centre for Synchrotron Science. Early career researchers played a prominent role at the meeting. Their achievements highlighted the promising capabilities of the region's next generation of synchrotron scientists.     

Monovalent cation localization in DNA A-tracts with different sequences

The free solution mobilities of 26-base pair (bp) DNA oligomers containing A-tracts with and without internal ApT steps have been measured by capillary electrophoresis, using the mobility of a 26-bp random-sequence oligomer as a reference. The background electrolytes (BGEs) contained mixtures of Li⁺ and tetrapropylammonium (TPA⁺) ions, keeping the total cation concentration constant at 0.3 M. The mobility ratios equaled 1.00 in 0.3 M TPA⁺, indicating that the A-tract and reference oligomers had the same B-form conformation in this BGE. With increasing [Li⁺], the mobility ratio decreased as Li⁺ ions became localized in the A-tract minor groove, suggesting that the A-tract was now in the B* conformation. If the A-tract contained an internal ApT step and the oligomer contained less than ∼50% A + T, the mobility ratio reached a reduced plateau value that remained constant as the [Li⁺] increased to 0.3 M. However, for A-tracts without an internal ApT step and for A-tracts embedded in oligomers containing more than 50% A + T, the mobility ratios increased again at high [Li⁺], eventually reaching a plateau value of 1.00. Hence, DNA A-tracts in solution appear to exist as mixtures of the B and B* conformations, with the fractional concentration of each conformer depending on the [Li⁺], the A-tract sequence, and the total A + T content of the oligomer.     

Shock Tube Measurements of the Rate Constant of the Reaction NCN + O2

The rate constant of the comparably slow bimolecular NCN radical reaction NCN + O₂ has been measured for the first time under combustion relevant conditions using the shock tube method. The thermal decomposition of cyanogen azide (NCN₃) served as a clean high‐temperature source of NCN radicals. NCN concentration–time profiles have been detected by narrow‐bandwidth laser absorption at cm^?1. The experiments behind incident shock waves have been performed with up to 17% O₂ in the reaction gas mixture. At such high O₂ mole fractions, it was necessary to take O₂ relaxation into account that caused a gradual decrease of the temperature during the experiment. Moreover, following fast decomposition of NCN₃ and collision‐induced intersystem crossing of the initially formed singlet NCN to its triplet ground state, an unexpected and slow additional formation of triplet NCN has been observed on a 100‐μs timescale. This delayed NCN formation was attributed to a fast recombination of ¹NCN with O₂ forming a ³NCNOO adduct acting as a reservoir species for NCN. Rate constant data for the reaction NCN + O₂ have been measured at temperatures between 1674 and 2308 K. They are best represented by the Arrhenius expression . No pressure dependence has been observed at pressures between 216 and 706 mbar.     

Highly trans‐Selective Arylation of Achmatowicz Rearrangement Products by Reductive γ‐Deoxygenation and Heck–Matsuda Reaction: Asymmetric Total Synthesis of (−)‐Musellarins A–C and Their Analogues

Fully functionalized pyranuloses derived from Achmatowicz rearrangement (AR) are versatile building blocks in organic synthesis. However, access to trans‐2,6‐dihydropyrans from pyranuloses remains underexplored. Herein, we report a new two‐step trans arylation of AR products to access 2,6‐trans‐dihydropyranones. This new trans‐arylation method built on numerous plausible, but unsuccessful, direct arylation reactions, including Ferrier‐type and Tsuji–Trost‐type reactions, was finally enabled by an unprecedented, highly regioselective γ‐deoxygenation of AR products by using Zn/HOAc and a diastereoselective Heck–Matsuda coupling. The synthetic utility of the reaction was demonstrated in the first asymmetric total synthesis of (?)‐musellarins A–C and 12 analogues in 11–12 steps. The brevity and efficiency of our synthetic route permitted preparation of enantiomerically pure musellarins and analogues (>20 mg) for preliminary cytotoxicity evaluation, which led us to identify two analogues with three‐to‐six times greater potency than the musellarins as promising new leads.     

Synthesis and pH‐Dependent Spectroscopic Behavior of 2,4,6‐Trisubstituted Pyridine Derivatives

Seven 2,4,6‐trisubstituted pyridine derivatives with N,N‐diethylaniline substituents at the 4‐position were synthesized, and their spectroscopic properties in the absence and presence of acid were studied. The spectral effects of protonation, molar absorptivities, pK_a values, and the structural origins of the observed spectral behavior were ascertained. The pyridine nitrogen was found to be more basic than the diethylamino nitrogen atom. Protonation of the pyridine ring nitrogen is associated with the appearance of a red‐shifted intramolecular charge transfer peak in the UV‐visible spectra. Favorable color indicating properties result from electron‐donating substitution at the 2 and 6 positions of pyridine, which provide a greater absorptivity of the red‐shifted peak associated with protonation of the pyridine nitrogen. These findings will assist in the design and optimization of these compounds for ion‐indicating and pH‐sensing applications.     

Phytosynthesis of Silver Nanoparticles Using Walnut (Juglans regia) Bark with Characterization of the Antibacterial Activity against Streptococcus mutans

A green method using Juglans regia bark extract was used to synthesize silver nanoparticles at room temperature with monitoring by absorption spectroscopy. The size and shape of the synthesized nanoparticles were characterized by infrared spectroscopy, transmission electron microscopy, scanning electron microscopy, high-resolution transmission electron microscopy, and small-angle X-ray scattering. The average particle size was from 10 to 30?nm. Gas chromatography–mass spectrometry (GC–MS) was used for the separation, identification, and quantification of components of the plant extracts. A possible mechanism for the synthesis of nanoparticles was elucidated based on the GC–MS results. The synthesized silver nanoparticles showed effective inhibition against Streptococcus mutans, which is the main causative agent for dental caries. The nanoparticles also showed promising antibiofilm activity by inhibiting the glucosyltransferase enzyme.     

Copper(II) halide salts and complexes of 4-amino-2-fluoropyridine: synthesis,structure and magnetic properties

Reaction of 4-amino-2-fluoropyridine (2-F-4-AP) with copper halides produced the neutral coordination complexes: (2-F-4-AP)₂CuX₂ (X = Cl(1), Br(2)). 1 crystallizes in the orthorhombic space group Pccn in a distorted square planar geometry. Magnetic susceptibility data were fit to the uniform chain Heisenberg model resulting in C = 0.439(6)emu-K/mole-Oe and J = ?28(1) K. 2 crystallizes in the monoclinic space group C2/m and is closer to distorted tetrahedral. Intermolecular Br?Cu contacts generate a square layer. Magnetic data show very weak ferromagnetic interactions [C = 0.42(1)emu-K/mol-Oe, J = 0.71(2) K]. Similarly, reaction of 2-F-4-AP with copper halides and aqueous HX in alcohol solvents produced the salts (2-F-4-APH)₂CuX₄ (X = Cl(3), Br(4)). 3 crystallizes in the triclinic space group P-1. Crystal packing reveals short Cl?Cl contacts which generate a structural ladder. However, analysis of the magnetic data suggests that only the rails of the ladder produce a viable magnetic superexchange pathway; the uniform Heisenberg chain model provides C = 0.449(1)emu-K/mol-Oe and J = -6.9(1) K. 4 is isostructural and is also best fit by a chain model [J = ?2.7(4) K]. The brominated complex (2-F-3-Br-4-APH)₂CuBr₄·2H₂O, 5, (2-F-3-Br-4-APH = 4-amino-3-bromo-2-fluoropyridinium) was serendipitously produced as a byproduct of the synthesis of 4 and was characterized by single-crystal X-ray diffraction.     

Pre-averaged kernel estimators for the drift function of a diffusion process in the presence of microstructure noise

We consider estimation of the drift function of a stationary diffusion process when we observe high-frequency data with microstructure noise over a long time interval. We propose to estimate the drift function at a point by a Nadaraya–Watson estimator that uses observations that have been pre-averaged to reduce the noise. We give conditions under which our estimator is consistent and asympotically normal. Its rate and asymptotic bias and variance are the same as those without microstructure noise. To use our method in data analysis, we propose a data-based cross-validation method to determine the bandwidth in the Nadaraya–Watson estimator. Via simulation, we study several methods of bandwidth choices, and compare our estimator to several existing estimators. In terms of mean squared error, our new estimator outperforms existing estimators.     

Applications of Vibrational Spectroscopy for Analysis of Connective Tissues

Advances in vibrational spectroscopy have propelled new insights into the molecular composition and structure of biological tissues. In this review, we discuss common modalities and techniques of vibrational spectroscopy, and present key examples to illustrate how they have been applied to enrich the assessment of connective tissues. In particular, we focus on applications of Fourier transform infrared (FTIR), near infrared (NIR) and Raman spectroscopy to assess cartilage and bone properties. We present strengths and limitations of each approach and discuss how the combination of spectrometers with microscopes (hyperspectral imaging) and fiber optic probes have greatly advanced their biomedical applications. We show how these modalities may be used to evaluate virtually any type of sample (ex vivo, in situ or in vivo) and how “spectral fingerprints” can be interpreted to quantify outcomes related to tissue composition and quality. We highlight the unparalleled advantage of vibrational spectroscopy as a label-free and often nondestructive approach to assess properties of the extracellular matrix (ECM) associated with normal, developing, aging, pathological and treated tissues. We believe this review will assist readers not only in better understanding applications of FTIR, NIR and Raman spectroscopy, but also in implementing these approaches for their own research projects.