Optimal boundary discretization by variational data assimilation

A variational data assimilation technique applied to the identification of the optimal discretization of interpolation operators and derivatives in the nodes adjacent to the boundary of the domain is discussed in frames of the linear shallow water model. The advantage of controlling the discretization of operators near the boundary rather than boundary conditions is shown. Assimilating data that have been produced by the same model on a finer grid, in a model on a coarse grid, we have shown that optimal discretization allows us to correct such errors of the numerical scheme as under‐resolved boundary layer and wrong wave velocity. Copyright © 2010 John Wiley & Sons, Ltd.     

Phosphorinane and Enol Rings in One Molecule. Evidence for Reciprocal Stabilization of Half-Chair Conformations

Abstract.

The X-ray crystal structure of 2-(2′,4′-dioxo-3′-pentyl)-5,5-dimethyl-2-oxo-1,3,2-dioxaphosphorinane (2) reveals significant half-chair distortion of the axially oriented cisenol ring. The molecule also undergoes in-plane deformations. R(O...O) = 2.410 Å in the enol moiety indicates a very strong hydrogen bonding. The enol content, δ_OH and thermodynamic parameters for the axial-equatorial conformational and keto-enol equilibriums were obtained from ¹H, ³¹P NMR and IR measurements in comparison with the planar 4,6-dimethyl isomer (1) containing equatorially oriented enol ring. The X-ray single crystal structure of 5,5-dimethyl-2-(methoxycarbonyl-3′-oxo-2′-butyl)-2-oxo-1,3,2-dioxaphosphorinane (3) reveals the unusual half-chair conformation of the dioxaphosphorinane cycle disposed a trans-enol ring substituent. ¹H, ³¹P NMR and IR solution data support the same structure displays a strong conformational preference while the minor forms are chair conformers with an axial or equatorial cis-enol ring.     

NOTE: Synthesis and Characterization of a Poly(acrylamide) with Pendant 1,4-piperazine-2,5-dione Moieties via Post-polymerization Cyclization

A poly(acrylamide) was synthesized from N ^α -Boc-N ^? -acrolyl-l-lysylglycine methyl ester via radical polymerization. This polymer typically had Mn ～ 100,000 g/mol, Mw ～ 300,000 g/mol, and a T_g of 93°C. Removal of Boc with TFA and cyclization with DABCO? in DMSO at 65°C afforded a soluble piperazinedione-containing polymer that had a T_g of 157°C and thermal stability up to 300°C. These results demonstrate a viable and efficient synthetic route to piperazinedione-containing polyacrylamides of high molecular weight. Related polymers that incorporate substituted indane moieties could be useful high T_g materials for fabrication of LC and NLO devices.     

Homochiral Ketals in Organic Synthesis. Enantioselective Synthesis of (4S, 5S)-4,5-Dihydroxycyclopent-2-En-1-One Isopropylidine Ketal

The title compound has been synthesized in 17% yield over six steps from 2-cyclopenten-1-one. The key step is catalytic osmylation of 4-bromo-2-cyclopenten-1-one 1,4-di-O-benzyl-D-threitol ketal to produce a chromatographically separable mixture of diastereomeric diols.     

Facile and convenient synthesis of aryl hydrazines via copper-catalyzed C–N cross-coupling of aryl halides and hydrazine hydrate

An efficient and convenient method for the synthesis of aryl hydrazines has been developed via copper-catalyzed cross-coupling of aryl bromides and hydrazine with a readily accessible ligand and water as a solvent. The multigram scale procedure is applicable to aryl bromides bearing both moderately electron-donating and electron-withdrawing substituents in the aromatic nucleus. No column chromatography is required to obtain aryl hydrazine hydrochlorides in good yields.     

Characterization of hydromedusan Ca2+-regulated photoproteins as a tool for measurement of Ca2+concentration

Calcium ion is a ubiquitous intracellular messenger, performing this function in many eukaryotic cells. To understand calcium regulation mechanisms and how disturbances of these mechanisms are associated with disease states, it is necessary to measure calcium inside cells. Ca²⁺-regulated photoproteins have been successfully used for this purpose for many years. Here we report the results of comparative studies on the properties of recombinant aequorin from Aequorea victoria, recombinant obelins from Obelia geniculata and Obelia longissima, recombinant mitrocomin from Mitrocoma cellularia, and recombinant clytin from Clytia gregaria as intracellular calcium indicators in a set of identical in vitro and in vivo experiments. Although photoproteins reveal a high degree of identity of amino acid sequences and spatial structures, and, apparently, have a common mechanism for the bioluminescence reaction, they were found to differ in the Ca²⁺ concentration detection limit, the sensitivity of bioluminescence to Mg²⁺, and the rates of the rise of the luminescence signal with a sudden change of Ca²⁺ concentration. In addition, the bioluminescence activities of Chinese hamster ovary cells expressing wild-type photoproteins also differed. The light signals of cells expressing mitrocomin, for example, slightly exceeded the background, suggesting that mitrocomin may be hardly used to detect intracellular Ca²⁺ without modifications improving its properties. On the basis of experiments on the activation of endogenous P2Y₂ receptor in Chinese hamster ovary cells by ATP, we suggest that wild-type aequorin and obelin from O. longissima are more suitable for calcium detection in cytoplasm, whereas clytin and obelin from O. geniculata can be used for calcium measurement in cell compartments with high Ca²⁺ concentration. Figure

Hydromedusan photoproteins differ in Ca²⁺ concentration detection limit, sensitivity of bioluminescence to Mg²⁺, and rates of rise of luminescence signal with a sudden change of [Ca²⁺] despite a high degree of identity of their amino acid sequences and spatial structures, and, apparently, a common mechanism for the bioluminescence reaction.     

Enumeration of non-labile oxygen atoms in dissolved organic matter by use of 16O/18O exchange and Fourier transform ion-cyclotron resonance mass spectrometry

We report a simple approach for enumeration of non-labile oxygen atoms in individual molecules of dissolved organic matter (DOM), using acid-catalyzed ¹⁶O/¹⁸O exchange and ultrahigh-resolution Fourier-transform ion-cyclotron-resonance mass spectrometry (FTICR-MS). We found that by dissolving DOM in H₂ ¹⁸O at 95 °C for 20 days it is possible to replace all oxygen atoms of DOM molecules (excluding oxygen from ether groups) with ¹⁸O. The number of exchanges in each molecule can be determined using high-resolution FTICR. Using the proposed method we identified the number of non-labile oxygen atoms in 231 molecules composing DOM. Also, using a previously developed hydrogen–deuterium (H/D)-exchange approach we identified the number of labile hydrogen atoms in 450 individual molecular formulas. In addition, we observed that several backbone hydrogen atoms can be exchanged for deuterium under acidic conditions. The method can be used for structural and chemical characterization of individual DOM molecules, comparing different DOM samples, and investigation of biological pathways of DOM in the environment.     

xMAP-based analysis of three most prevalent staphylococcal toxins in Staphylococcus aureus cultures

Detection of staphylococcal toxins presents a great interest for medical diagnostics. Screening of clinical samples for the presence of several types of staphylococcal toxins using traditional methods—biological tests on animals or cell cultures as well as ELISA—is laborious. Multiplex detection methods would simplify testing. We have designed an xMAP-based assay to detect three staphylococcal toxins—enterotoxins A and B (SEA and SEB) and toxic shock syndrome toxin (TSST)—in cultural supernatants obtained from different strains of Staphylococcus aureus. The limits of detection of SEA, SEB, and TSST multiplex detection in S. aureus growth medium were 10, 1,000, and 5 pg/mL, respectively. Fifty-nine samples of S. aureus cultural supernatants were tested with the xMAP assay. The developed assay has proved highly effective detection of the natural toxins in the samples obtained due to bacterial cells cultivation. In prospect, the developed test system can be used in clinical diagnostics and in monitoring of foodstuffs and environmental objects.     

Computational Insights into the Catalytic Mechanism of Is-PETase: An Enzyme Capable of Degrading Poly(ethylene) Terephthalate

Is-PETase has become an enzyme of significant interest due to its ability to catalyse the degradation of polyethylene terephthalate (PET) at mesophilic temperatures. We performed hybrid quantum mechanics and molecular mechanics (QM/MM) at the DSD-PBEP86-D3/ma-def2-TZVP/CHARMM27//rev-PBE-D3/dev2-SVP/CHARMM level to calculate the energy profile for the degradation of a suitable PET model by this enzyme. Very low overall barriers are computed for serine protease-type hydrolysis steps (as low as 34.1 kJ mol⁻¹). Spontaneous deprotonation of the final product, terephthalic acid, with a high computed driving force indicates that product release could be rate limiting.     

Development of Magnesium Anode-Based Transient Primary Batteries

Biodegradable primary batteries, also known as transient batteries, are essential to realize autonomous biodegradable electronic devices with high performance and advanced functionality. In this work, magnesium, copper, iron, and zinc – metals that exist as trace elements in the human body – were tested as materials for biomedical transient electronic devices. Different full cell combinations of Mg and X (where X = Cu, Fe, and Zn and the anodized form of the metals) with phosphate buffered saline (PBS) as electrolyte were studied. To form the cathodes, metal foils were anodized galvanostatically at a current density of 2.0 mA cm⁻² for 30 mins. Electrochemical measurements were then conducted for each electrode combination to evaluate full cell battery performance. Results showed that the Mg−Cu_anodized chemistry has the highest power density at 0.99 mW/cm². Nominal operating voltages of 1.26 V for the first 0.50 h and 0.63 V for the next 3.7 h were observed for Mg−Cu_anodized which was discharged at a current density of 0.70 mA cm⁻². Among the materials tested, Mg−Cu_anodized exhibited the best discharge performance with an average specific capacity of 2.94 mAh cm⁻², which is comparable to previous reports on transient batteries.