Coordination Number Of Atoms Research Articles

Using Latex Balls and Acrylic Resin Plates To Investigate the Stacking Arrangement and Packing Efficiency of Metal Crystals

A high-school third-year or undergraduate first-semester general chemistry laboratory experiment introducing simple-cubic, face-centered cubic, body-centered cubic, and hexagonal closest packing unit cells is presented. Latex balls and acrylic resin plates are employed to make each atomic arrangement. The volume of the vacant space in each cell is measured by weighing water poured into the unit cell model, and the packing efficiency of each unit is obtained from the volume of vacant space. The observed values are compared with the theoretical calculations. Students can easily understand experimentally and theoretically that the packing efficiency of the face-centered cubic is the same as that of the hexagonal closest packing and significantly greater than that of the body-centered cubic. Moreover, they can understand the number of the neighboring atoms for any atom (coordination number) in each cell.

Mechanisms of structural accommodation of Se deficiency in binary Ga2Se3–GeSe2 glasses: Results from 77Se MATPASS/CPMG NMR spectroscopy

The nature of the selenium coordination environments in the structure of binary Ga2Se3–GeSe2 chalcogenide glasses is investigated using two-dimensional 77Se magic angle turning-phase adjusted spinning sidebands/Carr–Purcell–Meiboom–Gill (MATPASS/CPMG) nuclear magnetic resonance (NMR) spectroscopy. The structural network of these glasses consists of corner and edge-sharing (Ga/Ge)Se4 tetrahedra in which the coordination numbers of Ga, Ge, and Se atoms are primarily 4, 4, and 2, respectively. Consequently, the addition of Ga2Se3 to GeSe2 results in the formation of Ge–Ge homopolar bonds to satisfy the coordination constraints of the constituent atoms. These Ge–Ge bonds are randomly distributed throughout the network such that any clustering of (Se3/2)Ge–Ge(Se3/2) ethane-like units is avoided to the maximum extent. However, for glasses containing ≥30mol% Ga2Se3, the appearance of three-coordinated Se atoms provides an alternate mechanism to accommodate for the Se deficiency in the limit where the Ge–Ge bonds are nearly saturated. These three-coordinated Se atoms are formed by corner-sharing between three GaSe4 tetrahedra that is reminiscent of oxygen triclusters shared by three AlO4 tetrahedra reported in peraluminous oxide glasses and liquids.

Adsorption of a Methylthio Radical on Silver Nanoparticles: Size Dependence

A systematic study of the adsorption of a methylthio on different sites of silver nanoparticles of 13, 55, 147, and 309 atoms with icosahedral symmetry as well as on the (111) surface is performed using density functional theory. Ab initio molecular dynamics were used to obtain the adsorption energies, atomic positions, and electronic properties of the lowest-energy configurations. Different adsorption sites and orientations of the molecule were tested. The electronic density of states also shows a size dependence, in which a transition from discrete to more band-like structure is found. Adsorption of a second methylthio is also studied. It was observed that final structures, adsorption energies, and electronic density of states strongly depended on the nanoparticle size and thus on the atomic coordination number, where bridge configurations had the lowest total energy and the highest adsorption energy for all sizes except Ag13.

State of uranium in glassy-crystalline materials for immobilization of radioactive slag

The valence state and local surrounding of uranium atoms in glassy-crystalline materials intended for immobilization of slag from a furnace for radioactive waste (RW) incineration and prepared by fusion of simulated slag with addition of sodium disilicate or tetraborate were determined by analysis of the spectra of X-ray L3-absorption edge fine structure (XAFS) in the near-edge (XANES) and extended (EXAFS) ranges. The averaged valence and coordination number of the uranium atoms are superpositions of the corresponding values for the coexisting phases.

Thickness- and microstructure-dependent mechanical properties induced by surface layers in nanofilms

The material properties of silica nanofilms were numerically investigated by using molecular dynamics and were theoretically confirmed by a homogenization method. Stress–strain curves under tensile deformations were obtained for two different microstructure films (α-quartz and amorphous) with various bulk thicknesses. Surface layers for both microstructure films formed by energetic relaxation were determined by coordination numbers of surface atoms, and they were shown to affect the mechanical properties of the nanofilms in a systematic manner, as predicted using the homogenization theory. We suggested a generalized prediction rule for effective material properties of nanostructured materials with interfacial phases such as surface layers in low dimensions, which is generally ignorable in the thick film limit.

Evolution of Carbon Nanofiber-Supported Pt Nanoparticles of Different Particle Sizes: A Molecular Dynamics Study

Molecular dynamics simulations employing the ReaxFF reactive force field have been carried out to analyze the structural evolution of fishbone-type carbon nanofiber-supported Pt nanoparticles, with particle size ranging from 5.6 to 30.7 Å. Simulated results indicate that upon adsorption the distribution of first-shell Pt–Pt coordination number and radial distribution function change significantly in Pt nanoparticles up to 2 nm in size and that the restructuring degree of the Pt nanoparticles decreases with particle size, which is attributed both to the reduced binding energy per Pt atom bonded to support and to the increased cohesive energy of the Pt nanoparticles. In the Pt10 particle, the majority of the Pt atoms are detached from the metal particle, leading to atomic adsorption of single Pt atoms on the support. As the Pt particle size is increased to ∼3 nm, however, the crystalline degree of Pt nanoparticles is even higher than that of the corresponding isolated nanoparticles because the strong metal–support interaction has a positive effect on the crystalline degree of the upper part of Pt nanoparticles. Two surface properties of the Pt nanoparticles, namely, Pt dispersion and coordination number of surface Pt atoms, are then computed and found to decrease and increase, respectively, with particle size. Thus, on-purpose control of particle size (and hence the metal–metal and metal–support interactions) is of crucial importance for tuning the superficial structures of supported active metal particles, which eventually determine the adsorption and catalytic properties of catalysts.

Control of regioselectivity over gold nanocrystals of different surfaces for the synthesis of 1,4-disubstituted triazole through the click reaction.

Gold nanocubes, octahedra, and rhombic dodecahedra were examined for facet-dependent catalytic activity in the formation of triazoles. Rhombic dodecahedra gave 100% regioselective 1,4-triazoles. The product yield was increased by decreasing the particle size. However, a mixture of 1,4- and 1,5-triazoles was obtained in lower yields when cubes and octahedra of similar sizes were used. The lowest Au-atom density on the {110} surface and largest unsaturated coordination number of surface Au atoms may explain their best catalytic efficiency and product regioselectivity. Various spectroscopic techniques were employed to verify the formation of the Au-acetylide intermediate and establish the reaction mechanism, in which phenylacetylene binds to the Au {110} surface through the terminal-binding mode to result in the exclusive formation of 1,4-triazoles. The smallest rhombic dodecahedra can give diverse 1,4-disubstituted triazoles in good yields by coupling a wide variety of alkynes and organic halides.

Intermetallic crystal structures as foams. Beyond Frank-Kasper.

In many intermetallic structures, the atoms and bonds divide space into tilings by tetrahedra. The well-known Frank-Kasper phases are examples. The dual tilings divide space into a tiling by polyhedra that is topologically a foam. The number of faces of the dual polyhedron corresponds to the atom coordination number in the direct structure, and face sharing by adjacent polyhedra corresponds to bonds in the direct structure. A number of commonly occurring intermetallic crystal structures are shown as their duals. A major advantage of this alternative mode of depiction is that coordination of all of the atoms can be seen simultaneously.

A DFT Study of Structural and Electronic Properties of ZnS Polymorphs and its Pressure‐Induced Phase Transitions

A systematic first‐principles investigation, by using the density functional formalism with the nonlocal B3LYP approximation including a long‐range dispersion correction, has been performed to calculate the structural and electronic properties and phase transitions under pressure of the three phases of ZnS (cubic zinc blende, ZB, hexagonal wurtzite, W, and cubic rock salt, RS). Numerical and analytical fittings have been carried out to determine the equilibrium unit cell geometry and equation of state parameters for the ZnS phases. The band structures, energy gap, density of states, and vibrational frequencies and their pressure dependences are investigated. The present results illustrate that both phases, W and ZB, present very similar enthalpy and the RS phase becomes thermodynamically more stable than ZB and W structures at 15.0 and 15.5 GPa, respectively. These phase transitions are accompanied by an increase of the first shell coordination number of Zn atom and by a cell volume collapse of 13.9% and 14.3% for ZB and W phases, respectively. The atomic contributions of the conduction and valence bands, as well the binding energy for the Zn 3d orbital have been obtained.

Mn-dimer 분자자성체의 전자구조 및 자기구조 계산

We have studied electronic and magnetic structure of Mn-dimer molecule using OpenMX method based on density functional method. The calculated density of states shows that the four O atoms split and energy levels. The energy splitting by the crystal field is smaller than bulk MnO with cubic structure, because of small coordination number of atoms. Total energy with antiferromagnetic spin configuration is lower than that of ferromagnetic configurations. Calculated exchange interaction J between Mn atoms is one order larger than that of the other Mn-O magnetic molecules. That comes from the direct exchange interaction between Mn 3d orbitals and the super-exchange interactions caused by strong -bonding of Mn-O orbitals.

CO2 hydrogenation with shape-controlled Pd nanoparticles embedded in mesoporous silica: Elucidating stability and selectivity issues

Shape-controlled Pd nanocubes and nanopolyedra particles were embedded in mesoporous silica shells and their catalytic properties for the CO2 hydrogenation were compared to a reference Pd/SiO2 catalyst prepared by wetness impregnation. Whereas the Pd impregnated silica exhibits a strong deactivation, the activity of both embedded solids is remarkably stable. This difference is due to a significant Pd particles sintering in the reference catalyst while no increase of particle size is observed for the core@shell solids. CH4 selectivity is shown to be correlated to the mean coordination number of surface atoms which controls the adsorption strength of CO as intermediate species.

Structural Study of Ferroelectric Phase Transition of Sn-doped SrTiO3

Recently, ferroelectricity was discovered in Sn-doped SrTiO3 (abbreviated by SSTO), in which Sr-atom was substituted by a few percent Sn-atom[1]. The ferroelctricity of SSTO was confirmed by means of the appearance of the dielectric anomaly, that reached several thousands and the clear D-E hysteresis loop in low temperature phase. In order to clarify the mechanism of ferroelectric phase transition of SSTO from the viewpoint of the crystal structure, we investigated the average crystal structure and the local structure around the substitutional Sn-atom of SSTO10 (10% Sn concentration, ferroelectric phase transition temperature 180K) by means of synchrotron-radiation powder X-ray diffraction and transmission XAFS spectrum of Sn:K-edge, respectively. From the results of MEM/Rietveld analysis of powder X-ray diffraction data, it was obtained that crystal structure of paraelectric phase of SSTO10 was cubic perovskite structure with the disorder state of Sn-atom. In ferroelectric phase, the crystal system was tetragonal, which was similar in structure to tetragonal ferroelectric structure of BaTiO3, and Sn-atom was order state. XAFS study revealed that the valence of Sn-ion was +2 charge and the local structure of Sn-atom was seemed as being the self-insistent state of SnO crystal structure. However, strangely, the coordination number of the nearest neighbor atom, that is O-atom, was 2 instead of 4. This is a mystery result and we have been analyzing. We have considered that the ferroelectricity of SSTO is induced by the distortion around the subsitituional Sn-atom. At the meeting, we are planning to discuss the precise crystal structure and the mechanism of the ferroelectric phase transition of SSTO.

Structural investigations on some cadmium-borotellurate glasses using ultrasonic, FT-IR and X-ray techniques

Glasses in the system 50B2O3–(50 − x)TeO2–xCdO with different CdO contents (0, 10, 20, 30, 40 and 50mol%), have been prepared by melt quenching technique. Elastic properties, X-ray and FT-IR spectroscopic studies have been employed to study the role of CdO on the structure of the investigated glass system. Elastic properties and Debye temperature have been investigated using sound wave velocity measurements at 4MHz at room temperature. The results showed that the density increase and the molar volume decrease while both sound velocities decrease with increase in x. Elastic properties, FT-IR and X-ray diffraction studies on the network structure of these glass structures, have revealed that Cd2+ ions are incorporated in the form of CdO6, decreasing the molar volume and compensate for the decrease in the average coordination number of tellurium atoms which was the reason for the increase in elastic moduli.

Structural Arrangements of Isomorphic Substitutions in Smectites: Molecular Simulation of the Swelling Properties, Interlayer Structure, and Dynamics of Hydrated Cs–Montmorillonite Revisited with New Clay Models

Three new structural models of montmorillonite with differently distributed Al/Si and Mg/Al substitutions in the tetrahedral and octahedral clay layers are systematically developed and studied by means of MD simulations to quantify the possible effects of such substitutional disorder on the swelling behavior, the interlayer structure, and mobility of aqueous species. A very wide range of water content, from 0 to 700 mgwater/gclay is explored to derive the swelling properties of Cs–montmorillonite. The determined layer spacing does not differ much depending on the clay model. However, at low water contents up to 1-layer hydrate (∼100 mgwater/gclay) the variation of specific locations of the tetrahedral and octahedral substitutions in the two TOT clay layers slightly but noticeably affects the total hydration energy of the system. Using atom–atom radial distribution functions and the respective atomic coordination numbers we have identified for the three clay models not only the previously observed binding sites for Cs+ on the clay surface but also new ones that are correlated with the position of tetrahedral substitution in the structure. The mobility of Cs+ ions and H2O diffusion coefficients, as expected, gradually increase both with increasing water content and with increasing distance from the clay surface, but they still remain 2 to 4 times lower than the corresponding bulk values. Only small differences were observed between the three Cs–montmorillonite models, but these differences are predicted to increase in the case of higher charge density of the clay layers and/or interlayer cations.

A theoretical study of structural and electronic properties of alkaline-earth fluoride clusters

The structural evolution and variation of electronic properties of alkaline-earth metal fluoride clusters (MF2)n (M=Mg, Ca, Sr, Ba; n=1–6) are investigated using density functional theory. All these clusters demonstrate ionic-bonding dominated through all sizes considered here, and generally show a preference of 3D structures when n⩾4. It is found that the structural evolution of (MgF2)n clusters are distinct from the rest of the alkaline-earth clusters owing to the competitive interplay of much smaller ionic radius of Mg and the stronger Mg–F bond. In the ground state configurations, (MgF2)n clusters prefer the planar building units, whereas the rest of the (MF2)n clusters prefer the 3D building units of a M2F3 type maximizing the coordination number of the constituent metal atoms. The variations of the binding energy, the ionization potential, the electron affinity and the HOMO–LUMO gap with the cluster size are explained in terms of the change in the ionic radius and the basicity of the constituent metal ions in going from (MgF2)n to (CaF2)n, (SrF2)n, and (BaF2)n.

Thermolysis preparation of ZnS nanoparticles from a nano-structure bithiazole zinc(II) coordination compound

Nano-scale and single crystals of a new tris-chelate Zn(II) compound, {[Zn(DADMBTZ)3](SCN)2⋅4H2O}n, (1), {DADMBTZ=2,2′-diamino-5,5′-dimethyl-4,4′-bithiazole} have been synthesized by the reaction of zinc(II) sulfate, ammonium thiocyanate and DADMBTZ using sonochemical and branched tube methods, respectively. The new nanoparticles were characterized by scanning electron microscopy (SEM), X-ray powder diffraction (XRD) and FT-IR spectroscopy. Compound (1) was structurally characterized by single crystal X-ray diffraction. Compound (1) form a tris-chelate complex with nearly C3 symmetry. The coordination number of zinc atom in the compound is six with coordinated environments of distorted octahedral, ZnN6. In reaction with DADMBTZ, the ligand DADMBTZ acts as bidentate in compound to form five-membered chelate rings with the same internal angles in coordination polyhedron. The crystal packing is mainly stabilized by N–H----N hydrogen bonding interactions. The thermal stability of compound (1) was studied by thermal gravimetric (TG) and differential thermal analyses (DTA). ZnS nanostructures were obtained by direct thermolyses of compound (1) at 400°C under argon atmosphere. The ZnS nanoparticles were characterized by scanning electron microscopy (SEM), X-ray powder diffraction (XRD) and Fourier transform infrared (FT-IR) spectroscopy.

Atomic-structural synergy for catalytic CO oxidation over palladium-nickel nanoalloys.

Alloying palladium (Pd) with other transition metals at the nanoscale has become an important pathway for preparation of low-cost, highly active and stable catalysts. However, the lack of understanding of how the alloying phase state, chemical composition and atomic-scale structure of the alloys at the nanoscale influence their catalytic activity impedes the rational design of Pd-nanoalloy catalysts. This work addresses this challenge by a novel approach to investigating the catalytic oxidation of carbon monoxide (CO) over palladium-nickel (PdNi) nanoalloys with well-defined bimetallic composition, which reveals a remarkable maximal catalytic activity at Pd:Ni ratio of ~50:50. Key to understanding the structural-catalytic synergy is the use of high-energy synchrotron X-ray diffraction coupled to atomic pair distribution function (HE-XRD/PDF) analysis to probe the atomic structure of PdNi nanoalloys under controlled thermochemical treatments and CO reaction conditions. Three-dimensional (3D) models of the atomic structure of the nanoalloy particles were generated by reverse Monte Carlo simulations (RMC) guided by the experimental HE-XRD/PDF data. Structural details of the PdNi nanoalloys were extracted from the respective 3D models and compared with the measured catalytic properties. The comparison revealed a strong correlation between the phase state, chemical composition and atomic-scale structure of PdNi nanoalloys and their catalytic activity for CO oxidation. This correlation is further substantiated by analyzing the first atomic neighbor distances and coordination numbers inside the nanoalloy particles and at their surfaces. These findings have provided new insights into the structural synergy of nanoalloy catalysts by controlling the phase state, composition and atomic structure, complementing findings of traditional density functional theory studies.

Graphitization Wear of Diamond Tool in Nanometric Cutting of Single Crystal Silicon

During ultra-precision cutting of brittle materials, the wear of diamond tool seriously affects the quality of machined surface. By molecular dynamics modeling of nanometric cutting, the generation of graphitization and its formation process at the cutting edge of tool are observed. By analyzing the process, the reason of the graphitization wear is mainly thermo-chemical reactions. By calculating the changes of coordination numbers of the tool atoms, graphitization conversion rate keeps increasing along the cutting process but gets stable after a certain length, which indicates the graphitization wear will occur in the same process.

Theoretical study of isomerism of acetylene compounds with aluminum clusters doped with 3d transition metals

Structural characteristics, vibrational frequencies, and energies of ten isomers of acetylene compounds with the centered aluminum cluster Al13 and its analogues Al12M doped with 3d transition metal atoms (M = Ti-Ni) in the states of different multiplicity have been calculated by the density functional theory method. In addition to “coordinated” intermediates in which the C2H2 molecule is coordinated through its C-C bond to the M vertex, an M-Al edge, or a trigonal face of the [MAl2] cluster, “fragment” isomers have been considered in which the acetylene molecule is broken into fragments (C2H + H, CH + CH, H + CH + C, and 2P + 2H) differently inserted into the aluminum cage and enlarging it to Al12MC2. For most compounds, low-lying isomers have structures 1–4 (the C2H2 molecule is coordinated to an Al2M face), 1–5 (two CH fragments are added to adjacent Al2M faces), and 1–8 (with a five-coordinate C* atom). Structure 1–1, in which the C2H2 molecule is coordinated through the C-C bond to the M dopant is unstable against transformation into 1–4 with a low barrier. An isomer with unusual structure 1–9 has been localized in which two five-coordinate C* atoms built into the aluminum cage are located in adjacent quasi-planar tetragonal [MAl3] faces and are bonded to the central aluminum atom (Alc) through the fifth bonds. The substitution of electronegative substituents X= F and Cl for H atoms in isomers 1–8 and 1–9 makes the latter more basic and clearly more favorable. The five-coordinate C* atoms in them are able to add acceptor ligands of the BH3 and AlH3 type and to increase the coordination number of the carbon atom to six with a considerable decrease in energy. The trends in the change in structural characteristics and relative energies of isomers with a change in M dopants along the 3d series, electronegativity of X substituents, and electronic state multiplicity have been analyzed.

Formic acid decomposition on Au catalysts: DFT, microkinetic modeling, and reaction kinetics experiments

A combined theoretical and experimental approach is presented that uses a comprehensive mean‐field microkinetic model, reaction kinetics experiments, and scanning transmission electron microscopy imaging to unravel the reaction mechanism and provide insights into the nature of active sites for formic acid (HCOOH) decomposition on Au/SiC catalysts. All input parameters for the microkinetic model are derived from periodic, self‐consistent, generalized gradient approximation (GGA‐PW91) density functional theory calculations on the Au(111), Au(100), and Au(211) surfaces and are subsequently adjusted to describe the experimental HCOOH decomposition rate and selectivity data. It is shown that the HCOOH decomposition follows the formate (HCOO) mediated path, with 100% selectivity toward the dehydrogenation products (CO2 + H2) under all reaction conditions. An analysis of the kinetic parameters suggests that an Au surface in which the coordination number of surface Au atoms is ≤4 may provide a better model for the active site of HCOOH decomposition on these specific supported Au catalysts. © 2014 American Institute of Chemical Engineers AIChE J, 60: 1303–1319, 2014