Glycosyl‐Substituted Dicarboxylates as Detergents for the Extraction,Overstabilization, and Crystallization of Membrane Proteins

To tackle the problems associated with membrane protein (MP) instability in detergent solutions, we designed a series of glycosyl‐substituted dicarboxylate detergents (DCODs) in which we optimized the polar head to clamp the membrane domain by including, on one side, two carboxyl groups that form salt bridges with basic residues abundant at the membrane–cytoplasm interface of MPs and, on the other side, a sugar to form hydrogen bonds. Upon extraction, the DCODs 8 b , 8 c , and 9 b preserved the ATPase function of BmrA, an ATP‐binding cassette pump, much more efficiently than reference or recently designed detergents. The DCODs 8 a , 8 b , 8 f , 9 a , and 9 b induced thermal shifts of 20 to 29 °C for BmrA and of 13 to 21 °C for the native version of the G‐protein‐coupled adenosine receptor A_2AR. Compounds 8 f and 8 g improved the diffraction resolution of BmrA crystals from 6 to 4 Å. DCODs are therefore considered to be promising and powerful tools for the structural biology of MPs.     

and interpolation between Banach lattices

We study the possibility of obtaining the -norm by an interpolation method starting from a couple of Banach lattice norms. We describe all couples of Banach lattice norms in such that the -norm is a strict interpolation norm between them. Further we consider the possibility of obtaining the -norm by any method which guarantees interpolation of not only linear operators (= bilinear forms on but also of all polylinear forms. Here we show that either one of the initial norms has to be proportional to the -norm, or both have to be weighted -norms.

     

yDNA versus xDNA pyrimidine nucleobases: computational evidence for dependence of duplex stability on spacer location

The structural and binding properties of the natural and x- and y-pyrimidines were compared using computational methods. Our calculations show that although the x-pyrimidines favor different orientations about the glycosidic bond compared to the natural pyrimidines, which could have implications for the formation and resulting stability of xDNA duplexes and jeopardize the selectivity of expanded nucleobases, y-pyrimidines have rotational profiles more similar to the natural bases. Increasing the pyrimidine size using a benzene spacer leads to relatively minor changes in the hydrogen-bond strength of isolated Watson-Crick base pairs. However, differences in the anomeric carbon distances in pairs composed of x- or y-pyrimidines suggest yDNA may yield a more optimal expanded structure. By stacking two monomers via their centers of mass, we find that the expanded nucleobases stack much stronger than the natural bases. Additionally, although replacing xT by yT changes the stacking energy by less than 5 kJ mol (-1), replacing xC by yC significantly strengthens complexes with the natural nucleobases (by up to 30%). Calculations on larger duplex models composed of four nucleobases reveal that x- and y-pyrimidines can increase duplex stability of natural helices by strengthening both the intra and interstrand stacking interactions. Furthermore, when the total stability (sum of all hydrogen-bonding and (intrastrand and interstrand) stacking interactions) of the larger models is considered, y-pyrimidines lead to more stable complexes than x-pyrimidines for all but three duplex sequences. Thus, through analysis of a variety of properties, our calculations suggest that the location of the benzene spacer affects the properties of expanded nucleobases and the stability of expanded duplexes, and therefore should be carefully considered when designing future expanded analogues.     

Fruit juice authentication by <Superscript>1</Superscript>H NMR spectroscopy in combination with different chemometrics tools

To discriminate orange juice from grapefruit juice in a context of fraud prevention, ¹H NMR data were submitted to different treatments to extract informative variables which were then analysed using multivariate techniques. Averaging contiguous data points of the spectrum followed by logarithmic transformation improved the results of the data analysis. Moreover, supervised variable selection methods gave better rates of classification of the juices into the correct groups. Last, independent-component analysis gave better classification results than principal-component analysis. Hence, ICA may be an efficient chemometric tool to detect differences in the ¹H NMR spectra of similar samples, and so may be useful for authentication of foods.     

Molecular dynamics simulation of thermomechanical properties of montmorillonite crystal. 1. Isolated clay nanoplate

The structure and mechanical properties of clay nanoparticles is a subject of growing interest because of their numerous applications in engineering. We present the results of molecular dynamics simulation for a single nanoplate of pyrophyllite - a 2:1 clay mineral consisting of two tetrahedral sheets of SiO4 and an intervening octahedral AlO6 sheet. Simulations were performed in the temperature interval from 5 to 750 K using the ionic-type potentials of Cygan et al. On this basis the temperature dependences of structural parameters, characterizing both tetrahedral and octahedral sheets as well as single lamella, have been studied. Two slightly different structures were observed in this wide temperature interval. The mechanical properties of the nanoplate were calculated from stress-strain diagrams, which have been obtained at relatively slow rates of deformation (for molecular simulations). Using different types of loading, we calculated the full elasticity tensor and estimated the influence of temperature on its components. We estimated also the bending and torsion stiffnesses of the nanoplate as specific characteristics of this type of particle. Because the nanoplate is atomically thin, a reasonable determination of the thickness is a nontrivial problem, both in the modeling of mechanical properties and in physical interpretation of the obtained data. We propose a procedure for its calculation.     

Focus on harsh environment mass spectrometry

Editorial

Focus on harsh environment mass spectrometry     

Mechanistic Evidence of a Ni(0/II/III) Cycle for Nickel Photoredox Amide Arylation

This work demonstrates the dominance of a Ni(0/II/III) cycle for Ni-photoredox amide arylation, which contrasts with other Ni-photoredox C-heteroatom couplings that operate via Ni(I/III) self-sustained cycles. The kinetic data gathered when using different Ni precatalysts supports an initial Ni(0)-mediated oxidative addition into the aryl bromide. Using NiCl₂ as the precatalyst resulted in an observable induction period, which was found to arise from a photochemical activation event to generate Ni(0) and to be prolonged by unproductive comproportionation between the Ni(II) precatalyst and the in situ generated Ni(0) active species. Ligand exchange after oxidative addition yields a Ni(II) aryl amido complex, which was identified as the catalyst resting state for the reaction. Stoichiometric experiments showed that oxidation of this Ni(II) aryl amido intermediate was required to yield functionalized amide products. The kinetic data presented supports a rate-limiting photochemically-mediated Ni(II/III) oxidation to enable C−N reductive elimination. An alternative Ni(I/III) self-sustained manifold was discarded based on EPR and kinetic measurements. The mechanistic insights uncovered herein will inform the community on how subtle changes in Ni-photoredox reaction conditions may impact the reaction pathway, and have enabled us to include aryl chlorides as coupling partners and to reduce the Ni loading by 20-fold without any reactivity loss.     

Gas-phase carbene radical anions: new mechanistic insights

The gas-phase reactivity of the CHCl*- anion has been investigated with a series of halomethanes (CCl4, CHCl3, CH2Cl2, and CH3Cl) using a FA-SIFT instrument. Results show that this anion primarily reacts via substitution and by proton transfer. In addition, the reactions of CHCl*- with CHCl3 and CH2Cl2 form minor amounts of Cl2*- and Cl-. The isotopic distribution of these two products is consistent with an insertion-elimination mechanism, where the anion inserts into a C-Cl bond to form an unstable intermediate, which eliminates either Cl2*- or Cl- and Cl*. Neutral and cationic carbenes are known to insert into single bonds; however, this is the first observation of such reactivity for carbene anions.     

Mixtures of interacting particles with well-defined composition field coupling chi parameters

This article proposes a systematic, quantitative treatment of the problem of associating a scalar Flory-Huggins-like chi parameter directly with the interaction potentials in a binary mixture of point particles. This work fulfills the need for a general, quantitative way to compare chi values in explicitly simulated ensembles of lattice and off-lattice polymer models with field theoretic calculations. Emphasis is placed on constructing particle models where chi is relatively well defined. In general, chi is defined through pair correlation functions, whose thermal fluctuations are coupled to local average composition and composition gradients. This implies that chi is composition dependent even in the simplest particle models. At the same time, by quantifying this effect, it is found that composition-independent chi may be defined to within a few percent for cases where the range of the potential is large relative to the interparticle distance. An explicit formula for chi in terms of interaction potentials is given.