Interatomic voids in analysis of computer model structures of liquids and glasses

To analyze the structure of noncrystalline systems (liquids, glasses), it is suggested that the functions to be calculated should include not only the conventional atom-atom radial distribution function and structural factor, but also the same functions for a system of points representing the centers of interatomic voids. The points are located at the nodes of Voronoi polyhedra or, which is equivalent, at the centers of the spheres circumscribed around the Delaunay simplices. The system of points (system {D}) is unambiguously defined by the atomic coordinates and conveys additional information on the structure of the system because each interatomic void is determined by the relative positions of several atoms. Using a homogeneous noncrystalline packing model of atoms and inhomogeneous models derived from it as an example, we demonstrate that system {D} is sensitive to the structural features on medium scales and may be used along with the conventional atom-atom functions to study structural correlations other than short-range order correlations.     

Structure of interparticle space in great noncrystalline packings of Lennard-Jones atoms and its influence on diffusional mobility of admixture particles

Models of 100,000 atoms interacting with Lennard-Jones potential have been constructed using the Monte Carlo method at different densities and temperatures. In these models, the structure of empty space is investigated in which the test particle with a diameter smaller than the diameter of matrix atoms can move. The percolation thresholds, when “infinite” cavities penetrating all model space arise, are found. A change of density and temperature of matrix preparation leads to a non trivial redistribution of volume between cavities of different type. By the method of molecular dynamics it is found that the usual (Einsteinian) law of diffusion is established rather quickly, on average. However, the laws for test particles moving in cavities of different type are more complex and specific to each kind of cavities. It should result in different course of chemical reaction in different local areas of a matrix.     

The competition between crystallization and demixing in polymer blends. V. Numerical modeling and quantitative evaluation of crystallization-induced composition inhomogeneities

It is well known that crystallization of one component in a polymer blend causes composition profiles around the growing spherulites. Amplitude and width of these profiles, respectively, depend on the ratio between the rates of diffusion and of spherulite growth. They can be determined by suitable experimental means. In the present article, the profiles are modeled, starting from Frank's solution of the diffusion equation in spherical coordinates under the boundary condition of moving walls that simultaneously are sources of the diffusing material. Modeled and experimentally determined profiles in PVDF/PEA and PCL/PS blends agree well. The analysis yields estimates for the diffusion coefficient D in polymeric melts as D ≅ (50 ··· 500) μm²/h. Finally, the interference of the composition profiles around several adjacent spherulites can be demonstrated. © 1996 John Wiley & Sons, Inc.     

分子排阻色谱硅质填料的制备及其对蛋白质的分离机理

利用自制的四种不同粒径的硅溶胶,通过堆积法来制备分子排阻色谱多孔硅质填料,该填料在进行化学键合改性后,形成二醇固定相。利用二醇固定相对蛋白质进行分离分析方面的研究。此填料粒径小,有利于蛋白质生物大分子的高效快速分离分析。     

Structural characteristics of close packings of hard spheres. Critical densities

For packings of similar hard spheres, there are several characteristic values of density. First, this is the maximal possible degree of space filling by spheres η = 0.74, realized for the crystalline packing of spheres. Another known value, η = 0.64, is the limiting (critical) value for disordered packings. We also indicate two more characteristic values of density: η = 0.60 and η = 0.66, in the vicinity of which qualitative changes in structure can occur. Computer models of the packings of hard spheres are investigated in the range of densities 0.52 < η < 0.72. Each packing consisted of 10,000 spheres in a cube with periodic boundary conditions. The structural characteristics were investigated using Delaunay simplices, defining the arrangement of the nearest four atoms. Simplices that are close to a regular tetrahedron or quartoctahedron (quarter of an octahedron) are considered. These forms are typical for the densest crystal structures. Variation of the fraction and ratio of these simplices is studied as a function of the packing density. According to the results, the threshold value, η = 0.60, corresponds to the density after which correlation of the disordered arrangement of spheres increases considerably. When η = 0.64, the structural organization changes more radically; high density demands the emergence of local crystal nuclei. The density η = 0.66 is the limiting density at which the crystalline nuclei can exist as independently distributed regions. Closer packings can only occur if a global crystal structure arises in them.     

From random sphere packings to regular pillar arrays: effect of the macroscopic confinement on hydrodynamic dispersion

Flow and mass transport in bulk and confined chromatographic supports comprising random packings of solid, spherical particles and hexagonal arrays of solid cylinders (regular pillar arrays) are studied over a wide flow velocity range by a numerical analysis scheme, which includes packing generation by a modified Jodrey-Tory algorithm, three-dimensional flow field calculations by the lattice-Boltzmann method, and modeling of advective-diffusive mass transport by a random-walk particle-tracking technique. We demonstrate the impact of the confinement and its cross-sectional geometry (circular, quadratic, semicircular) on transient and asymptotic transverse and longitudinal dispersion in random sphere packings, and also address the influence of protocol-dependent packing disorder and the particle-aspect ratio. Plate height curves are analyzed with the Giddings equation to quantify the transcolumn contribution to eddy dispersion. Confined packings are compared with confined arrays under the condition of identical bed porosity, conduit cross-sectional area, and laterally fully equilibrated geometrical wall and corner effects on dispersion. Fluid dispersion in a regular pillar array is stronger affected by the macroscopic confinement and does not resemble eddy dispersion in random sphere packings, because the regular microstructure cannot function as a mechanical mixer like the random morphology. Giddings' coupling theory fails to preserve the nature of transverse dispersion behind the arrays' plate height curves, which approach a linear velocity-dependence as transverse dispersion becomes velocity-independent. Upon confinement this pseudo-diffusive behavior can outweigh the performance advantage of the regular over the random morphology.     

Silver atoms in the structural channels of beryl

A silver atom in synthetic beryl is investigated by the EPR and electron spin echo (ESE) spectroscopy. It is established that silver ions were first introduced into the structural channels of beryl by thermodiffusion at 800υC. The Ag⁺ ions are then converted to the Agυ state by the X-ray irradiation of samples at room temperature. Charge changes in manganese and chromium impurities located at the aluminum positions are observed at the same conditions. Four different Agυ centers with isotropic hyperfine interactions (HFI) with ¹⁰⁷ Ag and ¹⁰⁹ Ag nuclei and hyperfine constants less than those for the free Ag atom are revealed by the EPR method. ESE investigations enable us to confirm the positions of silver atoms that are stable up to 230υC.     

Hartree-Fock energy partitioning in terms of Hirshfeld atoms.

A Hirshfeld decomposition scheme of the Hartree-Fock total molecular energy into atomic energies is presented. The calculations are performed by direct numerical integration and the results are compared for a set of 28 molecules containing different kinds of atoms. The calculated atomic energies show a strong dependency on changes of atomic electron population and hybridization. Linear correlations are found between the energy and the population for H, these being related to the electronegativity of this atom and to the external potential created by the remaining atoms. The proposed energy partitioning scheme appears to be useful for studies such as proton acidity, the anomeric effect and group transferability, and allows atomic virial ratios to be obtained. Finally, the atomic potential energies are found to mimic trends based on exact expressions as well as trends displayed by molecular quantities, thus lending credibility to the partitioning scheme used.     

Molecular dynamics simulation reveals structural and thermodynamic features of kinase activation by cancer mutations within the epidermal growth factor receptor

The epidermal growth factor receptor (EGFR) is a major target for drugs in treating lung carcinoma as it promotes cell growth and tumor progression. Structural studies have demonstrated that EGFR exists in an equilibrium between catalytically active and inactive forms, and dramatic conformational transitions occur during its activation. It is known that EGFR mutations promote such conformational changes that affect its activation and drug efficacy. The most common point mutation in lung cancer patients is a leucine to arginine substitution at amino acid 834 (L834R). In a recent article, we have studied changes in drug binding affinities due to cancer mutations of EGFR using ensemble molecular dynamics (MD) simulations. Here, we address an enhanced activation mechanism thought to be associated with this mutation. Using extended timescale MD simulations, the structural and energetic properties are studied for both active and inactive conformations of EGFR. The thermodynamic stabilities of these two conformations are characterized by free energy landscapes estimated from molecular mechanics/Poisson-Boltzmann solvent area calculations. Our study reveals that the L834R mutation introduces conformational changes in both states, adjusting the relative stabilities of active and inactive conformations and hence the activation of the EGFR kinase.     

氯化钠对朊病毒结构稳定性影响的分子动力学研究

朊病毒疾病是由正常构象的PrPC转化为致病构象的PrPSc引起的一类可传染的蛋白质构象病.采用分子动力学模拟的方法研究了0～500mmol/L的NaCl溶液体系对人朊病毒构象影响并深入探讨了其分子机制.研究发现NaCl可以降低朊病毒的结构稳定性,并引起其α-螺旋含量的急剧降低.进一步的研究表明高浓度NaCl溶液体系能够显著破坏朊病毒螺旋1内部的重要盐桥Asp144-Arg148和Asp147-Arg151,同时明显降低其主要氢键Arg151 N:Asp147 O,Tyr150 N:Glu146 O,Tyr149 N:Tyr145 O和Arg148 N:Asp144 O的稳定性,并诱导朊病毒的疏水核心发生明显扩张,促使朊病毒整体稳定性的下降,这些可能是NaCl促进朊病毒构象转换的重要原因.     

Influence of the pore structure on the properties of silica based reversed phase packings for LC

This paper describes the preparation and investigation of new, highly loaded, monomeric, silica based, reversed phase C18 and C30 packings. The influence of pore structure and endcapping on the properties of C18 and C30 packings is described. Using hydrothermal procedures, silicas with predictable pore size (9.3-25.5 nm) and surface area have been prepared. Silylation with long chain silanes substantially alters the pore structure of the silica: pore size and pore volume decrease. A new parameter, the volumetric surface coverage [mm3 x m(-2)] has been introduced. This parameter--calculated from on-column measured porosity data--indicates the pore volume portion occupied by the hydrocarbon chains. Endcapping does not significantly change the pore structure of the bonded phases. The reduced retentions (reduced with respect to unit area: [k/m2])--a good measure for comparing the retention behaviour of packings with different surface areas--are similar for most of the phases, demonstrating good accessibility of the pores for the solutes. Slightly lower retentions were found on the endcapped than on the non-endcapped phases for probes with dense pi-electron system (e.g. polyaromatic hydrocarbons) demonstrating the contribution of silanophilic interactions to the retention. The phases had been successfully used for various demanding separations, e.g. for the separation of flavonoids, carotenoids, resveratrol, and tocopherol isomers, fullerenes, and anions.     

The self-diffusion coefficient in stable and metastable states of the Lennard-Jones fluid

Molecular-dynamics simulations have been employed to calculate the self-diffusion coefficient of a Lennard-Jones fluid for 198 sets of state parameters in the range of temperatures 0.35 ≤ k_BT/? ≤ 2.0 and densities 0.005 ≤ ρσ³ ≤ 1.2. Calculations have been made in stable and metastable states to the boundary of spontaneous nucleation in a model containing 2048 interacting particles. Results of computations, performed in the parameter range of stable states, are compared with the results of previous papers. Equations have been formulated, which describe the dependences of the self-diffusion coefficient on temperature and density and on temperature and pressure in the whole range of parameters including both the stable and metastable (supersaturated vapor, superheated and supercooled liquid) states of fluid.     

On the accuracy of correlation energy calculated by the correlation factor method: first- and second-row atoms

Summary The correlation energy of two- and four-isoelectronic series, a representative example for which the existing spin-density functionals fails, is calculated using the Colle and Salvetti method, considering mono- and multideterminantal wave functions. The results are in agreement with experimental data, and show the potentiality of this method when it is applied to wave functions including the most relevant configurational features. Also, results for the ionization energies and electron affinities of first- and second-row atoms are reported.     

超临界L-J流体混合物互扩散性质的分子动力学模拟

采用分子动力学方法计算了超临界Lennard-Jones(L-J)流体混合物的扩散性质, 分析了超临界条件下二元L-J混合流体(Ar-Kr体系)中各组分的自扩散系数及Maxwell-Stefan互扩散系数随组分的变化情况. 结果表明, 与Darken公式能很好地应用于常规条件下的Ar-Kr体系不同, 超临界条件下的Maxwell-Stefan扩散系数明显大于Darken公式的预测值, 不同原子间的速度互相关函数不可忽略且为正相关.     

计算机辅助糖苷酶分子设计与改造研究进展

糖苷酶作为一种重要的生物催化剂,在工业生物催化领域有着广阔的应用前景.但天然糖苷酶存在催化活性低、热稳定性和底物选择性差等缺点,严重限制了它在规模化生产中的推广应用.近年,有关糖苷酶催化机制与结构功能关系的研究备受关注,特别是计算机辅助酶设计在相关研究领域发挥着越来越重要的作用.我们综述了糖苷酶分子设计改造过程中应用的计算机辅助方法:包括同源比对、分子对接以及动力学模拟;阐述了这些计算方法在糖苷酶的结构与功能关系解析、酶催化分子机制、酶催化性能改造方面的应用现状.最后,对开发智能精准的计算分析方法的新发展趋势进行了展望.     

Monte Carlo simulation of the local ordering of water molecules. I. Binary spatial correlations

The pair distribution functions (DFs) of the oxygen and hydrogen atoms over space around one of the water molecules were calculated during Monte Carlo simulation (Metropolis procedure for the NVT ensemble at normal density and 300 K). An analysis of the isosurfaces of the DF_OO and DF_OH constructed around the selected water molecule for several fixed values of local density allowed us to obtain detailed information about the most probable localization of water molecules in the second and third coordination spheres.     

The competition between crystallization and demixing in polymer blends. IV. Detection of composition inhomogeneities around growing spherulites

In polymer blends of an amorphous and a semicrystalline component, the crystallization kinetics and the resulting morphology are heavily determined by the diffusion ability of the whole chains and by the dwelling site of the amorphous polymer. Depending on the relative rates of spherulite growth and chain diffusion, radial composition profiles around the growing spherulites and a gradual increase of the melt bulk composition can develop. The resulting change in composition, particularly at the crystallization front, causes a corresponding temporal variation of the spherulite growth rate. In the present article, two experimental techniques are introduced to prove the existence and to determine the course of these concentration profiles. They are based on the composition dependences of the spherulite growth rate and the number density of primary nuclei. Their efficiency is demonstrated by measurements on PVDF/PEA blends. The blend composition at the crystal growth front was found to change by absolute 25%, and the width of the profile can amount to up to 70 μm. © 1996 John Wiley & Sons, Inc.     

New framework nanostructures of carbon atoms in <Emphasis Type="Italic">sp</Emphasis><Superscript>2</Superscript> and <Emphasis Type="Italic">sp</Emphasis><Superscript>3</Superscript> hybridized states

A new family of framework nanostructures including carbon atoms in _sp ² and sp ³ hybridized states is reported. Structure optimization was fulfilled using MM+ molecular mechanics and Hückel semiempirical methods. The energy characteristics of the structures have been evaluated. Comparative analysis of the stability of the title nanostructures has been performed in relation to their geometry and relative contents of sp ²/sp ³ atoms.     

Influence of the size of fixed-rigidity spheres on the structural and energy characteristics of hydrophobic hydration

Monte Carlo simulations of molecular configurations of aqueous solutions of spherical particles with a special potential of solute—water interaction were carried out. The influence of the particle size on the properties of hydration shells was investigated. Two regimes of hydrophobic hydration with a crossover point at 0.4 nm were found. Hydration of smaller particles causes insignificant changes in the properties of water. Particles larger than 0.4 nm break the liquid water structure. Breaking effects are more pronounced in the first hydration shell of particles. Dewetting of hard sphere surfaces predicted by the LCW phenomenological theory has peculiarities in the case of hydration of fixed-rigidity spheres. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1777–1786, September, 2008.