Interior Atoms Research Articles

Equilibrium configuration and continuum elastic properties of finite sized graphene

This paper presents a continuum mechanics approach to modelling the elastic deformationof finite graphene sheets based on Brenner’s potential. The potential energy of thegraphene sheet is minimized for determining the equilibrium configuration. The four edgesof the initially rectangular graphene sheet become curved at the equilibrium configuration.The curving of the sides is attributed to smaller coordination number for the atoms at theedges compared to that of the interior atoms. Considering two graphene models, with onlytwo or all four edges constrained to be straight, the continuum Young’s moduli of grapheneare computed applying the Cauchy–Born rule. The computed elastic constants of thegraphene sheet are found to conform to orthotropic material behaviour. The computedconstants differ considerably depending on whether a minimized or unminimizedconfiguration is used for computation.

Surface and Size Effects on the Specific Heat Capacity of Nanoparticles

Extending the elastic continuum model for fine particles, a theoretical model was proposed to include the different contributions of interior and surface atoms for the specific heat capacity. The effect of size and temperature and the softening of surface atom vibrations were studied, and a dimensionless variable was proposed to characterize the effect of particle size and temperature on the specific heat capacity of nanoparticles. The proposed model was used to fit experimental data for copper oxide nanoparticles.

Evolution of the Properties of AlnNnClusters with Size

A global optimization of stoichiometric (AlN)(n) clusters (n = 1-25, 30, 35, ..., 95, 100) has been performed using the basin-hopping (BH) method and describing the interactions with simple and yet realistic interatomic potentials. The results for the smaller isomers agree with those of previous electronic structure calculations, thus validating the present scheme. The lowest-energy isomers found can be classified in three different categories according to their structural motifs: (i) small clusters (n = 2-5), with planar ring structures and 2-fold coordination, (ii) medium clusters (n = 6-40), where a competition between stacked rings and globular-like empty cages exists, and (iii) large clusters (n > 40), large enough to mix different elements of the previous stage. All the atoms in small and medium-sized clusters are in the surface, while large clusters start to display interior atoms. Large clusters display a competition between tetrahedral and octahedral-like features: the former lead to a lower energy interior in the cluster, while the latter allow for surface terminations with a lower energy. All of the properties studied present different regimes according to the above classification. It is of particular interest that the local properties of the interior atoms do converge to the bulk limit. The isomers with n = 6 and 12 are specially stable with respect to the gain or loss of AlN molecules.

A finite-temperature dynamic coupled atomistic/discrete dislocation method

A method for simultaneously thermostatting an atomistic region and absorbing energetic pulses impinging on the atomistic/continuum interface from the atomistic region is developed to operate within the framework of the coupled atomistic/discrete dislocation method. The approach inserts an additional Langevin damping term and a random force term into the equations of motion for atoms in a ‘stadium’ boundary region near the atom/continuum interface, with the damping coefficient ramped linearly over the width of the region, as suggested by Holian and Ravelo. The remaining interior atom dynamics are computed using a standard MD algorithm with no artificial damping or thermostatting. The continuum region deformations are computed using static FEM updated stochastically over time scales comparable to the Debye frequency of the atoms using time-averaged displacements at the atom/continuum interface, thereby providing an evolution of the continuum region that tracks the atomistic deformation. The method is evaluated by studying the ability of the coupled system: (i) to equilibrate the inner atomistic region at a desired temperature under conditions of no external or internal loading, (ii) to produce the proper canonical thermal fluctuations and (iii) to absorb deformation pulses initiated in the interior region and incident upon the atomistic/continuum boundary. With an optimal maximum damping coefficient of approximately 1/2 of the Debye frequency, temperature stability is attained at values very close to the target temperature. The temperature variance agrees well with the canonical expectation for various temperatures. For the same damping parameters and at low temperature, high-energy deformation pulses propagate unimpeded up to the stadium boundary region and then are completely damped out upon approach to the atomistic/continuum interface with no measurable reflections. At higher temperatures, thermal fluctuations in the total energy make analyses difficult, but damping of high-energy deformation pulses is achieved within the limits of the thermal noise in the system while observation of the time-dependent displacements shows no observable reflections.

Stability of medium-sized neutral and charged silicon clusters

Using the full-potential linear-muffin-tin-orbital molecular-dynamics method based on the single-parent evolution algorithm, we have studied the stability for the medium-sized neutral, anionic, and cationic silicon clusters in detail. We have found the ground state structures of ${\mathrm{Si}}_{n}$ $(n=26--30)$. Our calculated results suggest that the compact structures containing interior atoms begin to compete for the ground state structures with the stacked prolate structures from $n=24$. The prolate structures transit into the spherical compact structures at $n=27$ for neutral silicon clusters, whereas the transition size occurs at $n=28$ for anionic and cationic silicon clusters. Starting from $n=29$, the stable structures with larger binding energies are basically the compact spherical structures. The results are in excellent agreement with the related experiments.

Finite size effect on critical transition temperature of superconductive nanosolids

A simple and unified model is developed for finite size effect on the critical transition temperature of superconductive nanosolids, which is based on the size-dependent Debye temperature of crystals within the McMillan expression. In the model, two material and structure dependent parameters of D 0 and α are used, which, respectively, are the critical size at which all atoms of a low-dimensional material are located on its surface, and the ratio of the mean square vibrational amplitude between surface atoms and interior atoms, In light of this model, the critical transition temperatures of superconductive nanosolids can decrease or increase with the dropping size of nanosolids depending on the bond strength changes of interfacial atoms. The predicated results are consistent with the available experimental results for superconductors MgB 2 and Nb thin films, Bi and Pb granular thin films and nanoparticles, Al thin films and nanoparticles.

Simultaneous determination of protein structure and dynamics

We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy--for obtaining experimental information at the atomic level about the structural and dynamical features of proteins--with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant advances in our ability to understand and utilize the structures of native proteins.

Formation of an icosahedral structure during the freezing of gold nanoclusters: surface-induced mechanism.

The freezing behavior of gold nanoclusters was studied by employing molecular dynamics simulations based on the semiempirical embedded-atom method. Investigations of the gold nanoclusters revealed that, just after freezing, ordered nanosurfaces with a fivefold symmetry were formed with interior atoms remaining in the disordered state. Further lowering of temperatures induced nanocrystallization of the interior atoms that proceeded from the surface towards the core region, finally leading to an icosahedral structure. These dynamic processes explain why the icosahedral cluster structure is dominantly formed in spite of its energetic metastability.

Melting behavior in ultrathin metallic nanowires

The thermal stability of helical multiwalled cylindrical gold nanowires is studied using molecular-dynamics simulations. From our simulation, the melting temperature of gold nanowires is lower than the bulk value, but higher than that of gold nanoclusters. It is interesting to find that the interior melting temperature in ultrathin nanowires is lower than that of the surface melting. The melting starts from the interior atoms, while the surface melting occurs at relatively higher temperature. This unique thermodynamic behavior is closely related to the interior structures. We propose that the surface melting represents the overall melting in ultrathin metallic nanowires.

Synthesis, structure, and bonding of Sc(6)MTe(2) (M = Ag, Cu, Cd): heterometal-induced polymerization of metal chains in Sc(2)Te.

Three new compounds, Sc(6)AgTe(2), Sc(6)Cu(0.80(2))Te(2.20(2)), and Sc(6)CdTe(2), were prepared by high-temperature solid state techniques, and the structures were determined by single-crystal X-ray diffraction to be orthorhombic, Pnma (No. 62, Z = 4) with a = 20.094(9) A, 19.853(5) A, 20.08(1) A, b = 3.913(1) A, 3.914(1) A, 3.915(2) A, and c = 10.688(2) A, 10.644(2) A, 10.679(5) A, respectively, at 23 degrees C. The compounds are isotypic with Sc(6)PdTe(2) and represent the first ternary metal-rich rare-earth-metal chalcogenides containing group 11 or group 12 elements. The structure can be viewed as heterometal sheets lying parallel to the b-c planes that are separated by isolated tellurium atoms. These sheets can also be viewed as a polymerization of two different types of metal chains in Sc(2)Te (blades and zigzag chains) by heterometal (M) replacements of some intervening tellurium atoms. Extended Hückel band calculations reveal that the interior atoms in the metal network achieve negative formal Mulliken charges while Sc atoms on the exterior that have tellurium neighbors have positive values. The heterometal-metal bonding enhances the overlap populations of zigzag chains and blades relative to those in Sc(2)Te. The calculation results also indicate that these compounds are metallic, as usual.

First-known high-nuclearity silver–nickel carbonyl cluster: nanosized [Ag16Ni24(CO)40]4– possessing a new 40-atom cubic Td closed-packed metal-core geometryDedicated by L. F. D. to Professor Dr. Wolfgang Beck, a close friend, for his many remarkable accomplishments in Transition-Metal Inorganic/Organometallic Chemistry during his highly distinguished professional career at the Institute für Anorganische Chemie der Ludwig-Maximilians-Universität, München.

The redox reaction of silver acetate with [Ni6(CO)12]2− (2) in acetonitrile has afforded in low yields (≤10%) a close-packed silver–nickel carbonyl cluster: namely, the pseudo-Td [Ag16Ni24(CO)40]4− tetraanion (1) as the [PPh3Me]+ salt. This well-defined, dark brown bimetallic cluster, which is air-unstable and light-sensitive, is the first example of a microscopic ccp chunk of quasi-silver metal that is stabilized by close-packed carbonyl-ligated transition-metal layers. The overall 40-atom metal-core geometry, which corresponds to a heretofore unknown 36-atom Td polyhedron encapsulating four interior atoms, may be described as a central ccp Ag16 kernel that is connected by direct Ag–Ni bonding with four tetrahedrally disposed equilateral triangular Ni6(CO)10 fragments. The particular close-packed condensation mode of each ν2 Ni6 triangular layer to one of the four tetrahedrally oriented Ag-centered hexagonal Ag7 layers of the Ag16 kernel results in each of the four tetrahedrally-connected interior Ag atoms in the Ag16Ni24 core having a localized hcp environment. Of the 10 carbonyl groups per ν2 Ni6 equilateral triangle, three are each terminally coordinated to a corner Ni atom, six are each edge-connected to one of the two pairs of linked Ni atoms along the three Ni3 edges, and the remaining one caps the inner triangle of the Ni6 triangle. Both its structure and composition were unambiguously established via a single-crystal X-ray diffraction analysis with a SMART CCD area detector diffractometry system. The maximum metal-core diameter in 1 is ca. 0.98 nm (av.) along each of the four three-fold axes.

A novel approach for identifying the surface atoms of macromolecules

A significant number of atoms lie buried beneath the “molecular surface” of proteins and other biologic macromolecules. Interactions between ligands and these macromolecules are dominated by interactions with the “surface atoms”. Although interactions with the “buried” or interior atoms of the macromolecule certainly contribute to the total intermolecular interaction energy, many computer-assisted drug design (CADD) strategies can benefit from the identification of those atoms “on the surface” of proteins and other macromolecules. We have developed a simple, yet novel method to distinguish the surface atoms of macromolecules from the interior atoms which is based on computing the atomic contributions to the solvent-accessible surface (SAS) area. This report describes that method and demonstrates that it compares very favorably with four alternative methods.

Spin-polarization of V/Mo(1 0 2 n−1) stepped structures

The magnetism of V/Mo(1 0 2 n−1) stepped surfaces with n=1−6 is investigated using the self-consistent tight-binding method in the unrestricted Hartree–Fock approximation with Hubbard Hamiltonian. These structures exhibit local magnetic moments with the least values on the kink atoms. The local moments of the edge atoms are affected by those of the kink atoms and cause a reduction in their values as compared with the moments of the interior atoms. The local moment of the kink atom is frustrated due to the ferromagnetic coupling with their nearest neighbors. The average magnetization increases as the step length increases.

The Importance of Solute−Solvent van der Waals Interactions with Interior Atoms of Biopolymers

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTThe Importance of Solute−Solvent van der Waals Interactions with Interior Atoms of BiopolymersJed W. Pitera and Wilfred F. van GunsterenView Author Information Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich, Switzerland Cite this: J. Am. Chem. Soc. 2001, 123, 13, 3163–3164Publication Date (Web):March 9, 2001Publication History Received1 November 2000Revised16 January 2001Published online9 March 2001Published inissue 1 April 2001https://doi.org/10.1021/ja0057474Copyright © 2001 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views453Altmetric-Citations48LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (32 KB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Chemical calculations,Free energy,Hollow structures,Solution chemistry,Solvation Get e-Alerts

Theoretical and spectroscopic studies of gap-states at ultrathin silicon oxide/silicon interfaces

The energy distribution of interface states in the Si forbidden gap at ultrathin thermal oxide/Si(111) interfaces is obtained from x-ray photoelectron spectroscopy measurements under bias. All the observed interface state spectra have peaked structure, indicating that they are due to Si dangling bonds. For thermal oxide layers formed at 350 °C, only one interface state peak is present near the midgap. The interface state peak has ∼0.1 eV width, showing that the effective correlation energy of the Si dangling bond interface state is less than ∼0.1 eV. For oxide layers produced above 550 °C, on the other hand, two peaks are observed, one above and the other below the midgap. It is found using a density functional theory method by employing clusters containing 27 bulk-like Si atoms (interior atoms, without H passivation) that an isolated Si dangling bond, with which no atoms in the oxide layer interact, has an energy level near the midgap. It is also found from the calculations that weak interaction of the Si dangling bond with a Si atom having an unpaired electron lowers the Si dangling bond energy below the midgap, while the interaction with an oxygen or Si atom having lone-pair electrons elevates it above the midgap. When the oxide layers are formed at low temperatures, the atomic density of the oxide layer is low, leading to a long distance between a Si dangling bond and the atom in the oxide layer, thus resulting in the isolated Si dangling bond interface state near the midgap. The higher the formation temperature of the oxide layer, the higher the atomic density, resulting in a shorter distance between a Si dangling bond and the interacting atom in the oxide layer. The interface state peaks are shifted from the midgap due to the weak interaction.

Evolution of the electronic structure and properties of neutral and charged aluminum clusters: A comprehensive analysis

Density-functional theory with generalized gradient approximation for the exchange-correlation potential has been used to calculate the global equilibrium geometries and electronic structure of neutral, cationic, and anionic aluminum clusters containing up to 15 atoms. The total energies of these clusters are then used to study the evolution of their binding energy, relative stability, fragmentation channels, ionization potential, and vertical and adiabatic electron affinities as a function of size. The geometries are found to undergo a structural change from two dimensional to three dimensional when the cluster contains 6 atoms. An interior atom emerges only when clusters contain 11 or more atoms. The geometrical changes are accompanied by corresponding changes in the coordination number and the electronic structure. The latter is reflected in the relative concentration of the s and p electrons of the highest occupied molecular orbital. Aluminum behaves as a monovalent atom in clusters containing less than seven atoms and as a trivalent atom in clusters containing seven or more atoms. The binding energy evolves monotonically with size, but Al7, Al7+, Al7−, Al11−, and Al13− exhibit greater stability than their neighbors. Although the neutral clusters do not conform to the jellium model, the enhanced stability of these charged clusters is demonstrated to be due to the electronic shell closure. The fragmentation proceeds preferably by the ejection of a single atom irrespective of the charge state of the parent clusters. While odd-atom clusters carry a magnetic moment of 1μB as expected, clusters containing even number of atoms carry 2μB for n⩽10 and 0 μB for n>10. The calculated results agree very well with all available experimental data on magnetic properties, ionization potentials, electron affinities, and fragmentation channels. The existence of isomers of Al13 cluster provides a unique perspective on the anomaly in the intensity distribution of the mass spectra. The unusual stability of Al7 in neutral, cationic, and anionic form compared to its neighboring clusters is argued to be due to its likely existence in a mixed-valence state.

Effects of the Electronic Structure on the Stability of Metallic Superlattices. Semi-Emipirical Calculations of the Total Energy

AbstractIn this work the total energy of metallic superlattices is evaluated at semi-empirical level. The superlattice has an heterogenous composition and it has two shapes, i.e.(i) two facingA/B wires and (ii) a hut-shaped island of the element A deposited on a rigid B substrate. The elements A and B are Ag, Cu, Pd, Pt and Fe. The calculations show the existence of competing bonding contributions. In fact, a strong bond arises from charge exchanges at the A/B interface and from the bulk-like bonds of interior atoms. On the contrary, surface atoms are undercoordinated and reduce the strength of bonding. These contributions act on opposite sense on the large structures and the geometry dependence of the binding energy suggests a self-limited growth, rather than Ostwald ripening.

The reactivity of copper clusters supported on carbon studied by XPS

Abstract The electronic structure and reactivity of metal clusters at solid surfaces is the subject of much interest, not least because of their importance in modelling industrial heterogeneous catalysts. In this article we investigate the reactivity of copper clusters deposited on a carbon substrate. In contrast with oxygen chemisorption at bulk copper surfaces at 298 K, two oxygen species are observed after exposure to dioxygen, reflecting the unusual properties of copper clusters supported on carbon. One of the oxygen species is atomic and adsorbed on the copper metal, whereas the second species is molecular and associated with the carbon substrate. The latter species is formed via spillover from the metal and can only be formed on the carbon surface in the absence of copper under much more extreme conditions of pressure and temperature. There are marked differences in the behaviour of the two oxygen states: the atomic species is unstable on heating to 540 K and is reactive towards ammonia at 298 K, being desorbed as water via an oxydehydrogenation reaction, whereas the molecular species is unaffected in both cases. The coverage of adsorbed imide, NH(a), formed from the oxydehydrogenation of ammonia is strongly dependent on reaction conditions, dynamic coadsorption from dioxygen ammonia mixtures leading to much higher surface concentrations than observed during the sequential adsorption of oxygen followed by ammonia. In the former case, the instantaneous concentration of adsorbed oxygen atoms remains low throughout much of the reaction due to their continuous removal by reaction with ammonia molecules. Preventing the development of oxygen islands, the interior atoms of which are relatively unreactive, is the key to maintaining a high reactivity.

A model for exploring particle size and temperature dependence of excess heat capacities of nanocrystalline substances

Einstein and Debye vibration modes are considered to be different in surface atoms and in interior atoms of fine solid particles. A model is constructed to predict particle size and temperature dependence of excess heat capacities of nanocrystalline substances. It is shown that excess heat capacity is not proportional to specific surface area. However, when specific surface area is far less than a characteristic area of a sample, the specific excess heat capacity can be viewed as independent of particle size. Several types of temperature dependence of excess heat capacity are predicted, including monotonous increase with increase in temperature, one-peak and two-peaks excess heat capacity vs. temperature curves. The proposed model has been used to fit experimental data of nanostructured silver and rutile

Properties of Silicon Nanoparticles: A Molecular Dynamics Study

Constant energy molecular dynamics simulations of silicon cluster growth have been conducted for clusters up to 480 atoms using the Stillinger−Weber empirical interatomic potential. It is found that the interior atoms of the 480-atom clusters, at the temperatures used, show bulklike characteristics. The cluster binding energy has been fit to an expression that separates the surface and bulk contributions to the energy over wide temperatures and size ranges. The average surface energy of an atom was found to be independent of cluster size and of a magnitude relative to the bulk, such that all cluster sizes were stable under the conditions studied here (600 < T < 2000 K). The photon density of states is similar to bulk silicon and does not show a strong cluster size dependence. Atomic self-diffusion coefficients have been calculated and compare quite well with experimental data on self-diffusion coefficient measurements of silicon surfaces.