Quantifying unfrozen water in frozen soil by high-field 2H NMR

To understand wintertime controls of biogeochemical processes in high latitude soils it is essential to distinguish between direct temperature effects and the effects of changes in water availability mediated by freezing. Efforts to separate these controls are hampered by a lack of adequate methods to determine the proportion of unfrozen water. In this study we present a high-field 2H2O NMR method for quantifying unfrozen water content in frozen soil. The experimental material consisted of the humic layer of a boreal spruce forest soil mixed with varying proportions of quartz sand and humidified with deuterium-enriched water. The relative standard deviation of unfrozen water content (measured as NMR signal integral) was less than 2% for repeated measurements on a given sample and 3.5% among all samples, based on a total of 16 measurements. As compared to 1H NMR, this 2H NMR method was found to be superior for several reasons: it is less sensitive to field inhomogeneity and paramagnetic impurities, it gives a bigger line shape difference between the ice and liquid signal, it shows a sharper response to water fusion, and it excludes the possibility of hydrogen in the organic material interfering with the measurement.     

Prediction of work piece geometry in electrochemical cavity sinking

A computer-implemented model for predicting ECM work piece geometry has been developed and experimentally verified with a commercial ECM machine for cavity sinking in copper and 302-stainless steel with 2N K NO₃ electrolyte. Constant tool piece feed rates of 7–10 × 10^?4 cm/s, and applied voltages of 11–25 V were used. The model predicts the dependence of work piece geometry on operating conditions and on the electrochemical and physical properties of the metal—electrolyte pair. Comparison of eight equilibrium and six unsteady state experimental cavity profiles in copper showed satisfactory agreement with predictions, as did five equilibrium profiles for cavity sinking in 302-stainless steel.     

Improvement of Aglycone π-Stacking Yields Nanomolar to Sub-nanomolar FimH Antagonists

Antimicrobial resistance has become a serious concern for the treatment of urinary tract infections. In this context, an anti-adhesive approach targeting FimH, a bacterial lectin enabling the attachment of E. coli to host cells, has attracted considerable interest. FimH can adopt a low/medium-affinity state in the absence and a high-affinity state in the presence of shear forces. Until recently, mostly the high-affinity state has been investigated, despite the fact that a therapeutic antagonist should bind predominantly to the low-affinity state. In this communication, we demonstrate that fluorination of biphenyl α-d -mannosides leads to compounds with perfect π–π stacking interactions with the tyrosine gate of FimH, yielding low nanomolar to sub-nanomolar K_D values for the low- and high-affinity states, respectively. The face-to-face alignment of the perfluorinated biphenyl group of FimH ligands and Tyr48 was confirmed by crystal structures as well as ¹H,¹⁵N-HSQC NMR analysis. Finally, fluorination improves pharmacokinetic parameters predictive for oral availability.     

Minimizing profile error when estimating the sieve-size distribution of iron ore pellets using ordinal logistic regression

Size measurement of pellets in industry is usually performed by manual sampling and sieving techniques. Automatic on-line analysis of pellet size based on image analysis techniques would allow non-invasive, frequent and consistent measurement. We evaluate the statistical significance of the ability of commonly used size and shape measurement methods to discriminate among different sieve-size classes using multivariate techniques. Literature review indicates that earlier works did not perform this analysis and selected a sizing method without evaluating its statistical significance. Backward elimination and forward selection of features are used to select two feature sets that are statistically significant for discriminating among different sieve-size classes of pellets. The diameter of a circle of equivalent area is shown to be the most effective feature based on the forward selection strategy, but an unexpected five-feature classifier is the result using the backward elimination strategy. The discrepancy between the two selected feature sets can be explained by how the selection procedures calculate a feature's significance and that the property of the 3D data provides an orientational bias that favours combination of Feret-box measurements. Size estimates of the surface of a pellet pile using the two feature sets show that the estimated sieve-size distribution follows the known sieve-size distribution.     

Experimental Validation of a Fundamental Model for PCR Efficiency

Recently a theoretical analysis of PCR efficiency has been published by Booth et al. (2010). The PCR yield is the product of three efficiencies: (i) the annealing efficiency is the fraction of templates that form binary complexes with primers during annealing, (ii) the polymerase binding efficiency is the fraction of binary complexes that bind to polymerase to form ternary complexes and (iii) the elongation efficiency is the fraction of ternary complexes that extend fully. Yield is controlled by the smallest of the three efficiencies and control could shift from one type of efficiency to another over the course of a PCR experiment. Experiments have been designed that are specifically controlled by each one of the efficiencies and the results are consistent with the mathematical model. The experimental data has also been used to quantify six key parameters of the theoretical model. An important application of the fully characterized model is to calculate initial template concentration from real-time PCR data. Given the PCR protocol, the midpoint cycle number (where the template concentration is half that of the final concentration) can be theoretically determined and graphed for a variety of initial DNA concentrations. Real-time results can be used to calculate the midpoint cycle number and consequently the initial DNA concentration, using this graph. The application becomes particularly simple if a conservative PCR protocol is followed where only the annealing efficiency is controlling.     

Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases

Nitriles, which are mostly needed and produced by the chemical industry, play a major role in various industry segments, ranging from high‐volume, low‐price sectors, such as polymers, to low‐volume, high‐price sectors, such as chiral pharma drugs. A common industrial technology for nitrile production is ammoxidation as a gas‐phase reaction at high temperature. Further popular approaches are substitution or addition reactions with hydrogen cyanide or derivatives thereof. A major drawback, however, is the very high toxicity of cyanide. Recently, as a synthetic alternative, a novel enzymatic approach towards nitriles has been developed with aldoxime dehydratases, which are capable of converting an aldoxime in one step through dehydration into nitriles. Because the aldoxime substrates are easily accessible, this route is of high interest for synthetic purposes. However, whenever a novel method is developed for organic synthesis, it raises the question of substrate scope as one of the key criteria for application as a “synthetic platform technology”. Thus, the scope of this review is to give an overview of the current state of the substrate scope of this enzymatic method for synthesizing nitriles with aldoxime dehydratases. As a recently emerging enzyme class, a range of substrates has already been studied so far, comprising nonchiral and chiral aldoximes. This enzyme class of aldoxime dehydratases shows a broad substrate tolerance and accepts aliphatic and aromatic aldoximes, as well as arylaliphatic aldoximes. Furthermore, aldoximes with a stereogenic center are also recognized and high enantioselectivities are found for 2‐arylpropylaldoximes, in particular. It is further noteworthy that the enantiopreference depends on the E and Z isomers. Thus, opposite enantiomers are accessible from the same racemic aldehyde and the same enzyme.     

Supramolecular Capsules Derived from Resorcin[4]arenes by H-Bonding and Metal Coordination: Synthesis,Characterization, and Single-Molecule Force Spectroscopy

Self-assembly by H-bonding and by metal-coordination of functionalized calix[4]arenes and cavitands to large supramolecular capsules is described. In addition, a new method of analyzing supramolecular recognition processes at the single molecule level is discussed. By measuring interaction forces in a hydrogen-bonded assembly using single-molecule force spectroscopy (SMFS), the dynamics of the self-assembly process can be evaluated. In the future, consequent application of this new technique will influence supramolecular design principles and the use of non-covalent interactions as construction elements in the field of nanotechnology.     

Chemoenzymatic Total Synthesis of Sorbicatechol Structural Analogues and Evaluation of Their Antiviral Potential

Sorbicillinoids are fungal polyketides characterized by highly complex and diverse molecular structures, with considerable stereochemical intricacy combined with a high degree of oxygenation. Many sorbicillinoids possess promising biological activities. An interesting member of this natural product family is sorbicatechol A, which is reported to have antiviral activity, particularly against influenza A virus (H1N1). Through a straightforward, one-pot chemoenzymatic approach with recently developed oxidoreductase SorbC, the characteristic bicyclo[2.2.2]octane core of sorbicatechol is structurally diversified by variation of its natural 2-methoxyphenol substituent. This facilitates the preparation of a focused library of structural analogues bearing substituted aromatic systems, alkanes, heterocycles, and ethers. Fast access to this structural diversity provides an opportunity to explore the antiviral potential of the sorbicatechol family.     

Two‐Step Protein Labeling by Using Lipoic Acid Ligase with Norbornene Substrates and Subsequent Inverse‐Electron Demand Diels–Alder Reaction

Inverse‐electron‐demand Diels–Alder cycloaddition (DA_inv) between strained alkenes and tetrazines is a highly bio‐orthogonal reaction that has been applied in the specific labeling of biomolecules. In this work we present a two‐step labeling protocol for the site‐specific labeling of proteins based on attachment of a highly stable norbornene derivative to a specific peptide sequence by using a mutant of the enzyme lipoic acid ligase A (LplA^W37V), followed by the covalent attachment of tetrazine‐modified fluorophores to the norbornene moiety through the bio‐orthogonal DA_inv . We investigated 15 different norbornene derivatives for their selective enzymatic attachment to a 13‐residue lipoic acid acceptor peptide (LAP) by using a standardized HPLC protocol. Finally, we used this two‐step labeling strategy to label proteins in cell lysates in a site‐specific manner and performed cell‐surface labeling on living cells.