A new and useful method for the macrocyclization of linear peptides

A new and useful procedure for the macrocyclization of linear peptides is described. The natural amino acid side chains of tyrosine (phenol), lysine (alkylamine), and histidine (imidazole) react in an intramolecular fashion with a pendent pyridine-N-oxide-carboxamide, which is selectively activated by the phosphonium salt, PyBroP. The reaction is mild, rapid, and efficient with a potentially large substrate scope. Multiple examples are provided with full characterization and analyses, including a novel aza-variant of the C-O-D ring system of vancomycin.     

Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples

To accurately determine the quantitative change of peptides and proteins in complex proteomics samples requires knowledge of how well each ion has been measured. The precision of each ions' calculated area is predicated on how uniquely it occupies its own space in m/z and elution time. Given an initial assumption that prior to the addition of the "heavy" label, all other ion detections are unique, which is arguably untrue, an initial attempt at quantifying the pervasiveness of ion interference events in a representative binary SILAC experiment was made by comparing the centered m/z and retention time of the ion detections from the "light" variant to its "heavy" companion. Ion interference rates were determined for LC-MS data acquired at mass resolving powers of 20 and 40 K with and without ion mobility separation activated. An ion interference event was recorded, if present in the companion dataset was an ion within ± its Δ mass at half-height, ±15 s of its apex retention time and if utilized by ±1 drift bin. Data are presented illustrating a definitive decrease in the frequency of ion interference events with each additional increase in selectivity of the analytical workflow. Regardless of whether the quantitative experiment is a composite of labeled samples or label free, how well each ion is measured can be determined given knowledge of the instruments mass resolving power across the entire m/z scale and the ion detection algorithm reporting both the centered m/z and Δ mass at half-height for each detected ion. Given these measurements, an effective resolution can be calculated and compared with the expected instrument performance value providing a purity score for the calculated ions' area based on mass resolution. Similarly, chromatographic and drift purity scores can be calculated. In these instances, the error associated to an ions' calculated peak area is estimated by examining the variation in each measured width to that of their respective experimental median. Detail will be disclosed as to how a final ion purity score was established, providing a first measure of how accurately each ions' area was determined as well as how precise the calculated quantitative change between labeled or unlabelled pairs were determined. Presented is how common ion interference events are in quantitative proteomics LC-MS experiments and how ion purity filters can be utilized to overcome and address them, providing ultimately more accurate and precise quantification results across a wider dynamic range.     

Elemental imaging at the nanoscale: NanoSIMS and complementary techniques for element localisation in plants

The ability to locate and quantify elemental distributions in plants is crucial to understanding plant metabolisms, the mechanisms of uptake and transport of minerals and how plants cope with toxic elements or elemental deficiencies. High-resolution secondary ion mass spectrometry (SIMS) is emerging as an important technique for the analysis of biological material at the subcellular scale. This article reviews recent work using the CAMECA NanoSIMS to determine elemental distributions in plants. The NanoSIMS is able to map elemental distributions at high resolution, down to 50 nm, and can detect very low concentrations (milligrams per kilogram) for some elements. It is also capable of mapping almost all elements in the periodic table (from hydrogen to uranium) and can distinguish between stable isotopes, which allows the design of tracer experiments. In this review, particular focus is placed upon studying the same or similar specimens with both the NanoSIMS and a wide range of complementary techniques, showing how the advantages of each technique can be combined to provide a fuller data set to address complex scientific questions. Techniques covered include optical microscopy, synchrotron techniques, including X-ray fluorescence and X-ray absorption spectroscopy, transmission electron microscopy, electron probe microanalysis, particle-induced X-ray emission and inductively coupled plasma mass spectrometry. Some of the challenges associated with sample preparation of plant material for SIMS analysis, the artefacts and limitations of the technique and future trends are also discussed.     

Coexistence of spin glass and antiferromagnetic orders in Ba3Fe2.15W0.85O8.72

Ba(3)Fe(2.15)W(0.85)O(8.72) has been grown as large single crystals using the floating-zone method, permitting very precise characterization of the nuclear and magnetic structures by neutron and synchrotron diffraction methods. The results of our structural investigation are combined with dc and ac magnetization and heat capacity measurements to give an unusually complete and detailed picture of a complex magnetic system. The compound crystallizes in the hexagonal perovskite structure (space group P6(3)/mmc) and reveals antiferromagnetic order below T(N) = 290 K. Frequency-dependent ac susceptibility and the presence of magnetic viscosity suggest the onset of a spin glass component in this material below T(f) = 60 K. These findings are discussed on the basis of detailed analysis of the crystalo-chemical properties, supported by ab initio (density functional theory) calculations.     

Production and validation of model iron-tannate dyed textiles for use as historic textile substitutes in stabilisation treatment studies

ABSTRACT: BACKGROUND: For millennia, iron-tannate dyes have been used to colour ceremonial and domestic objects shades of black, grey, or brown. Surviving iron-tannate dyed objects are part of our cultural heritage but their existence is threatened by the dye itself which can accelerate oxidation and acid hydrolysis of the substrate. This causes many iron-tannate dyed textiles to discolour and decrease in tensile strength and flexibility at a faster rate than equivalent undyed textiles. The current lack of suitable stabilisation treatments means that many historic iron-tannate dyed objects are rapidly crumbling to dust with the knowledge and value they hold being lost forever. This paper describes the production, characterisation, and validation of model iron-tannate dyed textiles as substitutes for historic iron-tannate dyed textiles in the development of stabilisation treatments. Spectrophotometry, surface pH, tensile testing, SEM-EDX, and XRF have been used to characterise the model textiles. RESULTS: On application to textiles, the model dyes imparted mid to dark blue-grey colouration, an immediate tensile strength loss of the textiles and an increase in surface acidity. The dyes introduced significant quantities of iron into the textiles which was distributed in the exterior and interior of the cotton, abaca, and silk fibres but only in the exterior of the wool fibres. As seen with historic iron tannate dyed objects, the dyed cotton, abaca, and silk textiles lost tensile strength faster and more significantly than undyed equivalents during accelerated thermal ageing and all of the dyed model textiles, most notably the cotton, discoloured more than the undyed equivalents on ageing. CONCLUSIONS: The abaca, cotton, and silk model textiles are judged to be suitable for use as substitutes for cultural heritage materials in the testing of stabilisation treatments.     

Floer cohomology and geometric composition of Lagrangian correspondences

We prove an isomorphism of Floer cohomologies under geometric composition of Lagrangian correspondences in exact and monotone settings.     

Entangled and sequential quantum protocols with dephasing

Sequences of commuting quantum operators can be parallelized using entanglement. This transformation is behind some optimal quantum metrology protocols and recent results on quantum circuit complexity. We show that dephasing quantum maps in arbitrary dimension can also be parallelized. This implies that for general dephasing noise the protocol with entanglement is not more fragile than the corresponding sequential protocol and, conversely, the sequential protocol is not less effective than the entangled one. We derive this result using tensor networks. Furthermore, we only use transformations strictly valid within string diagrams in dagger compact closed categories. Therefore, they apply verbatim to other theories, such as geometric quantization and topological quantum field theory. This clarifies and characterizes to some extent the role of entanglement in general quantum theories.     

First-principles optical spectra for F centers in MgO

The study of the oxygen vacancy (F center) in MgO has been aggravated by the fact that the positively charged and the neutral vacancy (F+ and F0, respectively) absorb at practically identical energies. Here we apply many-body perturbation theory in the G0W0 approximation and the Bethe-Salpeter approach to calculate the optical absorption and emission spectrum of the oxygen vacancy in all three charge states. We observe unprecedented agreement between the calculated and the experimental optical absorption spectra for the F0 and F+ center. Our calculations reveal that not only the absorption but also the emission spectra of different charge states peak at nearly the same energy, which leads to a reinterpretation of the F center's optical properties.     

Phonon-assisted optical absorption in silicon from first principles

The phonon-assisted interband optical absorption spectrum of silicon is calculated at the quasiparticle level entirely from first principles. We make use of the Wannier interpolation formalism to determine the quasiparticle energies, as well as the optical transition and electron-phonon coupling matrix elements, on fine grids in the Brillouin zone. The calculated spectrum near the onset of indirect absorption is in very good agreement with experimental measurements for a range of temperatures. Moreover, our method can accurately determine the optical absorption spectrum of silicon in the visible range, an important process for optoelectronic and photovoltaic applications that cannot be addressed with simple models. The computational formalism is quite general and can be used to understand the phonon-assisted absorption processes in general.