Atomic Packing Density Research Articles

Structure of eutectic alloys of Au with Si and Ge

Au–Si and Au–Ge alloy systems have a deep eutectic point in the Au-rich concentration region where the melting point falls down to 633 K. In order to investigate the liquid structure in relation to the glass-forming tendency of these alloys, high-energy X-ray diffraction measurements have been carried out at the eutectic composition and at compositions with excess amounts of Au or IVb element. The nearest neighbor correlations in the eutectic liquids are intense and sharp in the pair distribution function and exhibit a rather small temperature dependence in comparison with those alloys of other than the eutectic composition. Structural models for these liquid alloys are proposed with the aid of reverse Monte Carlo simulation. The reproduced atomic arrangements around the eutectic region exhibit a substitutional-type structure where the dense random packing of Au atoms is preserved and Si or Ge atoms occupy the Au-sites at random.

Diffusion compensation for argon, hydrogen, lead, and strontium in minerals: Empirical relationships to crystal chemistry

Inspection of available experimental data reveals log-linear compensation effects between activation energies and pre-exponential factors for Ar, H, Pb, and Sr diffusion in a wide array of minerals. As a result, diffusion of Ar, H, Pb, and Sr converges to the same rates, respectively, at isokinetic temperatures in these minerals. Ionic porosity, Z , defined as the fraction of the unit-cell volume in a mineral not occupied by ions, is a measure of atomic packing density in silicate, carbonate, and phosphate minerals. Experimental diffusion parameters exhibit first-order correlations with ionic porosity, which proxies for mean metal-oxygen bond length/strength in minerals. An empirical kinetics-porosity model systematizes Ar, H, Pb, and Sr diffusion in minerals for which experimental diffusion data exist. For Ar and H diffusion, linear correlations are documented between activation energy and total ionic porosity. Combination of these correlations with diffusional compensation effects, which are also documented, yields empirical relationships among elemental diffusivity, total ionic porosity, and temperature. Linear correlations are also observed between experimental diffusion coefficients for Pb and Sr at given temperatures and calculated ionic porosities. For most minerals, the empirical predictions are remarkably consistent with experimental data, which strengthens the link between crystal chemistry and diffusion kinetics.

Effect of grain orientation on tantalum magnetron sputtering yield

The differential sputter yields of tantalum grains during argon ion magnetron sputtering were measured and found to correlate with the atomic packing density in the uppermost atomic layer. Grains with their (110) planes aligned within 15° of the sputtering surface had the highest sputtering yield (0.95at./ion at 400eV). Simultaneously, grains oriented so that their (111) planes were within 15° of the sputtering surface had sputtering yields of around two times lower (0.47at./ion at 400eV). These results are consistent with the surface sputtering rather than the channeling model. A correlation was found between the number of free atoms on the surface as determined using a facetted surface model and the measured sputtering yield.

Design of Cu8Zr5-based bulk metallic glasses

Basic polyhedral clusters have been derived from intermetallic compounds at near-eutectic composition by considering a dense packing and random arrangement of atoms at shell sites. Using such building units, bulk metallic glasses can be formed. This strategy was verified in the Cu–Zr binary system, where we have demonstrated the existence of Cu8Zr5 icosahedral clusters in Cu61.8Zr38.2, Cu64Zr36, and Cu64.5Zr35.5 amorphous alloys. Furthermore, ternary bulk metallic glasses can be developed by doping the basic Cu–Zr alloy with a minority element. This hypothesis was confirmed in systems (Cu0.618Zr0.382)100−xNbx, where x=1.5 and 2.5at.%, and (Cu0.618Zr0.382)98Sn2. The present results may open a route to prepare amorphous alloys with improved glass forming ability.

A new Ti–Zr–Hf–Cu–Ni–Si–Sn bulk amorphous alloy with high glass-forming ability

The effect of Sn substitution for Cu on the glass-forming ability was investigated in Ti 41.5Zr 2.5Hf 5Cu 42.5− x Ni 7.5Si 1Sn x ( x = 0, 1, 3, 5, 7) alloys by using differential scanning calorimetry (DSC) and X-ray diffractometry. The alloy containing 5% Sn shows the highest glass-forming ability (GFA) among the Ti–Zr–Hf–Cu–Ni–Si–Sn system. Fully amorphous rod sample with diameters up to 6 mm could be successfully fabricated by the copper mold casting Ti 41.5Zr 2.5Hf 5Cu 37.5Ni 7.5Si 1Sn 5 alloy. The activation energies for glass transition and crystallization for Ti 41.5Zr 2.5Hf 5Cu 37.5Ni 7.5Si 1Sn 5 amorphous alloy are both larger than those values for the Sn-free alloy. The enhancement in GFA and thermal stability after the partial replacement of Cu by Sn may be contributed to the strong atomic bonding nature between Ti and Sn and the increasing of atomic packing density. The amorphous Ti 41.5Zr 2.5Hf 5Cu 37.5Ni 7.5Si 1Sn 5 alloy also possesses superior mechanical properties.

Structural changes in titanium dioxide nanocrystals during plastic deformation

The polygonization of 200 nm rutile crystals during dry ball-milling at 10gwas monitored in detail by means of transmission electron microscopy (TEM) and X-ray diffraction (XRD). The TEM results showed how to modify the Williamson–Hall method for a successful evaluation of crystal size and microstrain from XRD profiles. Macrostrain development was determined from the minute shift of the most intense reflection. In addition, changes in pycnometrical density were monitored. Accordingly, the primary crystal is disintegrated during milling into a mosaic of 12–35 nm pieces where the grain boundaries induce up to 1.2% microstrain in a lower layer of 6 nm thickness. Macrostrain in the interior of the crystals rises to 0.03%. The pycnometrical density, reflecting the packing density of atoms in the grain boundary, decreases steadily by 1.1%. The results bear relevance to our understanding of plastic flow and the mechanism of phase transitions of metal oxides during high-energy milling.

QSAR Analysis of the Structure—Toxicity Relationship of Aconitum and Delphinium Diterpene Alkaloids

The structure—toxicity relationship of a series of diterpene alkaloids isolated from plants of the genera Aconitum and Delphinium was found using a QSAR method. Structures were optimized by the semi-empirical AM1 quantum-chemical method and then used to find structure—toxicity trends. Several models for predicting toxicity based on topological 3D and physicochemical descriptors were developed using a genetic algorithm and multiple linear regression analysis. The resulting models showed a reliable dependence of toxicity of the diterpene alkaloids on such parameters as the atomic packing density in the molecular volume, surface polarity, number of C=O groups, and lipophilicity. The possible mechanism of biological activity was discussed in connection with these molecular features.

Efficient local packing in metallic glasses

A simple topological model in an earlier manuscript has provided additional support for the concept that efficient atomic packing is a fundamental principle in the formation of metallic glasses. In that work, an approach for defining and quantifying the local packing efficiency, P, was developed for solute-centered clusters that contained only solvent atoms in the first coordination shell. In the present work, this methodology is extended to allow quantification of P when more than one atomic species is present in the first coordination shell. This analysis is applied to several metallic glasses using published experimental data of partial coordination numbers. It is shown that packing in the first coordination shell is generally very efficient, even though the systems studied have significant differences in atomic species, compositions and relative atomic sizes. It is shown that packing is generally efficient around both solute and solvent atom species. Local packing efficiencies much less than unity are expected to be uncommon, since the global average packing efficiency is near unity and local packing efficiencies greater than unity are physically improbable. Deviations from efficiently packed configurations are discussed with respect to the local packing efficiencies in competing crystalline structures and with poorer glass forming ability. The values of P obtained for metallic glasses are essentially identical to the values obtained from a similar analysis of the competing crystalline structures. These results are consistent with frequent earlier reports of topological short range ordering in metallic glasses and with developments that have established the relationship between dense atomic packing and glass formation.

Exploring the electronic and mechanical properties of protein using conducting atomic force microscopy.

In interfacing man-made electronic components with specifically folded biomacromolecules, the perturbative effects of junction structure on any signal generated should be considered. We report herein on the electron-transfer characteristics of the blue copper metalloprotein, azurin, as characterized at a refined level by conducting atomic force microscopy (C-AFM). Specifically, the modulation of current-voltage (I-V) behavior with compressional force has been examined. In the absence of assignable resonant electron tunneling within the confined bias region, from -1 to 1 V, the I-V behavior was analyzed with a modified Simmons formula. To interpret the variation of tunneling barrier height and barrier length obtained by fitting with the modified Simmons formula, an atom packing density model associated with protein mechanical deformation was proposed and simulated by molecular dynamics. The barrier heights determined at the minimum forces necessary for stable electrical contact correlate reasonably well with those estimated from bulk biophysical (electroanalytical and photochemical) experiments previously reported. At higher forces, the tunnel barrier decreases to fall within the range observed with saturated organic systems. Molecular dynamics simulations revealed changes in secondary structure and atomic density of the protein with respect to compression. At low compression, where transport measurements are made, secondary structure is retained, and atomic packing density is observed to increase linearly with force. These predictions, and those made at higher compression, are consistent with both experimentally observed modulations of tunneling barrier height with applied force and the applicability of the atom packing density model of electron tunneling in proteins to molecular-level analyses.

Cytochrome c: the effect of temperature and pressure from molecular dynamics simulations

Cytochrome c has been extensively investigated due to its role in the process of electron transfer in the mitochondrial system. The effect of temperature and pressure on horse cytochrome c was investigated using normal mode analysis and Molecular Dynamics simulations. The conformational space of the molecule and the anharmonic component of oscillations were obtained further by molecular dynamics simulations for 1.5 ns in solvent environment. The simulated root means square fluctuations, radii of gyration, hydrogen bond arrangements and atomic packing densities reveal that the protein remains compact for the duration of the simulation; high temperature induced partial unfolding at surface regions was observed. The covalent bonding arrangement of the Fe (heme) was investigated during the simulation. These results provide insight into the stability of electron transport by cytochrome c under various pressures and temperatures and provide the regions that could be mutated to enhance the stability and electron transfer properties of the protein.

Glass forming ability and crystallization behavior of Ti-based amorphous alloys with high specific strength

Thermal stability and crystallization behavior of melt-spun Ti 50− x Cu 25Ni 15Sn 3Be 7Zr x ( x=0, 1, 3, 5 and 7) amorphous alloys have been investigated using differential scanning calorimetry (DSC), X-ray diffractometry and transmission electron microscopy. With increasing Zr content, x, from 0 to 7, both Δ T x(= T x− T g) and T rg(= T g/ T l) gradually increase from 45 to 56 K and from 0.53 to 0.60, respectively, indicating that the alloys containing Zr have a good glass forming ability, where T g, T x, and T l are glass transition, crystallization, and liquidus temperatures, respectively. The Ti 50Cu 25Ni 15Sn 3Be 7 alloy shows three endothermic events in the DSC curve; initially the alloy crystallizes by forming crystalline phase a few nanometers in scale, followed by decomposition into a mixture of Ti(Ni,Cu), TiCu, Ti 3Sn, and TiBe 12 phases at high temperature. On the other hand, the alloys containing Zr consist of only nanocrystalline phases around 10 nm in size even after the second endothermic event due to their increased atomic packing density. For the Ti 45Cu 25Ni 15Sn 3Be 7Zr 5 alloy, fully amorphous rods up to 5 mm in diameter are successfully fabricated by injection casting. The amorphous alloys exhibit high compressive strength around 2500 MPa with good ductility.

First-Principles Calculation of the Work Functions for the High-Index Copper Surfaces

We calculated the work functions (WFs) for the high-index copper surfaces, (112), (321), and (413), as well as the low-index surfaces, (111), (100), and (110), using the full-potential linearized augmented plane wave (FLAPW) method within both the local density approximation (LDA) and the generalized gradient approximation (GGA). It is found that the GGA lowers rigidly the WFs about 0.46–0.49 eV from the values obtained by the LDA, for all the surfaces, and the experimental values for low-index surfaces are in between the calculated values by the LDA and GGA. It is also found that the WF does not decrease further, for the surfaces with higher indices than (112). This result is different from that of the recent measurements by the Kelvin probe technique [Appl. Phys. Lett.79, 4337 (2001)], which shows a linear dependence of WF on the atomic packing density. The result of our calculation is consistent with the WF anisotropy model, which was recently applied to tungsten surfaces.

蛋白質分子の原子充填率の精密再評価

蛋白質分子の原子充填率の精密再評価

Die Packungsdichte der Atome in Modifikationen von Kohlenstoff und Silicium

Abstract The crystal chemistry of carbon and silicon is discussed with respect to the packing density of atoms in their crystalline modifications. The reduced atomic volumes of metallic carbon as calculated from diamond, hexagonal diamond and buckminsterfullerene C60 agree within less than 0.2, indicating the correctness of the reducing procedure. A much lower value calculated from graphite, rhombohedral graphite and a low-temperature modification of buckminsterfullerene remains unexplained. Two proposed crystal structures of a cubic body-centered form of carbon appear unacceptable. The reduced atomic volumes of diamond-type silicon and metastable γ-Si are in good agreement. Their values, calculated from six allotropic modifications (Si I, II, XI, V, VI, VII, and Si X) at pressures up to ≈200 GPa, are represented by an empirical exponential function of pressure. From this function, an isothermal equation of state is derived including the packing density of the atoms.

Synthesis of bulk metallic glass in the Ti-rich part of the Ti-Cu-Ni-Sn-Be-Zr alloy system

The glass forming ability and crystallization behaviour of melt spun Ti 50−xCu 25Ni 15Sn 3Be 7Zr x ( x = 0, 3 and 5) amorphous alloys were investigated using differential scanning calorimetry (DSC), X-ray diffractometry and transmission electron microscopy. With increasing Z r contents, x from 0 to 5, ? T x (= T x − T g ) and T rg(= T g T l ) , where T g = glass transition temperature, T x = crystallization temperature and T l = liquidus temperature, gradually increase from 45 K to 56 K and from 0.57 to 0.60, respectively. The Ti 50Cu 25Ni 15Sn 3Be 7 alloy shows three exothermic events in the DSC curve; initially the alloy crystallizes by forming a few nanometer scale crystalline phase, followed by decomposition into a mixture of Ti(Ni,Cu), TiCu, Ti 3Sn, and TiBe 12 phases at high temperature. Furthermore, the alloys containing Zr exhibit the formation of nanocrystalline phases of ∼10 nm size even after the second exothermic event due to their increased atomic packing density. For the Ti 45Cu 25Ni 15Sn 3Be 7Zr 5 alloy, fully amorphous rods up to 5 mm in diameter were successfully fabricated by injection casting.

Approach for the structure analysis of complex molecular systems at computer simulation

The structure of complex inhomogeneous systems is a current problem in the physics of liquids, glasses, polymers, molecular biology, and material science. To understand the physical properties of such materials, one should study the structure in “micro” and “macro” levels, which demands a unified rigorous approach for structure investigations. We demonstrate that the Voronoi–Delaunay technique, which is well known in mathematics and in computer simulations, can be used for this purpose. The Voronoi–Delaunay tessellation contains complete information about the structure of a computer model. The method is applied for studying the intermediate range order to show that the behavior of the so-called prepeak in the structure factor is defined by a motif of spatial distribution of voids in the model. A large model of dense packing of spherical atoms in the process of crystallization from non-crystalline phase is analyzed. The extended linear defects of the diverse types are revealed. Investigation of the free volume distribution in the lipid bilayer in water is carried out. The results obtained can help for understanding a mechanism of diffusion of small molecules across lipid membranes.

On mechanism of low-energy heavy ions scattering on a target surface with small atomic mass

In the present work, an experimental study of low-energy ( E 0=20–500 eV) heavy Cs + ions scattering on target surfaces with small atomic masses (Al, Si, Ni) has been performed for more accurate definition of mechanism of scattering and evaluation of an opportunity for use of heavy ions scattering as a tool of surface layer analysis. It is shown that the dependence of the relative energies of scattered ions versus the initial energy E/ E 0 ( E 0) for Si ( E b=4.64 eV/atom) and Ni ( E b=4.43 eV/atom) approximately coincide despite the fact that the mass of Ni atom is twice as large as that of the Si atom mass. At the same time their binding energies E b are approximately equal to each other. It is found that the scattering angles of Cs + ions considerably exceed a limiting scattering angle θ lim in a single collision. It has been established that the scattering of low-energy heavy ions by light targets is described by a non-binary mechanism of many-particle interactions (simultaneous ion interaction with several target atoms). It has been shown that during the many-particle interactions the structure of energy spectra disappears; high relative energy of scattering ions and their dependence on energy of bombardment is observed. It has been found that the energy of scattered ions depends on binding energy, melting temperature and packing density of target atoms.

ChemInform Abstract: Atomic Volume and Packing Density of Atoms in Metallic Elements.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Wulff-shape, minimal energy, maximal density

The Gibbs-Curie minimum energy principle leads to the Wulff-shape of dense atomic packing with respect to the underlying structure, periodic or aperiodic. We show that an appropriate maximum density also leads to Wulff shapes of crystals or quasicrystals. This underlines the close relation of minimal energy and maximal density. A final example shows the striking coincidance between experiment and mathematical model.

Atomvolumen und Packungsdichte der Atome in metallischen Elementen Atomic Volume and Packing Density of Atoms in Metallic Elements

In the body-centered cubic structure and in closest sphere-packings the atoms are arranged to give structures with equal densities. A measure of the packing density of atoms is derived. Several crystal structures of elements, including the bcc structure and the closest sphere packings, represent a state of maximum density in which the atomic volume is characteristic of each element. From any crystal structure of an element its atomic volume in this state can be calculated to a good approximation.