Planar Clusters Research Articles

Simulation of growth process of Pt-particles - first-principles calculations

First-principles calculations have been applied to investigate the interactions between Ptn (n = 1 ~ 4) clusters and a graphene sheet as models of Pt/C fuel-cell catalytic electrodes. A Pt atom is stably adsorbed on the bridge site between two carbon atoms with the adsorption energy of about 2eV. For the case of Pt2, both of the Pt atoms are adsorbed on the bridge site. For the case of Pt3, the triangular cluster is more stable than the linear cluster. For the case of Pt4, the tetrahedral cluster is more stable than the planar cluster. The adsorption energies on the surface without defects are 0.55 eV/adatom for Pt2 and 0.05 eV/adatom for Pt3. The interaction energy between the Pt cluster and the graphite surface per Pt atom becomes weaker as the number of Pt atoms increases. The adsorption energy for a Pt atom on the vacant site is 8.00 eV/adatom, which is stronger than the formation energy of a Pt-Pt bond (about 2 eV/bond) for small clusters.

Transformation of Sign of Nonlinear Refraction between Mo(W)/S/Cu Planar Metal Clusters

Optical nonlinear refractive properties of a series of Mo(W)/S/Cu planar square clusters are investigated using the Z-scan technique with the ns laser pulses at the wavelength of532nm. The result shows that the planar metal clusters containing the halogen ligands demonstrate the self-focusing effect, and the other planar metal clusters demonstrate the self-defocusing effect. These facts indicate that the halogen ligands can act as crucial factors in determining the sign of the nonlinear refraction of the Mo(W)/S/Cu planar metal clusters. The analysis of the experimental data shows that the planar clusters with halogen ligands possess greater refraction volume of the excited state than that of the ground state, while the other planar clusters possess the smaller refraction volume of the excited state than that of the ground state.

Molecular Dynamics Simulation Study of the Influence of Cluster Geometry on Formation of C60 Fullerene Clusters in Aqueous Solution

We have performed atomistic molecular dynamics simulations of linear (1-dimensional), planar (2-dimensional), and icosahedral (3-dimensional) clusters of C60 fullerenes in aqueous solution in order to investigate the influence of cluster geometry on their free energy of formation. As was found in our previous study of the potential of mean force (PMF) as a function of separation for a single pair of fullerenes in aqueous solution, the interaction between fullerenes for all cluster geometries was dominated by direct fullerene-fullerene interactions and not by water-induced hydrophobic interactions. A coarse-grained implicit solvent (CGIS) potential, given by the PMF for the fullerene pair in water obtained from atomistic simulations, was found to describe well the free energy of formation of the linear cluster, indicating that many-body effects, i.e., the influence of neighboring fullerenes on the water-induced interaction between a fullerene pair, are negligible for the 1-dimensional geometry. For the 2-dimensional and particularly the 3-dimensional geometry, however, many-body effects were found to strongly influence hydration, leading to complete dehydration of the central fullerene at close fullerene-fullerene separations for the icosahedral cluster. This strong influence of geometry on hydration translates into water-induced interactions that, while remaining repulsive, as is found for the fullerene pair, are not well described by the two-body CGIS potential obtained from the isolated fullerene pair, particularly for the 3-dimensional geometry.

A potential multipole theory for the hydrodynamics of bubble clouds

The occurrence of bubbles in clouds, or assemblies, is observed in a wide range of fluid flows. In an otherwise quiescent fluid, their free rise due to buoyancy may lead to transient planar clusters and ultimately to non-spherical bubble behaviour. This paper concentrates on the application of multipole methods to study the fluid dynamics of such clouds. Under the assumptions of an irrotational flow, the boundary-value problem for the fluid velocity potential is determined from the requirement that the fluid kinetic energy, in suitable integral form, is stationary with respect to a small variation in the potential. Two alternative formulations for the bubble dynamics are then presented. The first relates the trajectories of each spherical bubble to their driving forces through the Kelvin impulse. The coupled two-phase flow equations are posed in a convenient matrix form, and solved numerically to predict the transient behaviour of the assembly. To model the more general free-surface flow, a second novel approach uses a weighted residual method. Simulations on the rise of small spherical, buoyant, bubbles indicate that compact, transient, clusters are formed in a short length of time. As non-uniformities in the bubble radii strongly influence the interaction, the smaller bubbles tend to streamline around the larger ones, leading to dispersion.

”Developing paradigms of chemical bonding: adaptive natural density partitioning

A method of description of the chemical bonding combining the compactness and intuitive simplicity of Lewis theory with the flexibility and generality of canonical molecular orbital theory is presented, which is called adaptive natural density partitioning. The objects of chemical bonding in this method are n-center 2-electron bonds, where n goes from one (lone-pair) to the maximum number of atoms in the system (completely delocalized bonding). The algorithm is a generalization of the natural bonding orbital analysis and is based on the diagonalization of the blocks of the first-order density matrix in the basis of natural atomic orbitals. The results obtained by the application of the algorithm to the systems with non-classical bonding can be readily interpreted from the point of view of aromaticity/antiaromaticity concepts. The considered examples include Li4 cluster and a family of planar boron clusters observed in molecular beams.

DENSITY FUNCTIONAL THEORY STUDY OF BINDING ENERGIES,7LiNUCLEAR MAGNETIC SHIELDING, AND ELECTRIC FIELD GRADIENT TENSORS ON THE SMALL CLUSTERS OFLinHm(m ≤ n ≤ 4)

The binding energies, geometries,7Li magnetic shielding, and electric field gradient tensors of hydrogenated lithium clusters, LinHm(m ≤ n ≤ 4), were studied via density functional theory approach. We optimized the structures using B3LYP functional and 6-311++G (2d,2p) basis set. The calculated binding energies of lithium hydride clusters indicate that hydrogenation energy of LinHmclusters decreases as the number of hydrogen atoms within the cluster increases. Our calculations also showed that for n = 4 clusters, the three-dimensional structure is more stable than the planar one. The study of the trends in the7Li magnetic shielding isotropy, σiso, and anisotropies, Δσ, values are explained in terms of the interplay between the electronic and geometrical effects. The variations in the7Li nuclear quadrupole coupling constants, χ, and their associated asymmetry parameters, ηQ, for different isomers of the lithium hydride clusters and the influence of hydrogenation on the EFG tensors are also discussed. For n = 4, we obtained a noticeable difference in the χ value from the planar to the three-dimensional structures. The atoms in molecules (AIM) analysis at the Li–H bond critical point reveals remarkably different topographical properties of the charge density and associated Laplacian fields for the planar and three-dimensional lithium hydride clusters.

Dynamics of planar vortex clusters with binaries

AbstractWe study an N ‐vortex problem having J of them forming a cluster, which means the distances between the vortices in the cluster is much smaller by O (ε) than the distances, O (ℓ), to the N – J vortices outside of the cluster. With the strengths of N vortices being of the same order, the velocity and time scales for the motion of the J vortices relative to those of the N – J vortices are O (ε–1) and O (ε2) respectively. We show that this two‐time and two‐length scale problem can be converted to a standard two‐time scale problem and then the leading order solution of the N ‐vortex problem can be uncoupled to two problems, one for the motion of J vortices in the cluster relative to the center of the cluster and one for the motion of the N – J vortex plus the center of the cluster. For N = 3 and J = 2, the 3‐vortex problem is uncoupled to two binary vortices problems in the length scales ℓ and ℓε respectively. When perturbed in the scale ℓ, say by a fourth vortex even of finite strength, the binary problem becomes a 3‐vortex problem, admitting periodic solutions. Since 3‐vortex problems are solvable, the uncoupling enables us to solve 3‐cluster problems having at most three vortices in each cluster. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

The second Ca 2+ -binding domain of the Na + –Ca 2+ exchanger is essential for regulation: Crystal structures and mutational analysis

The Na(+)-Ca(2+) exchanger plays a central role in cardiac contractility by maintaining Ca(2+) homeostasis. Two Ca(2+)-binding domains, CBD1 and CBD2, located in a large intracellular loop, regulate activity of the exchanger. Ca(2+) binding to these regulatory domains activates the transport of Ca(2+) across the plasma membrane. Previously, we solved the structure of CBD1, revealing four Ca(2+) ions arranged in a tight planar cluster. Here, we present structures of CBD2 in the Ca(2+)-bound (1.7-A resolution) and -free (1.4-A resolution) conformations. Like CBD1, CBD2 has a classical Ig fold but coordinates only two Ca(2+) ions in primary and secondary Ca(2+) sites. In the absence of Ca(2+), Lys(585) stabilizes the structure by coordinating two acidic residues (Asp(552) and Glu(648)), one from each of the Ca(2+)-binding sites, and prevents a substantial protein unfolding. We have mutated all of the acidic residues that coordinate the Ca(2+) ions and have examined the effects of these mutations on regulation of exchange activity. Three mutations (E516L, D578V, and E648L) at the primary Ca(2+) site completely remove Ca(2+) regulation, placing the exchanger into a constitutively active state. These are the first data defining the role of CBD2 as a regulatory domain in the Na(+)-Ca(2+) exchanger.

Magnetism of Co overlayers and nanostructures on W(0 0 1): A first-principles study

The magnetic properties of Co nanostructures and a Co monolayer on W(0 0 1) have been studied in the framework of density functional theory. Different geometries such as planar and three-dimensional clusters have been considered, with cluster sizes varying between 2 and 13 atoms. The calculations were performed using the real-space linear muffin-tin orbital method (RS-LMTO-ASA). With respect to the stability of the magnetic state, we predict an antiferromagnetic (AFM) structure for the ground state of the planar Co clusters and a ferromagnetic (FM) state for the three-dimensional clusters. For the three-dimensional clusters, one of the AFM arrangements leads to frustration due to the competing FM and AFM exchange interactions between different atoms in the cluster, and gives rise to a non-collinear state with energy close to that of the FM ground state. The relative role of the Co–Co and Co–W exchange interactions is also investigated.

One-Dimensional Fast Migration of Vacancy Clusters in Metals

The migration of point defects, for example, crystal lattice vacancies and self-interstitial atoms (SIAs), typically occurs through three-dimensional random walk in crystalline solids. However, when vacancies and SIAs agglomerate to form planar clusters, the migration mode may change. We observed nanometer-sized clusters of vacancies exhibiting one-dimensional (1D) fast migration. The 1D migration transported a vacancy cluster containing several hundred vacancies with a mobility higher than that of a single vacancy random walk and a mobility comparable to a single SIA random walk. Moreover, we found that the 1D migration may be a key physical mechanism for self-organization of nanometer-sized sessile vacancy cluster (stacking fault tetrahedron) arrays. Harnessing this 1D migration mode may enable new control of defect microstructures such as effective defect removal and introduction of ordered nanostructures in materials, including semiconductors.

Rotational spectra of large Rydberg Matter clusters K 37, K 61 and K 91 give trends in K–K bond distances relative to electron orbit radius

Rotational spectra of planar clusters of Rydberg Matter (RM) have recently been reported for the first time, for clusters K 19 in excitation levels n B = 4, 5 and 6 [L. Holmlid, Mol. Phys. 105 (2007) 933–939]. From such spectra, the average bond distances in the clusters can be determined, and good agreement with theoretical predictions is found. K 19 is an example of a sixfold symmetric planar RM cluster, while other similar clusters have 37, 61 and 91 atoms. Rotational bands of the heavy clusters K 37, K 61 and K 91 are easily identified since they appear as closely spaced groups of lines on top of electronic, probably spin-flip transitions. The bond lengths for the heavy clusters are in the range 3–10 nm, found with a relative precision of approximately 2 × 10 −3. The cluster K 37 ( n B = 8) is the largest cluster observed with diameter of 58.9 nm and bond length of 9.82 ± 0.02 nm. The dimensional ratio d/r n , i.e. the ratio between the experimental interatomic distance and the theoretical electron orbiting radius, is larger for higher excitation levels, where the classical limit is approached and thus the electronic motion is more strongly confined to the cluster plane. The dimensional ratio is also larger for smaller clusters, which is probably due to larger edge effects giving larger average bond distances. The average value of d/r n is 2.865 ± 0.032, close to the theoretically predicted value 2.9. Intensity alternation for every second rotational line is often observed.

Concerted Diffusion, Clustering, and Magnetic Properties of Mn Dopants on a2×2−T4GaN(0001) Substrate

Based on first-principles calculations within density functional theory, we propose a kinetic pathway for Mn incorporation on reconstructed 2 x 2-T4 GaN(0001), characterized by concerted substitution of a Ga atom by a Mn adatom via a precursor surface site T4. The Mn dopants at low densities are randomly distributed, resulting in intrinsic diluted magnetic semiconductors (DMS). At high Mn densities, planar ferromagnetic clusters oriented in the (0001) plane can be readily formed at relatively low growth temperatures, but ferrimagnetic zigzag columns along the growth orientation will be formed at high temperatures. Furthermore, intrinsic DMS are more likely to be formed via codeposition of Mn+Ga+N at high growth rates. These findings help to explain the observed variations in both the magnetic ordering temperature TC and the magnetic nature of Ga1-xMnxN.

Decomposition of deformation density into orbital components

AbstractIn this research, deformation density matrix has been introduced as matrix representation of the density difference between the complex and fragments. The deformation density matrix is then diagonalized to obtain the magnitude of displaced charges as eigenvalues. Correspondingly, the eigenvectors reveal the spaces responsible for reorganization of the electrons because of the complex formation. The formalism has been applied on some CO2planar clusters, and the results showed that how the deformation density can be successfully separated into in‐plane and out‐of‐plane contributions. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Two-dimensional Ising model with competing interactions and its application to clusters and arrays ofπ-rings and adiabatic quantum computing

We study planar clusters consisting of loops including a Josephson $\ensuremath{\pi}$ junction ($\ensuremath{\pi}$-rings). Each $\ensuremath{\pi}$-ring carries a persistent current and behaves as a classical orbital moment. The type of particular state associated with the orientation of orbital moments at the cluster depends on the interaction between these orbital moments and can be easily controlled, i.e., by a bias current or by other means. We show that these systems can be described by the two-dimensional Ising model with competing nearest-neighbor and diagonal interactions and investigate the phase diagram of this model. The characteristic features of the model are analyzed based on the exact solutions for small clusters such as a five-site square plaquette as well as on a mean-field-type approach for the infinite square lattice of Ising spins. The results are compared with spin patterns obtained by Monte Carlo simulations for the $100\ifmmode\times\else\texttimes\fi{}100$ square lattice and with experiment. We show that the $\ensuremath{\pi}$-ring clusters may be used as a special type of superconducting memory elements. The obtained results may be verified in experiments and are applicable to adiabatic quantum computing where the states are switched adiabatically with the slow change of coupling constants.

A 1:1 cocrystal of 4-(dimethylamino)benzaldehyde and 6-phenyl-1,3,5-triazine-2,4-diamine

The crystal structure of the title compound, C(9)H(11)NO.C(9)H(9)N(5), contains one molecule of each component in the asymmetric unit. Approximately planar clusters of four molecules are formed by N-H...N and N-H...O hydrogen bonds, and further N-H...N hydrogen bonds link adjacent clusters to form pleated ribbons. pi-pi interactions are found between triazine and aldehyde benzene rings in different clusters, generating stacks along the monoclinic b axis. The intramolecular geometry of the two components is similar to that found in other crystal structures containing these molecules. Both molecules are approximately planar, except for methyl H atoms, with a small twist about the C-C bond linking the phenyl and triazine rings.

Colloquium: Soap bubble clusters

Soap bubble clusters and froths model biological cells, metallurgical structures, magnetic domains,liquid crystals, fire-extinguishing foams, bread, cushions, and many other materials and structures.Despite the simplicity of the governing principle of energy or area minimization, the underlyingmathematical theory is deep and still not understood, even for rather simple, finite clusters. Only withthe advent of geometric measure theory could mathematics treat surfaces which might haveunprescribed singularities and topological complexities. In 1884, Schwarz gave a rigorousmathematical proof that a single round soap bubble provides the least-area way to enclose a givenvolume of air. Similarly, the familiar double bubble provides the absolute least-area way to encloseand separate the two given volumes of air, although the proof did not come until 2000 and has aninteresting story, as this Colloquium explains in some detail. Whether a triple soap bubble provides theleast-area way to enclose and separate three given volumes of air remains an open conjecture today.Even planar bubble clusters remain mysterious. In about 200

Pressures inside bubbles in planar clusters

We provide theoretical estimates and undertake Surface Evolver experiments on the pressures inside bubbles in planar clusters. The equation of equilibrium implies that as the number, N, of unit bubbles become large, the average normalized pressure in an energy-minimizing cluster approaches 2−1/231/4 ≈ 0.9306. An equation is derived for the rigorous theoretical upper and lower bounds on the average pressure in terms of N. Surface Evolver experiments agree with these estimates.

Doping Golden Buckyballs: Cu@Au16‐ and Cu@Au17‐ Cluster Anions.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Halide Binding by the D212N Mutant of Bacteriorhodopsin Affects Hydrogen Bonding of Water in the Active Site

Bacteriorhodopsin (BR), a membrane protein found in Halobacterium salinarum, functions as a light-driven proton pump. The Schiff base region has a quadrupolar structure with positive charges located at the protonated Schiff base and Arg82, and the counterbalancing negative charges located at Asp85 and Asp212. The quadropole inside the protein is stabilized by three water molecules, forming a roughly planar pentagonal cluster composed of these waters and two oxygens of Asp85 and Asp212 (one from each carboxylate side chain). It is known that BR lacks proton-pumping activity if Asp85 or Asp212 is neutralized by mutation, but binding of Cl- has different functional effects in mutants at these positions. Binding of Cl- to D85T converts into a chloride ion pump (Sasaki, J., Brown, L. S., Chon, Y.-S., Kandori, H., Maeda, A., Needleman, R., and Lanyi, J. K. (1995) Science 269, 73-75). On the other hand, photovoltage measurements suggested that binding of Cl- to D212N restores the proton-pumping activity at low pH (Moltke, S., Krebs, M. P., Mollaaghababa, R., Khorana, H. G., and Heyn, M. P. (1995) Biophys. J. 69, 2074-2083). In this paper, we studied halide-bound D212N mutant BR in detail. Light-induced pH changes in a suspension of proteoliposomes containing D212N(Cl-) at pH 5 clearly showed that Cl- restores the proton-pumping activity. Spectral blue-shift induced by halide binding to D212N indicates that halides affect the counterion of the protonated Schiff base, whereas much smaller halide dependence of the lambdamax than in D85T suggests that the binding site is distant from the chromophore. In fact, the K minus BR difference Fourier-transform infrared (FTIR) spectra of D212N at 77 K exhibit little halide dependence for vibrational bands of retinal and protein. The only halide-dependent bands were the C=N stretch of Arg82 and some water O-D stretches, suggesting that these groups constitute a halide-binding pocket. A strongly hydrogen-bonded water molecule is observed for halide-bound D212N, but not for halide-free D212N, which is consistent with our hypothesis that such a water molecule is a prerequisite for proton-pumping activity of rhodopsins. We concluded that halide binding near Arg82 in D212N restores the water-containing hydrogen-bonding network in the Schiff base region. In particular, the ion pair formed by the Schiff base and Asp85 through a strongly hydrogen-bonded water is essential for the proton-pumping activity of this mutant and may be controlled by the halide binding to the distant site.

Global structure optimization study on Au 2-20

The geometries and electronic properties of the most stable small Aun clusters with n=2 to 20 are presented. An intensive search for low-energy minima of Aun clusters was carried through using a density-functional tight-binding method combined with genetic algorithms for an unbiased global structure optimization. The structural and energetic properties of the small gold clusters are compared with those of planar Aun clusters with n=5 to 15.