How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes

The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺), and (post-)transition metal (Zn²⁺, Cd²⁺, Hg²⁺, and Pb²⁺) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K⁺). Importantly, we establish the nature of the cation-GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations’ unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.     

Backbone rearrangement during olefin capture as the rate limiting step in molecular olefin polymerization catalysis and its effect on comonomer affinity

Available experimental data for several metallocenes indicate that the ethene/propene copolymerization ratio r_c can be much more temperature dependent than would be expected if competing insertion transition states (TS) are rate limiting. Detailed exploration of the reaction paths reveals in several cases the existence of a “capture‐like” transition state before the actual insertion, with free energies close to the insertion TS. Movement around these transition states does not just involve monomer and chain, but also clear distortion of the ligand skeleton to allow entry of the monomer. Taking these additional TSs into account leads to much improved agreement with experiment for a series of metallocenes and a constrained geometry catalyst system. Depending on catalyst and temperature, selectivity is determined by competing insertion/insertion, capture/insertion or capture/capture. It seems likely that this is a common situation especially for highly efficient catalysts, complicating (but not preventing) prediction of copolymerization performance. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 2807–2814     

Extraction of Reliable Molecular Information from Diffusion NMR Spectroscopy: Hydrodynamic Volume or Molecular Mass?

Measuring accurate translational self-diffusion coefficients (D_t) by NMR techniques with modern spectrometers has become rather routine. In contrast, the derivation of reliable molecular information therefrom still remains a nontrivial task. In this paper, two established approaches to estimating molecular size in terms of hydrodynamic volume (V_H) or molecular weight (M) are compared. Ad hoc designed experiments allowed the critical aspects of their application to be explored by translating relatively complex theoretical principles into practical take-home messages. For instance, comparing the D_t values of three isosteric Cp₂MCl₂ complexes (Cp=cyclopentadienyl, M=Ti, Zr, Hf), having significantly different molecular mass, provided an empirical demonstration that V_H is the critical molecular property affecting D_t. This central concept served to clarify the assumptions behind the derivation of D_t=ƒ(M) power laws from the Stokes–Einstein equation. Some pitfalls in establishing log (D_t) versus log (M) linear correlations for a set of species have been highlighted by further investigations of selected examples. The effectiveness of the Stokes–Einstein equation itself in describing the aggregation or polymerization of differently shaped species has been explored by comparing, for example, a ball-shaped silsesquioxane cage with its cigar-like dimeric form, or styrene with polystyrene macromolecules.     

Magnetoelectric effect in cobalt ferrite-barium titanate composites and their electrical properties

CoFe₂O₄-BaTiO₃ composites were prepared using conventional ceramic double sintering process with various compositions. Presence of two phases in the composites was confirmed using X-ray diffraction. The dc resistivity and thermoemf as a function of temperature in the temperature range 300 K to 600 K were measured. Variation of dielectric constant (ɛ′) with frequency in the range 100 Hz to 1 MHz and also with temperature at a fixed frequency of 1 kHz was studied. The ac conductivity was derived from dielectric constant (ɛ′) and loss tangent (tan δ). The nature of conduction is discussed on the basis of small polaron hopping model. The static value of magnetoelectric conversion factor has been studied as a function of magnetic field.     

On the convergence of the Fitness-Complexity algorithm

We investigate the convergence properties of an algorithm which has been recently proposed to measure the competitiveness of countries and the quality of their exported products. These quantities are called respectively Fitness F and Complexity Q. The algorithm was originally based on the adjacency matrix M of the bipartite network connecting countries with the products they export, but can be applied to any bipartite network. The structure of the adjacency matrix turns to be essential to determine which countries and products converge to non zero values of F and Q. Also the speed of convergence to zero depends on the matrix structure. A major role is played by the shape of the ordered matrix and, in particular, only those matrices whose diagonal does not cross the empty part are guaranteed to have non zero values as outputs when the algorithm reaches the fixed point. We prove this result analytically for simplified structures of the matrix, and numerically for real cases. Finally, we propose some practical indications to take into account our results when the algorithm is applied.     

Isolation of a bis-iodurated tetra-THF as a trace product from the oxidation of squalene with RuO₄ and its double ring expansion to a novel bis-THF-bis-THP compound

A novel bis-iodurated polyether compound, based on an unprecedented tetra-THF backbone, has been isolated as a trace by-product of the oxidation of squalene with the catalytic system RuO?(cat.)/NaIO?. The double erythro configuration of the central portion of the molecule furnishes the first indirect support of the previously postulated pathway operating in the oxidative pentacyclization of the isoprenoid substrate. A bidirectional double oxidative bis-cyclization is invoked to explain the formation of this compound. The isolated substance was successfully subjected to a double rearrangement-ring expansion to give a novel bis-THF-bis-THP compound.     

Fabrication of large-area ordered and reproducible nanostructures for SERS biosensor application

We propose a large-area SERS device with efficient fluorescence quenching capability. The substrate is based on anodic porous alumina templates with various pore size and wall thickness as small as 15 and 36 nm, respectively. The nano-patterned SERS substrate, with excellent control and reproducibility of plasmon-polaritons generation, shows very efficient enhanced Raman signal in the presence of intrinsically fluorescent molecules such as cresyl violet, rhodamine, and green fluorescent protein. This work demonstrates that, when the nanostructures are properly designed and fabricated, Raman and fluorescence spectroscopy can be used in combination in order to obtain complementary molecular informations. Theoretical simulation shows excellent agreement with the experimental findings. The enhancement factor is found to be 10(3)-10(4), with respect to flat gold surface when the molecules are supposed to be closely packed, with considerable fluorescence suppression, showing a promising disposable biosensor.     

Minimal agent based model for financial markets II

We present a detailed study of the statistical properties of the Agent Based Model introduced in paper I [Eur. Phys. J. B, DOI: 10.1140/epjb/e2009-00028-4] and of its generalization to the multiplicative dynamics. The aim of the model is to consider the minimal elements for the understanding of the origin of the stylized facts and their self-organization. The key elements are fundamentalist agents, chartist agents, herding dynamics and price behavior. The first two elements correspond to the competition between stability and instability tendencies in the market. The herding behavior governs the possibility of the agents to change strategy and it is a crucial element of this class of models. We consider a linear approximation for the price dynamics which permits a simple interpretation of the model dynamics and, for many properties, it is possible to derive analytical results. The generalized non linear dynamics results to be extremely more sensible to the parameter space and much more difficult to analyze and control. The main results for the nature and self-organization of the stylized facts are, however, very similar in the two cases. The main peculiarity of the non linear dynamics is an enhancement of the fluctuations and a more marked evidence of the stylized facts. We will also discuss some modifications of the model to introduce more realistic elements with respect to the real markets.