Hydration of copper(II) amino acids complexes

Hydration of the copper(II) bis‐complexes with glycine, serine, lysine, and aspartic acid was studied by DFT and MD simulation methods. The distances between copper(II) and water molecules in the 1st and 2nd coordination shells, the average number of water molecules and their mean residence times in the hydration shells were calculated. Good agreement was observed between the values obtained and those found by DFT and NMR relaxation methods. Influence of the functional groups of the ligands and the cis–trans isomerism of the complexes on the structural and dynamical parameters of the hydration shells was displayed and explained. Analysis of the MD trajectories reveals the competition for a copper(II) axial position between water molecules or water molecules and the functional chain groups of the ligands and confirms the suggestion on the pentacoordination of copper(II) in such complexes. MD simulations show that only one axial position of Cu(II) is basically occupied at each time step while in average the coordination number more than 5 is observed. © 2017 Wiley Periodicals, Inc.     

Dynamical Bifurcation in Gas‐Phase XH− + CH3Y SN2 Reactions: The Role of Energy Flow and Redistribution in Avoiding the Minimum Energy Path

The gas‐phase reactions of XH^? (X=O, S) + CH₃Y (Y=F, Cl, Br) span nearly the whole range of S_N2 pathways, and show an intrinsic reaction coordinate (IRC) (minimum energy path) with a deep well owing to the CH₃XH???Y^? (or CH₃S^????HF) hydrogen‐bonded postreaction complex. MP2 quasiclassical‐type direct dynamics starting at the [HX???CH₃???Y]^? transition‐state (TS) structure reveal distinct mechanistic behaviors. Trajectories that yield the separated CH₃XH+Y^? (or CH₃S^?+HF) products directly are non‐IRC, whereas those that sample the CH₃XH???Y^? (or CH₃S^????HF) complex are IRC. The IRCIRC/non‐IRC ratios of 90:10, 40:60, 25:75, 2:98, 0:100, and 0:100 are obtained for (X, Y)=(S, F), (O, F), (S, Cl), (S, Br), (O, Cl), and (O, Br), respectively. The properties of the energy profiles after the TS cannot provide a rationalization of these results. Analysis of the energy flow in dynamics shows that the trajectories cross a dynamical bifurcation, and that the inability to follow the minimum energy path arises from long vibration periods of the X?C???Y bending mode. The partition of the available energy to the products into vibrational, rotational, and translational energies reveals that if the vibrational contribution is more than 80 %, non‐IRC behavior dominates, unless the relative fraction of the rotational and translational components is similar, in which case a richer dynamical mechanism is shown, with an IRC/non‐IRC ratio that correlates to this relative fraction.     

Multipod structures of lamellae‐forming diblock copolymers in three‐dimensional confinement spaces: Experimental observation and computer simulation

The three‐dimensional (3D) confinement effect on the microphase‐separated structure of a diblock copolymer was investigated both experimentally and computationally. Block copolymer nanoparticles were prepared by adding a poor solvent into a block copolymer solution and subsequently evaporating the good solvent. The 3D structures of the nanoparticles were quantitatively determined with transmission electron microtomography (TEMT). TEMT observations revealed that various complex structures, including tennis‐ball, mushroom‐like, and multipod structures, were formed in the 3D confinement. Detailed structural analysis, showed that one block of the diblock copolymer slightly prefers to segregate into the particle surface compared with the other block. The observed structures were further elaborated using cell dynamics computer simulation. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1702–1709     

Impact of proliferation strategies on food web viability in a model with closed nutrient cycle

A food web model with a closed nutrient cycle is presented and analyzed via Monte Carlo simulations. The model consists of three trophic levels, each of which is populated by animals of one distinct species. While the species at the intermediate level feeds on the basal species, and is eaten by the predators living at the highest level, the basal species itself uses the detritus of animals from higher levels as the food resource. The individual organisms remain localized, but the species can invade new lattice areas via proliferation. The impact of different proliferation strategies on the viability of the system is investigated. From the phase diagrams generated in the simulations it follows that in general a strategy with the intermediate level species searching for food is the best for the survival of the system. The results indicate that both the intermediate and top level species play a critical role in maintaining the structure of the system.     

Simulation of local ion transport in lamellar block copolymer electrolytes based on electron micrographs

A method is presented to relate local morphology and ionic conductivity in a solid, lamellar block copolymer electrolyte for lithium batteries, by simulating conductivity through transmission electron micrographs. The electrolyte consists of polystyrene‐block‐poly(ethylene oxide) mixed with lithium bis(trifluoromethanesulfonyl) imide salt (SEO/LiTFSI), where the polystyrene phase is structural phase and the poly(ethylene oxide)/LiTFSI phase is ionically conductive. The electric potential distribution is simulated in binarized micrographs by solving the Laplace equation with constant potential boundary conditions. A morphology factor, f, is reported for each image by calculating the effective conductivity relative to a homogenous conductor. Images from two samples are examined, one annealed with large lamellar grains and one unannealed with small grains. The average value of f is 0.45 ± 0.04 for the annealed sample, and 0.37 ± 0.03 for the unannealed sample, both close to the value predicted by effective medium theory, 1/2. Simulated conductivities are compared to published experimental conductivities. The value of f_Unannealed/f_Annealed is 0.82 for simulations and 6.2 for experiments. Simulation results correspond well to predictions by effective medium theory but do not explain the experimental measurements. Observation of nanoscale morphology over length scales greater than the size of the micrographs (～1 μm) may be required to explain the experimental results. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 266–274     

A penalty method for numerically handling dispersive equations with incompatible initial and boundary data

This article is the numerical counterpart of a theoretical work in progress Qin and Teman, Applicable Anal (2011), 1–19, related to the approximation of evolution hyperbolic equations with incompatible data. The Korteweg‐de Vries and Schrödinger equations with incompatible initial and boundary data are considered here. For hyperbolic equations, the lack of regularity (compatibility) is known to produce large numerical errors which propagate throughout the spatial domain, destroying convergence. In this article, we numerically test the effectiveness of the penalty‐based method proposed in Qin and Teman, Applicable Anal (2011), 1–19, which replaces the hyperbolic equations with incompatible data by a system with compatible data. We observe that convergence is increased. As explained in the text, in the case of the Schrödinger equation, the impact of incompatible (nonregular) data is most severe, and the authors are not aware of any other method that can handle such severe incompatible data. © 2011 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2011     

Reaching multi‐nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling

We report an enhanced sampling technique that allows to reach the multi‐nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid–vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall‐clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc.     

Computation of the hindrance factor for the diffusion for nanoconfined ions: molecular dynamics simulations versus continuum-based models

We report the self-diffusion coefficients and hindrance factor for the diffusion of ions into cylindrical hydrophilic silica nanopores (hydrated silica) determined from molecular dynamics (MD) simulations. We make a comparison with the hindered diffusion coefficients used in continuum-based models of nanofiltration (NF). Hindrance factors for diffusion estimated from the macroscopic hydrodynamic theory were found to be in fair quantitative agreement with MD simulations for a protonated pore, but they strongly overestimate diffusion inside a deprotonated pore.     

Molecular dynamics simulations of displacement cascades in Fe-10%Cr systems

Molecular dynamics simulations of the displacement cascades in Fe-10%Cr systems are used to simulate the primary knocked-on atom events of the irradiation damage at temperatures 300,600,and 750 K with primary knockedon atom energies between 1 and 15 keV.The results indicate that the vacancies produced by the cascade are all in the central region of the displacement cascade.During the cascade,all recoil Fe and Cr atoms combine with each other to form Fe-Cr or Fe-Fe interstitial dumbbells as well as interstitial clusters.The number and the size of interstitial clusters increase with the energy of the primary knocked-on atom and the temperature.A few large clusters consist of a large number of Fe interstitials with a few Cr atoms,the rest are Fe-Cr clusters with small and medium sizes.The interstitial dumbbells of Fe-Fe and Fe-Cr are in the 111 and 110 series directions,respectively.     

Competitive Coordination of Chloride and Fluoride Anions Towards Trivalent Lanthanide Cations (La3+ and Nd3+) in Molten Salts

Molten salt electrolysis is a vital technique to produce high-purity lanthanide metals and alloys. However, the coordination environments of lanthanides in molten salts, which heavily affect the related redox potential and electrochemical properties, have not been well elucidated. Here, the competitive coordination of chloride and fluoride anions towards lanthanide cations (La³⁺ and Nd³⁺) is explored in molten LiCl-KCl-LiF-LnCl₃ salts using electrochemical, spectroscopic, and computational approaches. Electrochemical analyses show that significant negative shifts in the reduction potential of Ln³⁺ occur when F⁻ concentration increases, indicating that the F⁻ anions interact with Ln³⁺ via substituting the coordinated Cl⁻ anions, and confirm [LnCl_xF_y]^3−x−y (y_max=3) complexes are prevailing in molten salts. Spectroscopic and computational results on solution structures further reveal the competition between Cl⁻ and F⁻ anions, which leads to the formation of four distinct Ln(III) species: [LnCl₆]³⁻, [LnCl₅F]³⁻, [LnCl₄F₂]³⁻ and [LnCl₄F₃]⁴⁻. Among them, the seven-coordinated [LnCl₄F₃]⁴⁻ complex possesses a low-symmetry structure evidenced by the pattern change of Raman spectra. After comparing the polarizing power (Z/r) among different metal cations, it was concluded that Ln−F interaction is weaker than that between transition metal and F⁻ ions.