Unprecedented hour-long residence time of a cation in a left-handed G-quadruplex

Cations are critical for the folding and assembly of nucleic acids. In G-quadruplex structures, cations can bind between stacked G-tetrads and coordinate with negatively charged guanine carbonyl oxygens. They usually exchange between binding sites and with the bulk in solution with time constants ranging from sub-millisecond to seconds. Here we report the first observation of extremely long-lived K⁺ and NH₄⁺ ions, with an exchange time constant on the order of an hour, when coordinated at the center of a left-handed G-quadruplex DNA. A single-base mutation, that switched one half of the structure from left- to right-handed conformation resulting in a right–left hybrid G-quadruplex, was shown to remove this long-lived behaviour of the central cation.

An extremely long-lived cation has been detected in left-handed G-quadruplexes.     

New theoretical expressions for the five adsorption type isotherms classified by BET based on statistical physics treatment

New theoretical expressions to model the five adsorption isotherm types have been established. Using the grand canonical ensemble in statistical physics, we give an analytical expression to each of five physical adsorption isotherm types classified by Brunauer, Emett, and Teller, often called BET isotherms. The establishment of these expressions is based on statistical physics and theoretical considerations. This method allowed estimation of all the mathematical parameters in the models. The physicochemical parameters intervening in the adsorption process that the models present could be deduced directly from the experimental adsorption isotherms by numerical simulation. We determine the adequate model for each type of isotherm, which fixes by direct numerical simulation the monolayer, multilayer, or condensation character. New equations are discussed and results obtained are verified for experimental data from the literature. The new theoretical expressions that we have proposed, based on statistical physics treatment, are rather powerful to better understand and interpret the various five physical adsorption type isotherms at a microscopic level.     

The unexpected rearrangement of 1,5‐benzodiazepin‐2,4‐dione to a benzimidazol‐2‐one derivative during N,N'‐diglucosylation

Reaction of 1,5‐benzodiazepin‐2,4‐dione with 3‐O‐substituted‐5,6‐anhydro‐1,2‐isopropylidene‐α‐D‐glucofuranose gave the unexpected N,N'‐di‐glucofuranosyl benzimidazol‐2‐one by a novel rearrangement and ring closure reaction. A mechanism is proposed.     

Mechanism for resonant O electron stimulated desorption from condensed O2. Non-adiabatic transitions and dynamics

Absolute kinetic energy distributions and yields associated with ground state ³P and excited state ¹D oxygen atoms have been obtained for O⁻ anion electron stimulated desorption from condensed O₂ in the electron energy range 6–15 eV. The observed yields are understood as resulting essentially from dissociative electron attachment reactions via the two lowest ²Σ⁺_g O⁻₂ resonance states through adiabatic and non-adiabatic transitions to the limits O⁻(²P) + O(³P) and O⁻(²P) + O(¹D). The kinetic energy distributions show the prominent role of electron multiple collision processes and post-dissociation interactions of the O⁻ anions in the condensed phase.     

Structure determination of Na3DySi6O15 and crystal chemistry of zektzerite related compounds

The crystal structure of Na₃DySi₆O₁₅ has been solved and refined to an R₁=2.97% (wR₂=8.25%) for 1311 independent reflections. The compound was found to crystallize within the orthorhombic system with the space group Cmca (Z=8) and the lattice parameters: a=14.590(7) Å, b=17.813(4) Å, c=10.519(2) Å, V=2734.0 Å³, D_cal=3.11 g/cm³. The structure of Na₃DySi₆O₁₅ is a filled variant of the zektzerite with S like corrugated double chains of [SiO₄] tetrahedral, connected via Na⁺ and Dy³⁺ cations and running parallel to c-axis. The three-dimensional network results from the packing of these chains along [100] by skewering them in rods represented by the tunnels delimited by the S shape of the silicate chains. One of the main peculiar features of the Na₃DySi₆O₁₅ structure is the location of Na⁺ in tetrahedral sites with rather short Na-O bond lengths (2×2.243 and 2×2.262 Å).     

Influence of the building material and ventilation rate on the concentration of radon, thoron and their progenies in dwelling rooms using SSNTD and Monte Carlo simulation

A new Monte Carlo computer code was developed for determining the detection efficiencies of the CR-39 and LR-115 II solid state nuclear track detectors (SSNTD) for a-particles emitted by radon (²²²Rn) and thoron (²²⁰Rn) series inside the atmosphere of dwelling rooms. Alpha-activities due to radon, thoron and their decay products, were evaluated for the determination of the detection efficiencies of the SSNTD utilized for the emitted a-particles by measuring the corresponding track densities. The influence of the ventilation rate and building material on the concentration of radon, thoron and their progenies was investigated. Equilibrium factors between radon and its progeny and between thoron and its daughters have been evaluated in the air of the rooms.     

Staphylococcus aureus bicomponent gamma-hemolysins, HlgA, HlgB, and HlgC, can form mixed pores containing all components

Staphylococcal gamma-hemolysins are bicomponent toxins forming a protein family with leucocidins and alpha-toxin. Two active toxins (AB and CB) can be formed combining one of the class-S components, HlgA or HlgC, with the class-F component HlgB. These two gamma-hemolysins form pores with marked similarities to alpha-toxin in terms of conductance, nonlinearity of the current-voltage curve, and channel stability in the open state. AB and CB pores, however, are cation-selective, whereas alpha-toxin is anion-selective. gamma-Hemolysins' pores are hetero-oligomers formed by three or four copies of each component (indicated as 3A3B and 3C3B or 4A4B and 4C4B). Point mutants located on a beta-strand of the class-S component that forms part of the protomer-protomer contact region can prevent oligomer assembly. Interestingly, these mutants inhibit growth of pores formed not only by their natural components but also by nonstandard components. This lead to the hypothesis that mixed ABC pores could also be formed. By studying the conductance of pores, assembled in the presence of all three components (in different ratios), it was observed that the magnitudes expected for mixed pores were, indeed, present. We conclude that the gamma-hemolysin/leucocidin bicomponent toxin family may form a larger than expected number of active toxins by cross-combining various S and F components.     

Collisional dynamics of Ag19 on Pd(100): a molecular dynamics study

By means of molecular dynamics simulations based on realistic n-body potentials we investigate structural and dynamical features inherent to the energetic collision of a silver cluster (Ag₁₉) on the Pd(100) substrate. Both the system and the impact energy (E_i = 95 eV) adopted have been chosen to parallel an experimental study of size selected Ag cluster deposition on Pd(100). Our results indicate that the experimental cross section obtained via thermal energy atom scattering at the same collision energy is well reproduced by the simulations.The modeling allows to rationalize the collision outcome in terms of defect production and cluster atoms implantation. The adsorbed structures have an heterogenous nature and are mostly two-dimensional.     

Synthese De (1,2a)Benzimidazolo-1,3,5,2-triazaphosphorine-2-oxides

The reaction of hexamethylphosphotriamide or methylphosphonic bis(dimethylamide) compounds with amidines derived from N-Benzimidazoyl imidates 1 leads to (1,2a)benzimidazolo-1,3,5,2-tiazaphosphorine-2-oxides 4 in good yields. If the condensation is realized at room temperature, N-phosphonic amidines 3 can be isolated as intermediates. The isolated compounds 2 , 3 , and 4 are identified by spectroscopic methods: IR, 1 H, 13 C, 31 P, NMR, and M.S.