Molecular Dynamics Simulations of Metal Ion Binding to the His‐tag Motif

In our previous study, we have observed that the chelation of various metal ions to the His‐tag motifs mostly involves the i and i+2 His residues for Ni²⁺, Cu²⁺, Zn²⁺ and Co²+. In the present study, various 200 ps molecular dynamics simulations were further conducted to investigate the chelating pathway of various metal ions to the His‐tag motif with 6 His residues (His‐tag6) and the binding affinities of these metal binding pockets towards these metal ions. The results indicate that His‐tag6 with the chelated metal ion located in positions His(2,4) or His(3,5) exhibits the strongest affinity for Ni²+ and Cu²+.K⁺ was found to be preferred to chelate in His(1,3) and His(3,5) coordinations. However, Fe³+ was found to have higher affinity towards His(1,3) and His(2,4) binding pockets. Our results also suggest that Ni²⁺ exhibits the highest binding affinity towards His‐tag6 over the other metal ions. Most of the structural variations of the His‐tag6 motif were from the Histidyl side chains during metal ion binding. In addition, there is an inverse linear correlation between the final chelated distance and the charge/volume ratio of metal ion. There is a negative correlation between the metal binding affinity and the averaged potential energy generated from the MD simulations.     

Synthesis and characterization of [Ir(1,5-cyclooctadiene)(μ-H)]4: a tetrametallic Ir4H4-core, coordinatively unsaturated cluster

Reported herein is the synthesis of the previously unknown [Ir(1,5-COD)(μ-H)](4) (where 1,5-COD = 1,5-cyclooctadiene), from commercially available [Ir(1,5-COD)Cl](2) and LiBEt(3)H in the presence of excess 1,5-COD in 78% initial, and 55% recrystallized, yield plus its unequivocal characterization via single-crystal X-ray diffraction (XRD), X-ray absorption fine structure (XAFS) spectroscopy, electrospray/atmospheric pressure chemical ionization mass spectrometry (ESI-MS), and UV-vis, IR, and nuclear magnetic resonance (NMR) spectroscopies. The resultant product parallels--but the successful synthesis is different from, vide infra--that of the known and valuable Rh congener precatalyst and synthon, [Rh(1,5-COD)(μ-H)](4). Extensive characterization reveals that a black crystal of [Ir(1,5-COD)(μ-H)](4) is composed of a distorted tetrahedral, D(2d) symmetry Ir(4) core with two long [2.90728(17) and 2.91138(17) ?] and four short Ir-Ir [2.78680 (12)-2.78798(12) ?] bond distances. One 1,5-COD and two edge-bridging hydrides are bound to each Ir atom; the Ir-H-Ir span the shorter Ir-Ir bond distances. XAFS provides excellent agreement with the XRD-obtained Ir(4)-core structure, results which provide both considerable confidence in the XAFS methodology and set the stage for future XAFS in applications employing this Ir(4)H(4) and related tetranuclear clusters. The [Ir(1,5-COD)(μ-H)](4) complex is of interest for at least five reasons, as detailed in the Conclusions section.     

A pressure correction method for fluid–particle interaction flow: Direct‐forcing method and sedimentation flow

A direct‐forcing pressure correction method is developed to simulate fluid–particle interaction problems. In this paper, the sedimentation flow is investigated. This method uses a pressure correction method to solve incompressible flow fields. A direct‐forcing method is introduced to capture the particle motions. It is found that the direct‐forcing method can also be served as a wall‐boundary condition. By applying Gauss's divergence theorem, the formulas for computing the hydrodynamic force and torque acting on the particle from flows are derived from the volume integral of the particle instead of the particle surface. The order of accuracy of the present method is demonstrated by the errors of velocity, pressure, and wall stress. To demonstrate the efficiency and capability of the present method, sedimentations of many spherical particles in an enclosure are simulated. Copyright © 2010 John Wiley & Sons, Ltd.     

A free rectangular plate on the two-parameter elastic foundation

This paper provides a rigorous solution of a free rectangular plate on the V.Z. Vlazov two-parameter elastic foundation by the method of superposition[1]. In this paper we derive basic solutions under the various boundary conditions. To superpose these basic solutions the most generally rigorous solution of a free rectangular plate on the two-parameter elastic foundation can be obtained. The solution strictly satisfies the differential equation of a plate on the two-parameter elastic model foundation, the boundary conditions of the free edges and the free corner conditions. Some numerical examples are presented The calculated results show that when the plane dimension of plate is given and the ratio between the laver depth and the plate thick is equal to 15, the two-parameter elastic model is near the Winkler’s. It shows that the Winkler model can be applied to the thinner layer.     

Solitary waves in stratified fluids and their interaction

A systematic procedure is proposed for obtaining solutions for solitary waves in stratified fluids. The stratification of the fluid is assumed to be exponential or linear. Its comparison with existing results for an exponentially stratified fluid shows agreement, and it is found that for the odd series of solutions the direction of displacement of the streamlines from their asymptotic levels is reversed when the stratification is changed from exponential to linear. Finally the interaction of solitary waves is considered, and the Korteweg-de Vries equation and the Boussinesq equation are derived. Thus the known solutions of these equations can be relied upon to provide the answers to the interaction problem.     

Synthesis and electroluminescent properties of polyfluorene‐based conjugated polymers containing bipolar groups

A bipolar dibromo monomer, bis‐(4‐bromophenyl)[4‐(3,5‐diphenyl‐1,2,4‐ triazole‐4‐yl)‐phenyl]amine ( 9 ), containing electro‐rich triphenylamine and electro‐deficient 1,2,4‐triazole moieties was newly synthesized and characterized. Two fluorescent fluorene‐based conjugated copolymers ( TPAF , TPABTF ) were prepared via facile Suzuki coupling from the dibromo bipolar monomer, 4,7‐dibromo‐2,1,3‐benzothiadiazole ( BTDZ ), and 9,9‐dioctylfluorene. They were characterized by molecular weight determination, IR, NMR, DSC, TGA, solubility, absorption and photoluminescence spectra, and cyclic voltammetry. The polymers showed good solubility in common organic solvents such as dichloromethane, chloroform, tetrahydrofuran, and dichlorobenzene at room temperature. They had glass transition temperatures (T_g) higher than 135 °C and 5% degradation temperatures in nitrogen atmosphere were higher than 428 °C. Single layer polymer light‐emitting diodes (PLED) of ITO/PEDOT:PSS/polymer/metal showed a blue emission at 444 nm and Commission Internationale de I'Eclairage (CIE) 1931 color coordinates of (0.16, 0.13) for TPAF . The device using TPABTF as emissive material showed electroluminescence at 542 nm with CIE1931 of (0.345, 0.625), low turn‐on voltage of 5 V, a maximum electroluminance of 696 cd/m², and a peak efficiency of 2.02 cd/A. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 6231–6245, 2009     

Estimation of the Moments of the Residence Time and First Passage Time from Experimentally Measurable Permeation Parameters via a New Formulation of the Transmission Matrix

Siegel's analysis on membrane transport in the Laplace domain [J. Phys. Chem. 95 (1991) 2556] in terms of transmission matrix, T(s), has been extended to a more useful formulation. This is achieved by combining uses of the matrix transport equations appropriate for void initial condition, or for saturated equilibrium, or of Dirac delta functional type and the theorem det[T(s)] = 1. This formulation enables us to expand T(s) in power series of the Laplace variable, s, with the expansion coefficients as the algebraic functions of the experimentally measurable transport parameters. Utility of the formulation is illustrated in the estimation of the experimentally inaccessible time moments for the first passage or residence times. It was also applied to the percutaneous drug delivery to obtain from the experimental data. The higher moments of the time lag or time lead using a graphic method.     

Communication: rovibrationally selected study of the N2+(X; v+=1, N+= 0-8) + Ar charge transfer reaction using the vacuum ultraviolet laser pulsed field ionization-photoion method

By employing an electric field pulsing scheme for vacuum ultraviolet laser pulsed field ionization-photoion (PFI-PI) measurements, we have been able to prepare a rovibrationally selected PFI-PI beam of N(2)(+)(v(+) = 1, N(+)) with not only high intensity and high quantum state purity, but also high kinetic energy resolution, allowing absolute total cross sections [σ(v(+) = 1, N(+))] for the N(2)(+)(X; v(+) = 1, N(+)) + Ar, N(+) = 0-8 charge transfer reaction to be measured at center-of-mass collision energies (E(cm)) down to thermal energies. The σ(v(+) = 1, N(+) = 0-8) values determined at E(cm) = 0.04-10.00 eV are in good agreement with the theoretical predictions based on the Landau-Zener-Stu?ckelberg formulism. Taking into account the experimental uncertainties, the σ(v(+) = 1, N(+)), N(+) = 0-8, measured at E(cm) = 1.56 eV are found to be independent of N(+).     

Insights into the Kramers’ flux‐over‐population rate for chemical reactions in liquid phases through the matrix transport equation

Kramers’ equation models a chemical reaction as a Brownian particle diffusing over a potential barrier under the influence of medium viscosity. In the case of high viscosity, the equation reduces to a simpler Smoluchowski equation. In this report, we have contrived an equivalent matrix‐transport equation that relates the ordered pair (activity, flux) of the output (activated complex) to that of the input (reactant). With an initial condition of the Dirac delta type placed at the location of the reactant, and a reflecting boundary condition set on the reactant state, and an absorbing boundary condition on the activated complex state, we are able to prove the equality relation between the mean first passage time, , for the diffusion and the inverse of the rate constant, k^?1, for the reaction counterpart. We have also derived , where λ_i is the ith eigenvalue of the Smoluchowski differential operator stipulated with the above‐mentioned boundary conditions. We have also deduced that, in the long time limit, the number of particles remaining inside the diffusion domain decays exponentially with a relaxation time just the same as the concentration of the reactant does for a first‐order reaction system.     

粉状白钨酸的研究——Ⅵ.多种偏钨酸盐的PMR谱研究

本文采用PMR技术,研究了由粉状白钨酸制得的偏钨酸钾、钠、铵以及有机铵([C_2H_5-NH_3]~ 、[(C_2H_5)_2NH_2]~ 的阴离子结构;通过测定分子中不可交换氢的数目和氢峰的化学位移,肯定了它们都具有Keggin结构,并讨论了影响化学位移的因素。