A New Thiolate-Bound Dimanganese Cluster as a Structural and Functional Model for Class Ib Ribonucleotide Reductases

In class Ib ribonucleotide reductases (RNRs) a dimanganese(II) cluster activates superoxide (O₂⋅⁻) rather than dioxygen (O₂), to access a high valent Mn^III−O₂−Mn^IV species, responsible for the oxidation of tyrosine to tyrosyl radical. In a biomimetic approach, we report the synthesis of a thiolate-bound dimanganese complex [Mn^II₂(BPMT)(OAc)₂](ClO)₄ (BPMT=(2,6-bis{[bis(2-pyridylmethyl)amino]methyl}-4-methylthiophenolate) ( 1 ) and its reaction with O₂⋅⁻ to form a [(BPMT)MnO₂Mn]²⁺ complex 2 . Resonance Raman investigation revealed the presence of an O−O bond in 2 , while EPR analysis displayed a 16-line S_t=1/2 signal at g=2 typically associated with a Mn^IIIMn^IV core, as detected in class Ib RNRs. Unlike all other previously reported Mn−O₂−Mn complexes, generated by O₂⋅⁻ activation at Mn₂ centers, 2 proved to be a capable electrophilic oxidant in aldehyde deformylation and phenol oxidation reactions, rendering it one of the best structural and functional models for class Ib RNRs.     

SLE Boundary Visits

We study the probabilities with which chordal Schramm–Loewner evolutions (SLE) visit small neighborhoods of boundary points. We find formulas for general chordal SLE boundary visiting probability amplitudes, also known as SLE boundary zig-zags or order refined SLE multi-point Green’s functions on the boundary. Remarkably, an exact answer can be found to this important SLE question for an arbitrarily large number of marked points. The main technique employed is a spin chain–Coulomb gas correspondence between tensor product representations of a quantum group and functions given by Dotsenko–Fateev type integrals. We show how to express these integral formulas in terms of regularized real integrals, and we discuss their numerical evaluation. The results are universal in the sense that apart from an overall multiplicative constant the same formula gives the amplitude for many different formulations of the SLE boundary visit problem. The formula also applies to renormalized boundary visit probabilities for interfaces in critical lattice models of statistical mechanics: we compare the results with numerical simulations of percolation, loop-erased random walk, and Fortuin–Kasteleyn random cluster models at Q = 2 and Q = 3, and find good agreement.     

Assessment of priority pesticides,degradation products,and pesticide adjuvants in groundwaters and top soils from agricultural areas of the Ebro river basin

Gas chromatography-mass spectrometry (GC/MS) was employed for the determination of 30 widely used pesticides including various transformation products and alkylphenols in water and agricultural soils with the aim of assessing the impact of these compounds in agricultural soils and the underlying aquifer. The extraction, clean-up, and analytical procedures were optimized for both water and soil samples to provide a highly robust method capable of determining target analytes at the ppb–ppt level with high precision. For water samples, different solid-phase extraction cartridges and conditions were optimized; similarly, pressurized liquid extraction conditions were tested to provide interference-free extracts and high sensitivity. Instrumental LODs of 3–4 pg were obtained. The multi-residue extraction procedures were applied to the analysis of groundwaters and agricultural soils from the Ebro river basin (NE Spain). Most ubiquitous herbicides detected were triazines but some acetanilides and organophosphorus pesticides were also found; the pesticide additive tributylphosphate was found in all water samples. Levels varied between 0.57 and 5.37 μg/L in groundwater, whereas nonylphenol was the sole compound detected in soil. Alkylphenols are used as adjuvants in pesticide formulations and are present in sludges employed as soil fertilizers. Occurrence was found to be similar to other environmental studies.     

A generalized anisotropic and asymmetric yield criterion with adjustable complexity

During the past decades, numerous yield criteria for orthotropic materials, possibly showing tension–compression asymmetry, were developed. Although they were applied successfully to forming simulations, they are usually only adequate for a specific class of materials. The aim of this work is to present a generalized, pressure-independent criterion for plane stress states on the base of a two-dimensional Fourier series. Its complexity is adjustable through the number of considered Fourier coefficients, and thus, albeit using an associated flow rule, virtually any number of experimental data can be captured exactly. The criterion is applicable for materials with or without tension–compression asymmetry.     

New Nitriminotetrazoles – Synthesis,Structures and Characterization

The reactions of 5‐nitriminotetrazole ( 4 ) with 1‐methyl‐5‐aminotetrazole ( 2 ) as well as 2‐methyl‐5‐aminotetrazole ( 3 ) were investigated. In the first reaction 2 was protonated yielding 1‐methyl‐5‐aminotetrazolium 5‐nitrimino‐1H‐tetrazolate monohydrate ( 7 ). In the latter case no protonation could be observed and a co‐crystallization of 5‐nitraminotetrazole and 2‐methyl‐5‐aminotetrazole was obtained. In this compound a new tautomer of 4 could be found. Both products were determined by low temperature single crystal X‐ray diffraction, IR, Raman and multinuclear (¹H, ¹³C, ¹⁵N) NMR spectroscopy, elemental analysis as well as differential scanning calorimetry. In addition the heats of formation were calculated using experimentally obtained heats of combustion. With these and the X‐ray densities several detonation parameter were computed using the EXPLO5 software. In addition the sensitivities towards impact, friction and electrostatic discharge were determined. Further, two crystal structures of the important starting materials in energetic research 5‐nitriminotetrazole monohydrate ( 4 ·H₂O) and 1‐methyl‐5‐nitriminotetrazolemonohydrate ( 5 ·H₂O) are presented and compared with the water‐free compounds. The heats of formation of 4 , 4 ·H₂O, 5 , 5 ·H₂O have been calculated by the atomization method using the CBS basis set. Inclusion of crystal water decrease heats of formation about 265 kJ mol^?1. Also the influence of crystal water on sensitivities (impact, friction, electrostatic discharge) but also performance is discussed.     

Crystal structure and ionic conductivity of three polymorphic phases of rubidium trifluoromethyl sulfonate, RbSO3CF3

The crystal structures of three polymorphic phases of rubidium trifluoromethyl sulfonate (RbSO3CF3, rubidium 'triflate') were solved from X-ray powder diffraction data. At room temperature, rubidium triflate crystallizes in the monoclinic space group Cm with lattice parameters of a = 19.9611(5) A, b = 23.4913(7) A, c = 5.1514(2) A, beta = 102.758(2) degrees; Z = 16. At T = 321 K, a first-order phase transition occurs toward a monoclinic phase in space group P2(1) with lattice parameters at T = 344 K of a = 10.3434(5) A, b = 5.8283(3) A, c = 5.1982(3) A, beta = 104.278(6) degrees; Z = 2). At T = 461 K, another phase transition, this time of second order, occurs toward an orthorhombic phase in space group Cmcm with lattice parameters at T = 510 K of a = 5.3069(2) A, b = 20.2423(10) A, c = 5.9479(2) A; Z = 4. As a common feature within all three crystal structures of rubidium triflate, the triflate anions are arranged in double layers with the lipophilic CF3 groups facing each other. The rubidium ions are located between the SO3 groups. The general packing is similar to the packing in cesium triflate. Rubidium triflate can be classified as a solid electrolyte with a specific ionic conductivity of sigma = 9.89 x 10(-9) S/cm at T = 384 K and sigma = 3.84 x 10(-6) S/cm at T = 481 K.     

Revisiting the structure and dynamics of hydrated Cd2+ in aqueous solutions: Insights from the RI-SCS-MP2/MM molecular dynamics simulation

The spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd²⁺ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 Å for the average distance between water and Cd²⁺. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd²⁺ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd²⁺ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.     

On the applicability of elastic network normal modes in small-molecule docking

Incorporating backbone flexibility into protein-ligand docking is still a challenging problem. In protein-protein docking, normal mode analysis (NMA) has become increasingly popular as it can be used to describe the collective motions of a biological system, but the question of whether NMA can also be useful in predicting the conformational changes observed upon small-molecule binding has only been addressed in a few case studies. Here, we describe a large-scale study on the applicability of NMA for protein-ligand docking using 433 apo/holo pairs of the Astex data sets. On the basis of sets of the first normal modes from the apo structure, we first generated for each paired holo structure a set of conformations that optimally reproduce its C(α) trace with respect to the underlying normal mode subspace. Using AutoDock, GOLD, and FlexX we then docked the original ligands into these conformations to assess how the docking performance depends on the number of modes used to reproduce the holo structure. The results of our study indicate that, even for such a best-case scenario, the use of normal mode analysis in small-molecule docking is restricted and that a general rule on how many modes to use does not seem to exist or at least is not easy to find.