Coordination Number Of Atoms Research Articles

Oxidation of formic acid on stepped Au(997) surface

The adsorption and reaction of formic acid (HCOOH) on clean and atomic oxygen-covered Au(997) surfaces were studied by temperature-programmed desorption/reaction spectroscopy (TPRS) and X-ray photoelectron spectroscopy (XPS). At 105 K, HCOOH molecularly adsorbs on clean Au(997) and interacts more strongly with low-coordinated Au atoms at (111) step sites than with those at (111) terrace sites. On an atomic oxygen-covered Au(997) surface, HCOOH reacts with oxygen atoms to form HCOO and OH at 105 K. Upon subsequent heating, surface reactions occur among adsorbed HCOO, OH, and atomic oxygen and produce CO2, H2O, and HCOOH between 250 and 400 K. The Au(111) steps bind surface adsorbates more strongly than the Au(111) terraces and exhibit larger barriers for HCOO(a) oxidation reactions. The surface reactions also depend on the relative coverages of co-existing surface species. Our results elucidate the elementary surface reactions between formic acid and oxygen adatoms on Au surfaces and highlight the effects of the coordination number of the Au atoms on the Au catalysis.

Atomic Ordering and Sn Segregation in Pt–Sn Nanoalloys Supported on CeO2 Thin Films

The stability and atomic ordering in Pt–Sn nanoalloys supported on CeO2 thin films have been studied by means of synchrotron radiation photoelectron spectroscopy and density functional calculations. Using CO molecules as a probe, we explored the development of the surface structure of supported Pt–Sn nanoalloys with respect to a reference Pt/CeO2 model system. We found a significant decrease in the density of CO adsorption sites on supported Pt–Sn nanoalloys caused by Sn segregation to the surface upon annealing. Additionally, we found that atomic ordering in Pt–Sn nanoalloys is driven by the balance between the surface segregation energy of Sn atoms and the energy of heteroatomic bond formation. Our calculations demonstrate a clear tendency for Sn segregation to the nanoalloy surface. For Pt105Sn35 and Pt1097Sn386 nanoparticles, we calculated a surface stoichiometry of Pt2Sn which is only slightly dependent on temperature in thermodynamic equilibrium. The analysis of Bader charges in Pt–Sn nanoalloys revealed a strong correlation between the charge and the coordination number of Sn atoms with respect to Pt neighbors. In particular, the magnitude of the charge transfer from Sn to Pt increases as a function of the Sn coordination number.

Synthesis of Lewis Base Adducts of Barium Bis[bis(trimethylsilyl)amide

Transmetalation of Sn{N(SiMe3)2}2 with barium metal in 1,2‐dimethoxyethane (DME) yields [(dme)2Ba{N(SiMe3)2}2] (1). The neutral ether ligand can be substituted by stronger Lewis bases such as tetramethylethylenediamine (tmeda) and pentamethyldiethylenetriamine (pmdeta) leading to the formation of [(tmeda)Ba{N(SiMe3)2}2] (2) and [(pmdeta)Ba{N(SiMe3)2}2] (3). The tetrahydropyran adduct [(thp)3Ba{N(SiMe3)2}2] (4) can be isolated after addition of tetrahydropyran (thp) to coligand‐free [Ba{N(SiMe3)2}{µ‐N(SiMe3)2}]2. The Ba–N bond lengths to the amido ligands are dictated by the coordination number of the metal atom. A comparitive analysis with alternative methods of preparation shows that the metathetical approach requires the use of exact stoichiometry because bariates form with any excess KN(SiMe3)2.

Formation of Second-Generation Nanoclusters on Metal Nanoparticles Driven by Reactant Gases.

Heterogeneous catalysis occurs at the interface between a solid catalyst and the reactants. The structure of metal catalyst nanoparticles at the metal-gas interface is a key factor that determines catalytic selectivity and activity. Here we report that second-generation nanoclusters are formed on the initial catalyst nanoparticles as a result of interaction with the reactant molecules when the nanoparticles are in a gas phase at Torr pressure or higher. The formation of the second-generation nanoclusters is manifested by a decrease of the average coordination number of the metal atoms and a shift of their core level energies in the presence of gases. The formation of second-generation nanoclusters increases the number of undercoordinated sites, which are the most active for catalysis in many cases.

Effect of pressure on the stability and ability to drying of water-saturated gases

The inorganic salts-based solid phase adsorbents are often used as driers of gases or weakly polar liquids (for example – ethanol) as the cations of metal elements have the ability to readily form aquacomplex compounds, which easily solidify and form crystalline hydrates. However, since there is often a need to conduct drying gas from other pressure than atmospheric pressure, there is a need to carry out the dependence of properties of inorganic salts, which form crystalline hydrates, from the pressure. Results based on the use of four different inorganic adsorbents have shown that the pressure increase accelerates dehydration and generally deepens its extent. It is caused both by van der Waals bonds and a more effective mechanism for the formation of bonds of the donor-acceptor mechanism. Effect of pressure increase on various adsorbents is uneven and is linked to the strength of relationships, which are formed by a cationic mechanism, and is also associated with coordination number of the central atom, its radius, the distance to its electron shells and the position in the periodic table. The results make it possible to develop an adsorbent for effective drying gas to replace traditional gas drier, such as phosphorus (V) oxide, and sulfate (sulfuric) acid.

Reaction mechanism of ethylene glycol decomposition on Pt model catalysts: A density functional theory study

Understanding and controlling bond beak sequence is important in catalytic processes. The DFT-GGA method combined with slab model was performed to study the ethylene glycol decomposition on various Pt model catalysts such as close-packed Pt(111), stepped Pt(211) and a more open one, Pt(100). Calculation results show that the adsorption energies of ethylene glycol and other decomposition species depend on the coordination number of surface atom, that is, low coordination number correspond to high adsorption energy. Moreover, it was found that final products of ethylene glycol decomposition are CO and H2 on all model catalysts, but the reaction mechanism varies: On Pt(111), the first step is OH bond scission, followed by CH bond cleavage, namely C2H6O2→HOCH2CH2O+H→HOCH2CHO+2H→HOCH2CO+3H→OCH2CO+4H→OCHCO+5H→CO+HCO+5H→2CO+6H→2CO+3H2; On Pt(211) and Pt(100), however, it is a second OH bond cleavage that follows the initial OH bond scission, that is, C2H6O2→HOCH2CH2O+H→OCH2CH2O+2H→OCHCH2O+3H→OCHCHO+4H→2HCO+4H→2CO+6H→2CO+3H2 on Pt(211), and C2H6O2→HOCH2CH2O+H→OCH2CH2O+2H→OCHCH2O+3H→OCCH2O+4H→CO+H2CO+4H→CO+HCO+5H→2CO+6H→2CO+3H2 on Pt(100) For the catalytic order of ethylene glycol to form H2, it may be determined based on the rate-controlling step, and it is Pt(111)>Pt(211)>Pt(100).

A comparative study on local atomic configurations characterized by cluster-type-index method and Voronoi polyhedron method

To assess strengths and weaknesses of cluster-type-index method (CTIM) and Voronoi polyhedron method (VPM) in the characterization of local structures, the similarity and difference between CTIM clusters and Voronoi polyhedrons (VPs) in under-cooled liquids and rapidly solidified solids of silvers are analyzed from the configurational view of point. By tracking identification numbers of atoms, it is found that one kind of VPs usually corresponds to several kinds of CTIM clusters with same or higher coordination number of central atoms, and the local structures of fcc lattices and hcp lattices can hardly be distinguished from each other merely based on their Voronoi polyhedron indexes 〈0, 12, 0, 0〉. In CTIM, the fcc and hcp basic clusters can be characterized by (12, 12/1421) and (12, 6/1421, 6/1422), respectively, but their total are less than the population of 〈0, 12, 0, 0〉 VPs in the same simulated system. A careful analysis of VPs with and without refinement reveals that the diminishment of shell atoms associated with tiny Voronoi polygons should be responsible for low coordination numbers of central atoms in VPs relative to their counterparts of CTIM clusters. The CTIM based on Honeycutt-Andersen (H-A) pair analysis can identify more kinds of atomic clusters, but its multi-indexes nature makes the feature extraction from various local atomic configurations more difficult.

Finite-size effect on the dynamic and sensing performances of graphene resonators: the role of edge stress

We have studied the finite-size effect on the dynamic behavior of graphene resonators and their applications in atomic mass detection using a continuum elastic model such as modified plate theory. In particular, we developed a model based on von Karman plate theory with including the edge stress, which arises from the imbalance between the coordination numbers of bulk atoms and edge atoms of graphene. It is shown that as the size of a graphene resonator decreases, the edge stress depending on the edge structure of a graphene resonator plays a critical role on both its dynamic and sensing performances. We found that the resonance behavior of graphene can be tuned not only through edge stress but also through nonlinear vibration, and that the detection sensitivity of a graphene resonator can be controlled by using the edge stress. Our study sheds light on the important role of the finite-size effect in the effective design of graphene resonators for their mass sensing applications.

Systematic Study of Mutually Inclusive Influences of Temperature and Substitution on the Coordination Geometry of Co(II) in a Series of Coordination Polymers and Their Properties

In this contribution we have extended our current research goal of designing functional metal–organic frameworks (MOFs) using bispyrazole type ligands. Accordingly, ten new cobalt-based MOFs have been synthesized using a simple bispyrazole ligand, 4,4′-methylene-bispyrazole (H2MBP), and isophthalic acid (H2IPA) and its four 5-substituted derivatives R-H2IPA (R = COOH, OH, tBu, NH2). The major aim of this study was to validate the mutual influence of temperature and substitutions on the final structural self-assembly. Five different isophthalic acid derivatives were used to study the influence of substituents while each reaction was carried out at two different temperatures to assess the temperature effect. A clear correlation was observed between the reaction temperature and the coordination number of the cobalt atoms which consequently changes the self-assembly pattern. We have also shown that the periodical change in coordination number did bring about some systematic changes in the structural network v...

Surface Structure of Hydroxyapatite from Simulated Annealing Molecular Dynamics Simulations.

The surface structure of hydroxyapatite (HAP) is crucial for its bioactivity. Using a molecular dynamics simulated annealing method, we studied the structure and its variation with annealing temperature of the HAP (100) surface. In contrast to the commonly used HAP surface model, which is sliced from HAP crystal and then relaxed at 0 K with first-principles or force-field calculations, a new surface structure with gradual changes from ordered inside to disordered on the surface was revealed. The disordering is dependent on the annealing temperature, Tmax. When Tmax increases up to the melting point, which was usually adopted in experiments, the disordering increases, as reflected by its radial distribution functions, structural factors, and atomic coordination numbers. The disordering of annealed structures does not show significant changes when Tmax is above the melting point. The thickness of disordered layers is about 10 Å. The surface energy of the annealed structures at high temperature is significantly less than that of the crystal structure relaxed at room temperature. A three-layer model of interior, middle, and surface was then proposed to describe the surface structure of HAP. The interior layer retains the atomic configurations in crystal. The middle layer has its atoms moved and its groups rotated about their original locations. In the surface layer, the atomic arrangements are totally different from those in crystal. In particular for the hydroxyl groups, they move outward and cover the Ca(2+) ions, leaving holes occupied by the phosphate groups. Our study suggested a new model with disordered surface structures for studying the interaction of HAP-based biomaterials with other molecules.

Formation of Mixed Bond‐Angle Linkages in Zinc Boromolybdate Glasses

The short and medium range structure of glassy MoO3–ZnO–B2O3 has been studied by neutron diffraction and reverse Monte Carlo simulation. The partial atomic pair correlation functions and coordination numbers are presented that are not yet reported for this system. We have established that the first neighbor distances do not depend on concentration within limit of error, the actual values are rB‐O = 1.38 Å, rMo‐O = 1.72 Å, and rZn‐O = 1.97 Å. It is found that ZnO takes part in the glassy structure as network former, as ZnO4 tetrahedral are linked both to MoO4 and to BO3 and BO4 groups. It is revealed that BO4/BO3 increases with increasing B2O3 content. We have found that only small amount of boroxol ring is present, BO3 and BO4 groups are organized into superstructure units, and a small part is in isolated BO3 triangles. The BO3 and BO4 units are linked to MoO4 or ZnO4 forming mixed [4]Mo‐O‐[3]B, [4]Mo‐O‐[4]B, [4]Mo‐O‐[4]Zn, [3]B‐O‐[4]Zn, [4]B‐O‐[4]Zn bond linkages.

Polymeric zinc complexes with 2,2′-dipyridylamine and different benzenepolycarboxylato ligands: Synthesis, structure, characterization and antimicrobial activity

A series of new zinc complexes containing the 2,2′-dipyridylamine (dipya) ligand and anions of four benzenepolycarboxylic (BPC) acids, namely phthalic (H2pht), isophthalic (H2ipht), terephthalic (H2tpht) and pyromellitic (H4pyr), have been synthesized by ligand exchange reactions. The complexes were characterized based on elemental analysis, FTIR spectroscopy and thermal (TG/DSC) analysis. The complexes were found to have the formulae [Zn(dipya)(pht)] (1), [Zn(dipya)(ipht)]n (2), {[Zn(dipya)(tpht)]·H2O}n (3) and [Zn2(dipya)2(pyr)] (4). Compounds 2 and 3 have been obtained as single crystals and their crystal structures were determined from X-ray diffraction data. In both structures the coordination number of the Zn atoms is five and they are linked by bridging BPC ligands. In 2, the ipht ligand is coordinated in a tridentate manner via chelate and monodentate COO groups, whereas two crystallographically different tpht ligands in 3 are coordinated as bis-chelate and bis-monodentate ligands, respectively. These combined modes of ipht and tpht anions resulted in zigzag chains of 2 and 3. Two-dimensional pseudo-layers in 2 and a three-dimensional network in 3 are governed by hydrogen bonds and C–H⋯O interactions which are formed between the zigzag chains, and by additional C–H⋯π interactions in 3. The antimicrobial activity of complexes 1–4 was screened in vitro against some Gram-positive bacteria (Bacillus subtilis, Enterococcus faecalis, Listeria monocytogenes and Staphylococcus aureus), some Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa and Salmonella enteritidis) and yeast Candida albicans. Complex 2 showed the most potent inhibitory effect against the tested microorganisms.

Evidence for faster etching at the mask-substrate interface: atomistic simulation of complex cavities at the micron-/submicron-scale by the continuous cellular automaton

We combine experiments and simulations to study the acceleration of anisotropic etching of crystalline silicon at the mask-substrate interface, as a function of the coordination number of the substrate atoms located at the junction between obtuse-angled {1 1 1} facets and the mask layer. Atomistic simulations based on the use of the continuous cellular automaton (CCA) conclude that the interface atoms react faster with the etchant, thus initiating a step flow process that results in increased etch rates for the obtuse facets. By generating a wide range of complex cavities on high-index silicon wafers with a single-side, single-step etching, the comparison of the experimental and simulated results strongly indicates that the CCA method is suitable for accurately describing not only the development of micron-scaled structures but also, for the first time, the formation of submicron shapes. The study also describes the acceleration of obtuse facets formed through double-side etching, obtaining results in good agreement with previous experiments.

High pressure structural, electronic, and optical properties of polymorphic InVO4 phases

In the present work, we report a detailed density functional theory calculation on polymorphic InVO4 phases by means of projector augmented wave method. The computed first-order structural phase transformation from orthorhombic (Cmcm) to monoclinic (P2/c) structure is found to occur around 5.6 GPa along with a large volume collapse of 16.6%, which is consistent with previously reported experimental data. This transformation also leads to an increase in the coordination number of vanadium atom from 4 to 6. The computed equilibrium and high pressure structural properties of both InVO4 phases, including unit cell parameters, equation of state, and bulk moduli, are in good agreement with the available experimental data. In addition, compressibility is found to be highly anisotropic and the b-axis being more compressible than the other for both the structures. Electronic band structures for both the phases were calculated, and the band gaps for orthorhombic and monoclinic InVO4 are found to be 4.02 and 1.67 eV, respectively, within the Tran-Blaha Modified Becke-Johnson potential as implemented in linearized augmented planewave method. We further examined the optical properties such as dielectric function, refractive index, and absorption spectra for both the structures. From the implications of these results, it can be proposed that the high pressure InVO4 phase can be more useful than orthorhombic phase for photo catalytic applications.

Evolution of the germanium–oxygen coordination number in lithium–lead–germanate glasses

Lithium–lead–germanate glasses in the xLi2O·(100-x)[7GeO2·3PbO] system, where 0≤x≤40mol% Li2CO3 exhibit a “germanate anomaly”, which is a maximum in their density profiles with the addition of Li2CO3 up to 20mol%. The structural characterization of the samples was performed by investigations of Raman spectroscopy and X-ray scattering analysis.An EXAFS analysis of the spectra collected at the germanium K-edge for series of lithium–lead–germanate glasses is also presented. With the EXAFS-extracted structural parameters were reconstructed to the local neighborhood of Ge atoms and were verified current opinions on the germanate anomaly in the considered glasses. The formation of higher-coordinated Ge species in the glassy network can be correlated with the density anomaly.Several structural mechanisms can be summarized by increasing of lithium carbonate in the lead–germanate glassy: i) depolymerization of germanate network; ii) conversion of 3- to 4-membered [GeO4] rings; iii) transformation of connected [GeO6] structural units into isolated [GeO6] structural units and a conversion part of higher to lower coordination number of germanium atoms.

Structure of Glassy Ag–Ge–Se by Neutron Diffraction with Isotope Substitution

Abstract The structure of glassy Ag0.077Ge0.212Se0.711, which lies at y = 0.077 on the Ag y (Ge0.23Se0.77)1−y tie-line, was investigated by using the method of neutron diffraction with silver isotope substitution. Two glass transition temperatures were found from a characterisation of the material using modulated differential scanning calorimetry, which indicates a mixed phase material. The diffraction method provides site-specific information on the Ag coordination environment, and gives an average of 3.5(1) Ag–Se nearest-neighbours with a bond distance of 2.65(1) Å together with 0.9(1) Ag–Ag next nearest-neighbours at a distance of 2.9(2) Å. The incorporation of silver does not appear to have a marked effect on the coordination number of Se to other matrix (Ge or Se) atoms, which supports the notion that Ag forms dative bonds with Se lone-pair electrons. A model is given for predicting the change in the Se to matrix atom coordination number when a monovalent metal such as Ag is added to a Se rich Ge–Se base glass.

Bonding nature of the amorphous structure studied by a combination of cutoff and electronic localization function

The analysis of the local structure of covalent glass is one of the major challenges for analyzing the amorphous structure. Usually, people use a cutoff distance to determine the coordinated atoms and relevant structural information, such as coordination number and bond angles. Recently, the electron localization function (ELF) has been used to analyze the local structure of amorphous Ge2Sb2Te5. But how to determine the EFL threshold and cutoff distance has not been reported. Here, according to the ab-initio calculations, we systematically investigate the relationship between the bond number and the ELF threshold, and also the cutoff distance in amorphous GeTe. The reasonable value of the ELF threshold and the cutoff distance are determined according to the inflection point and slope change of the bond number with ELF value respectively. Furthermore, the minimal ELF value distributions of Ge-Ge, Ge-Te and Te-Te bonds are presented. The comparison shows that the majority of removed bonds in structural analysis are weak Ge-Te bonds due to the low localization degree of electron. In contrast, the stronger Ge-Ge bonds are almost unchanged when changing the ELF threshold value from 0.58 to 0.63 because of the high localization degree of electron. The average minimal ELF value of Ge-Te bonds in crystalline GeTe is calculated, and it is close to the ELF threshold that is determined by the inflection point. t is easy to find that the Ge-Te bonds which are removed by increasing the ELF threshold are relatively weak. Therefore, these weaker bonds should be removed in structure analysis, which also means that the ELF threshold determined by the inflection point are reasonable value. Finally, based on the EFL threshold value, the coordination number and bond angle distribution of Ge in amorphous GeTe are obtained. The analysis of the coordination number of the Ge atoms shows that as the ELF threshold increases from 0.58 to 0.63, the 5- fold Ge atoms almost disappear because they are against the (8-N) rule. Furthermore, when the ELF threshold value is 0.58, the bond angle distribution analysis of Ge atoms shows that the local structure is a configuration that is mainly defectively octahedral (3-fold Ge) and distorted tetrahedral (4-fold Ge), but it remains unchanged when the threshold value increases to 0.63. It further demonstrates that all the removed chemical bonds are weaker ones as the ELF threshold increases. This approach is useful to improve the accuracy of amorphous structure analysis by obtaining the more reasonable inter-atomic bonding information. And it should be applied to the structural analyses of other systems generally.

Nanoparticle size evaluation of catalysts by EXAFS: Advantages and limitations

In this article we determine particle size of nanocatalysts using the first-shell fitting results of Extended X-ray Absorption Fine Structure (EXAFS) measurements. The EXAFS technique measures the average coordination number of nanoparticles in the path of X-ray beam. Since nanoparticles can be found in variety of cluster structures with varying coordination number of surface atoms, the discussion is limited to the structures of face centered cubic (fcc) lattice in which most metals of interest for catalysis crystalize. Two nanoparticle structures, namely cuboctahedron and icosahedron, were analyzed and their calculated average coordination numbers compared to those determined by EXAFS. It was found that the particle size determined using EXAFS corresponds best to the diameter of the sphere that has the same volume as the nanoparticle. This volume-corrected sphere was calculated for a number of platinum group metals. It is further shown that the model for particle size evaluation can be extended to bimetallic and trimetallic nanoparticles. Advantages and limitations of the technique in assessing the particle size are discussed.

Beyond the staple motif: a new order at the thiolate-gold interface.

Staple motifs in the form of -RS(AuSR)x- (x = 1, 2, 3, etc.) are the most common structural feature at the interface of the thiolate-protected gold nanoclusters, Aun(SR)m. However, the recently solved structure of Au92(SR)44, in which the facets of the Au84 core are protected mainly by the bridging thiolates, challenges the staple hypothesis. Herein, we explore the surface sensitivity of the thiolate-gold interface from first principles density functional theory. We find that the interfacial structures of thiolates on gold are surface sensitive: while a staple motif (such as -RS-Au-SR-) is preferred on Au(111), a bridging motif (-RS-) is preferred on Au(100) and Au(110). We show that this surface sensitivity is closely related to the coordination number of the surface Au atom on the different surfaces. We further confirm the preference of the bridging motif for self-assembled monolayers of two different ligands (methylthiolate and 4-tert-butylbenzenethiolate) on Au(100). With this surface sensitivity, we categorize the structure-known Aun(SR)m clusters into three groups: (1) no bridging; (2) ambiguous bridging; (3) distinct bridging. We further employ the surface sensitivity of the thiolate-Au interface to predict the protecting motifs of face-centered cubic (fcc) gold nanoparticles of different shapes. Our study provides a unifying view of the Aun(SR)m structures with guidelines for structure predictions for larger Aun(SR)m clusters of a fcc core.

Structural optimization of Pt–Pd–Rh trimetallic nanoparticles using improved genetic algorithm

Metallic nanoparticles have received considerable attention due to their superior catalytic properties. In this study, we proposed an improved genetic algorithm to optimize atomic structures of Pt–Pd–Rh trimetallic nanoparticles with various sizes and compositions. In the improved genetic algorithm, a layered coordinate ranking method and an effective fitness function were introduced to enhance its searching capability. The optimized results show that Pt and Pd atoms prefer to segregate on the surface, while Rh atoms tend to aggregate inside. Meanwhile, Pd atoms exhibit stronger surface segregation than Pt ones. Furthermore, the distribution of atomic coordination number was investigated.