Non‐enzymatic Ribonucleotide Reduction in the Prebiotic Context

Model studies of prebiotic chemistry have revealed compelling routes for the formation of the building blocks of proteins and RNA, but not DNA. Today, deoxynucleotides required for the construction of DNA are produced by reduction of nucleotides catalysed by ribonucleotide reductases, which are radical enzymes. This study considers potential non‐enzymatic routes via intermediate radicals for the ancient formation of deoxynucleotides. In this context, several mechanisms for ribonucleotide reduction, in a putative H₂S/HS^. environment, are characterized using computational chemistry. A bio‐inspired mechanistic cycle involving a keto intermediate and HSSH production is found to be potentially viable. An alternative pathway, proceeding through an enol intermediate is found to exhibit similar energetic requirements. Non‐cyclical pathways, in which HSS^. is generated in the final step instead of HS^., show a markedly increased thermodynamic driving force (ca. 70 kJ mol^?1) and thus warrant serious consideration in the context of the prebiotic ribonucleotide reduction.     

Statistics of polymer capture by a nanopore: A Brownian dynamics simulation study

We investigate the statistics of polymer capture by a nanopore using Brownian dynamics simulations. It is found that when the velocity flux is greater than a critical velocity flux, the capture picture is a random selection process, otherwise it tends to a statistical process governed by energetic considerations. In addition, the chain ends capture probability decreases as the chain length increases and satisfies a power-law scaling of P0(N)~N-0.8.     

Baeyer–Villiger oxidation of cyclohexanone by molecular oxygen with Fe–Sn–O mixed oxides as catalysts

Fe–Sn–O mixed oxides were synthesized and used as catalysts for Baeyer–Villiger oxidation of cyclohexanone, which showed both high catalytic activity and selectivity. X‐ray powder diffraction and scanning electron microscopy suggested that the Fe–Sn–O catalysts had a tetragonal structure with a grain size of 29.3 nm. An ε‐caprolactone yield as high as 98.8% was obtained in a small‐scale experiment (5 mmol of cyclohexanone). In a scale‐up test (20 mmol of cyclohexanone), the cyclohexanone conversion and ε‐caprolactone yield were 96.7 and 96.5%, respectively. In addition, the catalysts can be reused five times without any major decline in catalytic activity. Copyright © 2015 John Wiley & Sons, Ltd.     

Solvent‐Dependent Structure of the I3− Ion Derived from Photoelectron Spectroscopy and Ab Initio Molecular Dynamics Simulations

Ab initio molecular dynamics (MD) simulations of the solvation of LiI₃ in four different solvents (water, methanol, ethanol, and acetonitrile) are employed to investigate the molecular and electronic structure of the I₃^? ion in relation to X‐ray photoelectron spectroscopy (XPS). Simulations show that hydrogen‐bond rearrangement in the solvation shell is coupled to intramolecular bond‐length asymmetry in the I₃^? ion. By a combination of charge analysis and I 4 d core‐level XPS measurements, the mechanism of the solvent‐induced distortions has been studied, and it has been concluded that charge localization mediates intermolecular interactions and intramolecular distortion. The approach involving a synergistic combination of theory and experiment probes the solvent‐dependent structure of the I₃^? ion, and the geometric structure has been correlated with the electronic structure.     

Electrically Switchable Magnetic Molecules: Inducing a Magnetic Coupling by Means of an External Electric Field in a Mixed‐Valence Polyoxovanadate Cluster

Herein we evaluate the influence of an electric field on the coupling of two delocalized electrons in the mixed‐valence polyoxometalate (POM) [GeV₁₄O₄₀]^8? (in short V₁₄) by using both a t‐J model Hamiltonian and DFT calculations. In absence of an electric field the compound is paramagnetic, because the two electrons are localized on different parts of the POM. When an electric field is applied, an abrupt change of the magnetic coupling between the two delocalized electrons can be induced. Indeed, the field forces the two electrons to localize on nearest‐neighbors metal centers, leading to a very strong antiferromagnetic coupling. Both theoretical approaches have led to similar results, emphasizing that the sharp spin transition induced by the electric field in the V₁₄ system is a robust phenomenon, intramolecular in nature, and barely influenced by small changes on the external structure.     

Molecular scale simulations on thermoset polymers: A review

This article reviews the field of molecular simulations of thermoset polymers. This class of polymers is of interest in applications ranging from structural components for aerospace to electronics packaging and predictive simulations of their response is playing an increasing role in understanding the molecular origin of their properties and complementing experiments in the search for tailored materials for specific applications. It focuses on modeling and simulation of the process of curing to predict the molecular structure of these polymers and their thermomechanical response by all-atom molecular dynamics simulations. Results from Monte Carlo and coarse-grained simulations are briefly summarized. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 103–122     

Free volume characteristics of 2,2-bistrifluoromethyl-4,5-difluoro-1,3-dioxole-co-tetrafluoroethylene copolymers: Effect of composition and molecular weight

2,2-bistrifluoromethyl-4,5-difluoro-1,3-dioxole-co-tetrafluoroethylene (PDD-TFE) copolymer is a good candidate to prepare gas separation membranes with excellent permeability due to its free volume characteristics. However, the influence of PDD-TFE copolymer structure on its free volume characteristics is less studied. In this paper, PDD-TFE copolymers with different compositions and molecular weights were synthesized, and their free volume characteristics were analyzed by positron annihilation lifetime spectroscopy and a molecular dynamics simulation. It indicated that the molar fraction of PDD in copolymers had a significant effect on free volume characteristics, while the molecular weight of copolymers exerted a slight influence on free volume when the molecular weight exceeded a critical region (intrinsic viscosity [η] > 68 ml g⁻¹). PDD-TFE copolymers with greater PDD molar fractions (i.e., 72% and 84%) showed bimodal distributions in positron lifetime and free volume size distributions, while PDD-TFE copolymers with lower PDD molar fractions (i.e., 27% and 35%) exhibited a single peak. The long-lifetime parameter τ₃ was assigned to micro-cavities formed by [-(TFE)_y-PDD-] segments and τ₄ was attributed to micro-cavities formed by [-(PDD)_x-TFE-] segments. The cis and trans transitions of PDD led to a local multilayer spiral structure with a 2.6–4.3 Å layer spacing, which would also increase the free volume of copolymers.     

Modification of an implicit approach based on nonstandard rules for structural dynamics analysis

The present study aims to modify a recently suggested implicit approach consisted of the approximate Euler method and closed-form exponential mapping (herein referred to as the Liu scheme) for the dynamic analysis of structures. Such modification has been developed based upon nonstandard rules. The equation of motion is formulated in the augmented dynamic space to apply the exponential mapping as a group preserving scheme. The formulation of the proposed method involves the hyperbolic sine and cosine functions. The method is therefore prone to divergence due to the behavior of the hyperbolic functions in structures with a high ratio of stiffness to mass. In the present study, to consider the properties of the structural equation into the formulation of the time step size and thereby avoid the divergence, a parameter, known as stability parameter, is thus derived from the exact solution of the equation of motion based on nonstandard rules. Embedding this parameter into the proposed method improves its stability. Afterward, for evaluating the performance of the proposed method, it is applied to several structures with different loading patterns while implemented in programing environment of the Matlab software. The results are compared to those of several commonly used numerical methods in structural applications. It is found that the proposed method has acceptable convergence and accuracy, and low time consumption compared to several commonly used methods. Furthermore, its stability is guaranteed by embedding the stability parameter into the proposed method.     

Self-similar asymptotic behavior for the solutions of a linear coagulation equation

In this paper we consider the long-time asymptotics of a linear version of the Smoluchowski equation which describes the evolution of a tagged particle moving in a random distribution of fixed particles. The volumes v of these particles are independently distributed according to a probability distribution which decays asymptotically as a power law $v^{?\sigma }$. The validity of the equation has been rigorously proved in [22] taking as a starting point a particle model and for values of the exponent $\sigma >3$, but the model can be expected to be valid, on heuristic grounds, for $\sigma >\frac{5}{3}$. The resulting equation is a non-local linear degenerate parabolic equation. The solutions of this equation display a rich structure of different asymptotic behaviors according to the different values of the exponent σ. Here we show that for $\frac{5}{3}<\sigma <2$ the linear Smoluchowski equation is well-posed and that there exists a unique self-similar profile which is asymptotically stable.