New Theoretical Developments in Exploring Electronically Excited States: Including Localized Configuration Interaction Singles and Application to Large Helium Clusters

NASA Astrophysics Data System (ADS)

Closser, Kristina Danielle

This thesis presents new developments in excited state electronic structure theory. Contrasted with the ground state, the electronically excited states of atoms and molecules often are unstable and have short lifetimes, exhibit a greater diversity of character and are generally less well understood. The very unusual excited states of helium clusters motivated much of this work. These clusters consist of large numbers of atoms (experimentally 103--109 atoms) and bands of nearly degenerate excited states. For an isolated atom the lowest energy excitation energies are from 1s → 2s and 1s → 2 p transitions, and in clusters describing the lowest energy band minimally requires four states per atom. In the ground state the clusters are weakly bound by van der Waals interactions, however in the excited state they can form well-defined covalent bonds. The computational cost of quantum chemical calculations rapidly becomes prohibitive as the size of the systems increase. Standard excited-state methods such as configuration interaction singles (CIS) and time-dependent density functional theory (TD-DFT) can be used with ≈100 atoms, and are optimized to treat only a few states. Thus, one of our primary aims is to develop a method which can treat these large systems with large numbers of nearly degenerate excited states. Additionally, excited states are generally formed far from their equilibrium structures. Vertical excitations from the ground state induce dynamics in the excited states. Thus, another focus of this work is to explore the results of these forces and the fate of the excited states. Very little was known about helium cluster excited states when this work began, thus we first investigated the excitations in small helium clusters consisting of 7 or 25 atoms using CIS. The character of these excited states was determined using attachment/detachment density analysis and we found that in the n = 2 manifold the excitations could generally be interpreted as superpositions of atomic states with surface states appearing close to the atomic excitation energies and interior states being blue shifted by up to ≈2 eV. The dynamics resulting from excitation of He_7 were subsequently explored using ab initio molecular dynamics (AIMD). These simulations were performed with classical adiabatic dynamics coupled to a new state-following algorithm on CIS potential energy surfaces. Most clusters were found to completely dissociate and resulted in a single excited atomic state (90%), however, some trajectories formed bound, He*2 (3%), and a few yielded excited trimers (<0.5%). Comparisons were made with available experimental information on much larger clusters. Various applications of this state following algorithm are also presented. In addition to AIMD, these include excited-state geometry optimization and minimal energy path finding via the growing string method. When using state following we demonstrate that more physical results can be obtained with AIMD calculations. Also, the optimized geometries of three excited states of cytosine, two of which were not found without state following, and the minimal energy path between the lowest two singlet excited states of protonated formaldimine are offered as example applications. Finally, to address large clusters, a local variation of CIS was developed. This method exploits the properties of absolutely localized molecular orbitals (ALMOs) to limit the total number of excitations to scaling only linearly with cluster size, which results in formal scaling with the third power of the system size. The derivation of the equations and design of the algorithm are discussed in detail, and computational timings as well as a pilot application to the size dependence of the helium cluster spectrum are presented.

Kramers degeneracy and relaxation in vanadium, niobium and tantalum clusters

NASA Astrophysics Data System (ADS)

Diaz-Bachs, A.; Katsnelson, M. I.; Kirilyuk, A.

2018-04-01

In this work we use magnetic deflection of V, Nb, and Ta atomic clusters to measure their magnetic moments. While only a few of the clusters show weak magnetism, all odd-numbered clusters deflect due to the presence of a single unpaired electron. Surprisingly, for the majority of V and Nb clusters an atomic-like behavior is found, which is a direct indication of the absence of spin–lattice interaction. This is in agreement with Kramers degeneracy theorem for systems with a half-integer spin. This purely quantum phenomenon is surprisingly observed for large systems of more than 20 atoms, and also indicates various quantum relaxation processes, via Raman two-phonon and Orbach high-spin mechanisms. In heavier, Ta clusters, the relaxation is always present, probably due to larger masses and thus lower phonon energies, as well as increased spin–orbit coupling.

Structural and electronic properties of Aun-xPtx (n = 2-14; x ⩽ n) clusters: The density functional theory investigation

NASA Astrophysics Data System (ADS)

Yuan, H. K.; Kuang, A. L.; Tian, C. L.; Chen, H.

2014-03-01

The structural evolutions and electronic properties of bimetallic Aun-xPtx (n = 2-14; x ⩽ n) clusters are investigated by using the density functional theory (DFT) with the generalized gradient approximation (GGA). The monatomic doping Aun-1Pt clusters are emphasized and compared with the corresponding pristine Aun clusters. The results reveal that the planar configurations are favored for both Aun-1Pt and Aun clusters with size up to n = 13, and the former often employ the substitution patterns based on the structures of the latter. The most stable clusters are Au6 and Au6Pt, which adopt regular planar triangle (D3h) and hexagon-ring (D6h) structures and can be regarded as the preferential building units in designing large clusters. For Pt-rich bimetallic clusters, their structures can be obtained from the substitution of Pt atoms by Au atoms from the Ptn structures, where Pt atoms assemble together and occupy the center yet Au atoms prefer the apex positions showing a segregation effect. With respect to pristine Au clusters, AunPt clusters exhibit somewhat weaker and less pronounced odd-even oscillations in the highest occupied and lowest unoccupied molecular-orbital gaps (HOMO-LUMO gap), electron affinity (EA), and ionization potential (IP) due to the partially released electron pairing effect. The analyses of electronic structure indicate that Pt atoms in AuPt clusters would delocalize their one 6s and one 5d electrons to contribute the electronic shell closure. The sp-d hybridizations as well as the d-d interactions between the host Au and dopant Pt atoms result in the enhanced stabilities of AuPt clusters.

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

NASA Technical Reports Server (NTRS)

Kahn, L. R.

1982-01-01

Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

Structural, electronic, and magnetic properties of Y(n)O (n=2-14) clusters: Density functional study.

PubMed

Yang, Zhi; Xiong, Shi-Jie

2008-09-28

The geometries stability, electronic properties, and magnetism of Y(n)O clusters up to n=14 are systematically studied with density functional theory. In the lowest-energy structures of Y(n)O clusters, the equilibrium site of the oxygen atom gradually moves from an outer site of the cluster, via a surface site, and finally, to an interior site as the number of the Y atoms increases from 2 to 14. Starting from n=12, the O atom falls into the center of the cluster with the Y atoms forming the outer frame. The results show that clusters with n=2, 4, 8, and 12 are more stable than their respective neighbors, and that the total magnetic moments of Y(n)O clusters are all quite small except Y(12)O cluster. The lowest-energy structure of Y(12)O cluster is a perfect icosahedron with a large magnetic moment 6mu(B). In addition, we find that the total magnetic moments are quenched for n=2, 6, and 8 due to the closed-shell electronic configuration. The calculated ionization potentials and electron affinities are in good agreement with the experimental results, which imply that the present theoretical treatments are satisfactory.

Size dependent fragmentation of argon clusters in the soft x-ray ionization regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gisselbrecht, Mathieu; Lindgren, Andreas; Burmeister, Florian

Photofragmentation of argon clusters of average size ranging from 10 up to 1000 atoms is studied using soft x-ray radiation below the 2p threshold and multicoincidence mass spectroscopy technique. For small clusters (=10), ionization induces fast fragmentation with neutral emission imparting a large amount of energy. While the primary dissociation takes place on a picosecond time scale, the fragments undergo slow degradation in the spectrometer on a microsecond time scale. For larger clusters ({>=}100) we believe that we observe the fragmentation pattern of multiply charged species on a time-scale which lasts a few hundred nanoseconds. The reason for these slowermore » processes is the large number of neutral atoms which act as an efficient cooling bath where the excess energy ('heat') dissipates among all degrees of freedom. Further degradation of the photoionic cluster in spectrometer then takes place on the microsecond time scale, similar to small clusters.« less

Atomic structure of a decagonal Al-Pd-Mn phase

NASA Astrophysics Data System (ADS)

Mihalkovič, Marek; Roth, Johannes; Trebin, Hans-Rainer

2017-12-01

We present a detailed structure solution for the 16 -Å decagonal quasicrystal in the Al-Pd-Mn system by means of cluster decoration and ab initio energy minimization. It is based on structure models of the ɛ and other approximant phases. The ɛ phases can be represented as subsets of a hexagon-boat-star (HBS) tiling. The decagonal phase comprises further HBS tiles. We have constructed several fictitious HBS approximants and optimized their structures individually. All tiles are decorated by two types of atomic clusters: the pseudo-Mackay icosahedron (PMI) and the large bicapped pentagonal prism (LBPP). It turns out that, whereas the PMI clusters can be kept essentially unchanged, the LBPP clusters must be adjusted in occupancy with Al atoms depending on their positions in the various tiles. In this way we obtain cluster decorations for all tiles of the decagonal quasicrystal. The calculations were confirmed by evaluation of an effective tile Hamiltonian.

Penning ionization electron spectroscopy of CO 2 clusters in collision with metastable rare gas atoms

NASA Astrophysics Data System (ADS)

Maruyama, Ryo; Tanaka, Hideyasu; Yamakita, Yoshihiro; Misaizu, Fuminori; Ohno, Koichi

2000-09-01

Penning ionization electron spectra (PIES) of CO 2 clusters have been observed for the first time. An unusually fast electron band with excess kinetic energies of 1.4-2.9 eV with respect to the monomer band for the ionic X state was observed for CO 2 clusters in collision with He*(2 3S) atoms. While for PIES with Ne*(3 3P), no such unusual band was observed. The unusual band is ascribed to autoionization into stable structures of ionic clusters to which direct ionization processes are almost impossible due to very small Franck-Condon overlaps associated with a very large geometry difference between the ionic and neutral clusters.

Composition design for Laves phase-related body-centered cubic-V solid solution alloys with large hydrogen storage capacities.

PubMed

Wang, H B; Wang, Q; Dong, C; Yuan, L; Xu, F; Sun, L X

2008-03-19

This paper analyzes the characteristics of alloy compositions with large hydrogen storage capacities in Laves phase-related body-centered cubic (bcc) solid solution alloy systems using the cluster line approach. Since a dense-packed icosahedral cluster A(6)B(7) characterizes the local structure of AB(2) Laves phases, in an A-B-C ternary system, such as Ti-Cr (Mn, Fe)-V, where A-B forms AB(2) Laves phases while A-C and B-C tend to form solid solutions, a cluster line A(6)B(7)-C is constructed by linking A(6)B(7) to C. The alloy compositions with large hydrogen storage capacities are generally located near this line and are approximately expressed with the cluster-plus-glue-atom model. The cluster line alloys (Ti(6)Cr(7))(100-x)V(x) (x = 2.5-70 at.%) exhibit different structures and hence different hydrogen storage capacities with increasing V content. The alloys (Ti(6)Cr(7))(95)V(5) and Ti(30)Cr(40)V(30) with bcc solid solution structure satisfy the cluster-plus-glue-atom model.

Effect of charge and composition on the structural fluxionality and stability of nine atom tin-bismuth Zintl analogues.

PubMed

Gupta, Ujjwal; Reber, Arthur C; Clayborne, Penee A; Melko, Joshua J; Khanna, Shiv N; Castleman, A W

2008-12-01

Synergistic studies of bismuth doped tin clusters combining photoelectron spectra with first principles theoretical investigations establish that highly charged Zintl ions, observed in the condensed phase, can be stabilized as isolated gas phase clusters through atomic substitution that preserves the overall electron count but reduces the net charge and thereby avoids instability because of coulomb repulsion. Mass spectrometry studies reveal that Sn(8)Bi(-), Sn(7)Bi(2)(-), and Sn(6)Bi(3)(-) exhibit higher abundances than neighboring species, and photoelectron spectroscopy show that all of these heteroatomic gas phase Zintl analogues (GPZAs) have high adiabatic electron detachment energies. Sn(6)Bi(3)(-) is found to be a particularly stable cluster, having a large highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap. Theoretical calculations demonstrate that the Sn(6)Bi(3)(-) cluster is isoelectronic with the well know Sn(9)(-4) Zintl ion; however, the fluxionality reported for Sn(9)(-4) is suppressed by substituting Sn atoms with Bi atoms. Thus, while the electronic stability of the clusters is dominated by electron count, the size and position of the atoms affects the dynamics of the cluster as well. Substitution with Bi enlarges the cage compared with Sn(9)(-4) making it favorable for endohedral doping, findings which suggest that these cages may find use for building blocks of cluster assembled materials.

Analysis of Helium Segregation on Surfaces of Plasma-Exposed Tungsten

NASA Astrophysics Data System (ADS)

Maroudas, Dimitrios; Hu, Lin; Hammond, Karl; Wirth, Brian

2015-11-01

We report a systematic theoretical and atomic-scale computational study of implanted helium segregation on surfaces of tungsten, which is considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations, including molecular statics to understand the origin of helium surface segregation, targeted molecular-dynamics (MD) simulations of near-surface cluster reactions, and large-scale MD simulations of implanted helium evolution in plasma-exposed tungsten. We find that small, mobile helium clusters (of 1-7 He atoms) in the near-surface region are attracted to the surface due to an elastic interaction force. This thermodynamic driving force induces drift fluxes of these mobile clusters toward the surface, facilitating helium segregation. Moreover, the clusters' drift toward the surface enables cluster reactions, most importantly trap mutation, at rates much higher than in the bulk material. This cluster dynamics has significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure.

Impurity-doped Si10 cluster: Understanding the structural and electronic properties from first-principles calculations

NASA Astrophysics Data System (ADS)

Majumder, Chiranjib; Kulshreshtha, S. K.

2004-12-01

Structural and electronic properties of metal-doped silicon clusters ( MSi10 , M=Li , Be, B, C, Na, Mg, Al, and Si) have been investigated via ab initio molecular dynamics simulation under the formalism of the density functional theory. The exchange-correlation energy has been calculated using the generalized gradient approximation method. Several stable isomers of MSi10 clusters have been identified based on different initial configurations and their relative stabilities have been analyzed. From the results it is revealed that the location of the impurity atom depends on the nature of interaction between the impurity atom and the host cluster and the size of the impurty atom. Whereas Be and B atoms form stable isomers, the impurity atom being placed at the center of the bicapped tetragonal antiprism structure of the Si10 cluster, all other elements diffuse outside the cage of Si10 cluster. Further, to understand the stability and the chemical bonding, the LCAO-MO based all electron calculations have been carried out for the lowest energy isomers using the hybrid B3LYP energy functional. Based on the interaction energy of the M atoms with Si10 clusters it is found that p-p interaction dominates over the s-p interaction and smaller size atoms interact more strongly. Based on the binding energy, the relative stability of MSi10 clusters is found to follow the order of CSi10>BSi10>BeSi10>Si11>AlSi10>LiSi10>NaSi10>MgSi10 , leading one to infer that while the substitution of C, B and Be enhances the stability of the Si11 cluster, others have an opposite effect. The extra stability of the BeSi10 clusters is due to its encapsulated close packed structure and large energy gap between the HOMO and LUMO energy levels.

Theoretical research program to predict the properties of molecules and clusters containing transition metal atoms

NASA Technical Reports Server (NTRS)

Walch, S.

1984-01-01

The primary focus of this research has been the theoretical study of transition metal (TM) chemistry. A major goal of this work is to provide reliable information about the interaction of H atoms with iron metal. This information is needed to understand the effect of H atoms on the processes of embrittlement and crack propagation in iron. The method in the iron hydrogen studies is the cluster method in which the bulk metal is modelled by a finite number of iron atoms. There are several difficulties in the application of this approach to the hydrogen iron system. First the nature of TM-TM and TM-H bonding for even diatomic molecules was not well understood when these studies were started. Secondly relatively large iron clusters are needed to provide reasonable results.

Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures

NASA Astrophysics Data System (ADS)

Angelié, C.; Soudan, J.-M.

2017-05-01

The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, gp(Ep), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat -1 /3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat < 150, the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve.

Inorganic material profiling using Arn+ cluster: Can we achieve high quality profiles?

NASA Astrophysics Data System (ADS)

Conard, T.; Fleischmann, C.; Havelund, R.; Franquet, A.; Poleunis, C.; Delcorte, A.; Vandervorst, W.

2018-06-01

Retrieving molecular information by sputtering of organic systems has been concretized in the last years due to the introduction of sputtering by large gas clusters which drastically eliminated the compound degradation during the analysis and has led to strong improvements in depth resolution. Rapidly however, a limitation was observed for heterogeneous systems where inorganic layers or structures needed to be profiled concurrently. As opposed to organic material, erosion of the inorganic layer appears very difficult and prone to many artefacts. To shed some light on these problems we investigated a simple system consisting of aluminum delta layer(s) buried in a silicon matrix in order to define the most favorable beam conditions for practical analysis. We show that counterintuitive to the small energy/atom used and unlike monoatomic ion sputtering, the information depth obtained with large cluster ions is typically very large (∼10 nm) and that this can be caused both by a large roughness development at early stages of the sputtering process and by a large mixing zone. As a consequence, a large deformation of the Al intensity profile is observed. Using sample rotation during profiling significantly improves the depth resolution while sample temperature has no significant effect. The determining parameter for high depth resolution still remains the total energy of the cluster instead of the energy per atom in the cluster.

Path integral Monte Carlo study on the structure and absorption spectra of alkali atoms (Li, Na, K) attached to superfluid helium clusters

NASA Astrophysics Data System (ADS)

Nakayama, Akira; Yamashita, Koichi

2001-01-01

Path integral Monte Carlo calculations have been performed to investigate the microscopic structure and thermodynamic properties of the AkṡHeN (Ak=Li, Na, K,N⩽300) clusters at T=0.5 K. Absorption spectra which correspond to the 2P←2S transitions of alkali atoms are also calculated within a pairwise additive model, which employs diatomic Ak-He potential energy curves. The size dependences of the cluster structure and absorption spectra that show the influence of the helium cluster environment are examined in detail. It is found that alkali atoms are trapped in a dimple on the helium cluster's surface and that, from the asymptotic behavior, the AkṡHe300 cluster, at least semiquantitatively, mimics the local structure of experimentally produced large helium clusters in the vicinity of alkali atoms. We have successfully reproduced the overall shapes of the spectra and explained their features from a static and structural point of view. The positions, relative intensities, and line widths of the absorption maxima are calculated to be in moderate agreement with experiments [F. Stienkemeier, J. Higgins, C. Callegari, S. I. Kanorsky, W. E. Ernst, and G. Scoles, Z. Phys. D 38, 253 (1996)].

Clustering biomolecular complexes by residue contacts similarity.

PubMed

Rodrigues, João P G L M; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J

2012-07-01

Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions. Albeit widely used, these measures suffer from several theoretical and technical limitations (e.g., choice of regions for fitting) that impair their application in multicomponent systems (N > 2), large-scale studies (e.g., interactomes), and other time-critical scenarios. We present here a simple similarity measure for structural clustering based on atomic contacts--the fraction of common contacts--and compare it with the most used similarity measure of the protein docking community--interface backbone RMSD. We show that this method produces very compact clusters in remarkably short time when applied to a collection of binary and multicomponent protein-protein and protein-DNA complexes. Furthermore, it allows easy clustering of similar conformations of multicomponent symmetrical assemblies in which chain permutations can occur. Simple contact-based metrics should be applicable to other structural biology clustering problems, in particular for time-critical or large-scale endeavors. Copyright © 2012 Wiley Periodicals, Inc.

Electronic and molecular structure of carbon grains

NASA Technical Reports Server (NTRS)

Almloef, Jan; Luethi, Hans-Peter

1990-01-01

Clusters of carbon atoms have been studied with large-scale ab initio calculations. Planar, single-sheet graphite fragments with 6 to 54 atoms were investigated, as well as the spherical C(sub 60) Buckminsterfullerene molecule. Polycyclic aromatic hydrocarbons (PAHs) have also been considered. Thermodynamic differences between diamond- and graphite-like grains have been studied in particular. Saturation of the peripheral bonds with hydrogen is found to provide a smooth and uniform convergence of the properties with increasing cluster size. For the graphite-like clusters the convergence to bulk values is much slower than for the three-dimensional complexes.

Atomic-scale structure and electronic properties of GaN/GaAs superlattices

NASA Astrophysics Data System (ADS)

Goldman, R. S.; Feenstra, R. M.; Briner, B. G.; O'Steen, M. L.; Hauenstein, R. J.

1996-12-01

We have investigated the atomic-scale structure and electronic properties of GaN/GaAs superlattices produced by nitridation of a molecular beam epitaxially grown GaAs surface. Using cross-sectional scanning tunneling microscopy (STM) and spectroscopy, we show that the nitrided layers are laterally inhomogeneous, consisting of groups of atomic-scale defects and larger clusters. Analysis of x-ray diffraction data in terms of fractional area of clusters (determined by STM), reveals a cluster lattice constant similar to bulk GaN. In addition, tunneling spectroscopy on the defects indicates a conduction band state associated with an acceptor level of NAs in GaAs. Therefore, we identify the clusters and defects as nearly pure GaN and NAs, respectively. Together, the results reveal phase segregation in these arsenide/nitride structures, in agreement with the large miscibility gap predicted for GaAsN.

Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin [Ensemble averaged structure-function relationship for composite nanocrystals: magnetic bcc Fe clusters with catalytically active fcc Pt skin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petkov, Valeri; Prasai, Binay; Shastri, Sarvjit

Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction,more » respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.« less

Bonding reactivity descriptor from conceptual density functional theory and its applications to elucidate bonding formation

NASA Astrophysics Data System (ADS)

Zhou, Pan-Pan; Liu, Shubin; Ayers, Paul W.; Zhang, Rui-Qin

2017-10-01

Condensed-to-atom Fukui functions which reflect the atomic reactivity like the tendency susceptible to either nucleophilic or electrophilic attack demonstrate the bonding trend of an atom in a molecule. Accordingly, Fukui functions based concepts, that is, bonding reactivity descriptors which reveal the bonding properties of molecules in the reaction were put forward and then applied to pericyclic and cluster reactions to confirm their effectiveness and reliability. In terms of the results from the bonding descriptors, a covalent bond can readily be predicted between two atoms with large Fukui functions (i.e., one governs nucleophilic attack while the other one governs electrophilic attack, or both of them govern radical attacks) for pericyclic reactions. For SinOm clusters' reactions, the clusters with a low O atom ratio readily form a bond between two Si atoms with big values of their Fukui functions in which they respectively govern nucleophilic and electrophilic attacks or both govern radical attacks. Also, our results from bonding descriptors show that Si—Si bonds can be formed via the radical mechanism between two Si atoms, and formations of Si—O and O—O bonds are possible when the O content is high. These results conform with experimental findings and can help experimentalists design appropriate clusters to synthesize Si nanowires with high yields. The approach established in this work could be generalized and applied to study reactivity properties for other systems.

Sc20C60: a volleyballene

NASA Astrophysics Data System (ADS)

Wang, Jing; Ma, Hong-Man; Liu, Ying

2016-06-01

An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable.An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable. Electronic supplementary information (ESI) available: Sc20C60: a Volleyballene_SI. See DOI: 10.1039/c5nr07784b

Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10(1)0).

PubMed

Hellström, Matti; Spångberg, Daniel; Hermansson, Kersti

2015-12-15

We assess the consequences of the interface model-embedded-cluster or periodic-slab model-on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic-slab calculations indicate a delocalized charge-transfer state. Our example is Cu atom adsorption on ZnO(10(1)0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded-cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom-centered and plane-waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10(1)0), as long as care is taken to account for the effects of CT. © 2015 Wiley Periodicals, Inc.

Structural, electronic, vibrational and optical properties of Bin clusters

NASA Astrophysics Data System (ADS)

Liang, Dan; Shen, Wanting; Zhang, Chunfang; Lu, Pengfei; Wang, Shumin

2017-10-01

The neutral, anionic and cationic bismuth clusters with the size n up to 14 are investigated by using B3LYP functional within the regime of density functional theory and the LAN2DZ basis set. By analysis of the geometries of the Bin (n = 2-14) clusters, where cationic and anionic bismuth clusters are largely similar to those of neutral ones, a periodic effect by adding units with one to four atoms into smaller cluster to form larger cluster is drawn for the stable structures of bismuth clusters. An even-odd alteration is shown for the properties of the clusters, such as the calculated binding energies and dissociation energies, as well as frontier orbital energies, electron affinities, ionization energies. All the properties indicate that the Bi4 cluster is the most possible existence in bismuth-containing materials, which supports the most recent experiment. The orbital compositions, infrared and Raman activities and the ultraviolet absorption of the most possible tetramer bismuth cluster are given in detail to reveal the periodic tendency of adding bismuth atoms and the stability of tetramer bismuth cluster.

Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petkov, Valeri; Prasai, Binay; Shastri, Sarvjit

2017-09-12

Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction,more » respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.« less

Generation of nanoclusters by ultrafast laser ablation of Al: Molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miloshevsky, Alexander; Phillips, Mark C.; Harilal, Sivanandan S.

The laser ablation of materials induced by an ultrashort femtosecond pulse is a complex phenomenon, which depends on both the material properties and the properties of the laser pulse. The unique capability of a combination of molecular dynamics (MD) and Momentum Scaling Model (MSM) methods is developed and applied to a large atomic system for studying the process of ultrafast laser-material interactions, behavior of matter in a highly non-equilibrium state, material disintegration, and formation of nanoparticles (NPs). Laser pulses with several fluences in the range from 500 J/m2 to 5000 J/m2 interacting with a large system of aluminum atoms aremore » simulated. The response of Al material to the laser energy deposition is investigated within the finite-size laser spot. It is found that the shape of the plasma plume is dynamically changing during an expansion process. At several tens of picoseconds it can be characterized as a long hollow ellipsoid surrounded by atomized and nano-clustered particles. The time evolution of NP clusters in the plume is investigated. The collisions between the single Al atoms and generated NPs and fragmentation of large NPs determine the fractions of different-size NP clusters in the plume. The MD-MSM simulations show that laser fluence greatly affects the size distribution of NPs, their polar angles, magnitude and direction vectors of NP velocities. These results and predictions are supported by the experimental data and previous MD simulations.« less

Cluster size dependence of high-order harmonic generation

NASA Astrophysics Data System (ADS)

Tao, Y.; Hagmeijer, R.; Bastiaens, H. M. J.; Goh, S. J.; van der Slot, P. J. M.; Biedron, S. G.; Milton, S. V.; Boller, K.-J.

2017-08-01

We investigate high-order harmonic generation (HHG) from noble gas clusters in a supersonic gas jet. To identify the contribution of harmonic generation from clusters versus that from gas monomers, we measure the high-order harmonic output over a broad range of the total atomic number density in the jet (from 3×1016 to 3 × 1018 {{cm}}-3) at two different reservoir temperatures (303 and 363 K). For the first time in the evaluation of the harmonic yield in such measurements, the variation of the liquid mass fraction, g, versus pressure and temperature is taken into consideration, which we determine, reliably and consistently, to be below 20% within our range of experimental parameters. By comparing the measured harmonic yield from a thin jet with the calculated corresponding yield from monomers alone, we find an increased emission of the harmonics when the average cluster size is less than 3000. Using g, under the assumption that the emission from monomers and clusters add up coherently, we calculate the ratio of the average single-atom response of an atom within a cluster to that of a monomer and find an enhancement of around 100 for very small average cluster size (∼200). We do not find any dependence of the cut-off frequency on the composition of the cluster jet. This implies that HHG in clusters is based on electrons that return to their parent ions and not to neighboring ions in the cluster. To fully employ the enhanced average single-atom response found for small average cluster sizes (∼200), the nozzle producing the cluster jet must provide a large liquid mass fraction at these small cluster sizes for increasing the harmonic yield. Moreover, cluster jets may allow for quasi-phase matching, as the higher mass of clusters allows for a higher density contrast in spatially structuring the nonlinear medium.

Dynamics of the Coulomb explosion of large hydrogen iodide clusters irradiated by superintense ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Krainov, V. P.; Roshchupkin, A. S.

2001-12-01

Dynamics of the inner and outer above-barrier ionization and of the Coulomb explosion are calculated for large hydrogen iodide clusters irradiated by superintense ultrashort laser pulses. We have found that the Coulomb forces predominate in the expansion of these clusters in comparison with the hydrodynamic forces. The energy distribution of the iodine multiple atomic ions in laser focal volume is derived. Results of our calculations are in a good agreement with the recent experimental data of Tisch et al. [Phys. Rev. A 60, 3076 (1999)].

Structural, electronic and magnetic properties of Ti n Mo ( n = 1 - 7) clusters

NASA Astrophysics Data System (ADS)

Zhang, Ge; Zhai, Zhongyuan; Sheng, Yong

2017-04-01

The ground state structures of TinMo and Tin+1 (n = 1 - 7) clusters and their structural, electronic and magnetic properties are investigated with the density functional method at B3LYP/LanL2DZ level. One Mo atom substituted Tin+1 structure is the dominant growth pattern, and the TinMo clusters exhibit enhanced structural stabilities according to the averaged binding energies. The electronic properties are also discussed by investigating chemical hardness and HOMO-LUMO energy gap. The results reveal that Ti3Mo and Ti5Mo keep higher chemical stabilities when compared with the other clusters. For all the studied clusters, the Mo atoms always get electrons from Ti atoms and present negative charges. Moreover, the doping of Mo in the bare titanium clusters can alter the magnetic moments of them. Ti3Mo and Ti5Mo show relatively large total magnetic moments, which may be related to the presence of exchange splitting behavior in their densities of states. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-70589-8

Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales.

PubMed

Huang, Shiping

2017-11-13

The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids. To this end, Green's function molecular dynamics (GFMD) is used to study both how the contact cluster evolves from the atomic scale to the macroscopic scale and the interaction between clusters. It is found that the interaction between clusters has a strong effect on their formation. The formation and distribution of the contact clusters is far more complicated than that predicted by the asperity model. Ignorance of the interaction between them leads to overestimating the contacting force. In real contact, contacting clusters are smaller and more discrete due to the interaction between the asperities. Understanding the exact nature of the contact area with the normal load is essential to the following research on friction.

Analysis of the electron density features of small boron clusters and the effects of doping with C, P, Al, Si, and Zn: Magic B7P and B8Si clusters

NASA Astrophysics Data System (ADS)

Saha, P.; Rahane, A. B.; Kumar, V.; Sukumar, N.

2016-05-01

Boron atomic clusters show several interesting and unusual size-dependent features due to the small covalent radius, electron deficiency, and higher coordination number of boron as compared to carbon. These include aromaticity and a diverse array of structures such as quasi-planar, ring or tubular shaped, and fullerene-like. In the present work, we have analyzed features of the computed electron density distributions of small boron clusters having up to 11 boron atoms, and investigated the effect of doping with C, P, Al, Si, and Zn atoms on their structural and physical properties, in order to understand the bonding characteristics and discern trends in bonding and stability. We find that in general there are covalent bonds as well as delocalized charge distribution in these clusters. We associate the strong stability of some of these planar/quasiplanar disc-type clusters with the electronic shell closing with effectively twelve delocalized valence electrons using a disc-shaped jellium model. {{{{B}}}9}-, B10, B7P, and B8Si, in particular, are found to be exceptional with very large gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, and these are suggested to be magic clusters.

Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales

NASA Astrophysics Data System (ADS)

Huang, Shiping

2017-11-01

The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids. To this end, Green's function molecular dynamics (GFMD) is used to study both how the contact cluster evolves from the atomic scale to the macroscopic scale and the interaction between clusters. It is found that the interaction between clusters has a strong effect on their formation. The formation and distribution of the contact clusters is far more complicated than that predicted by the asperity model. Ignorance of the interaction between them leads to overestimating the contacting force. In real contact, contacting clusters are smaller and more discrete due to the interaction between the asperities. Understanding the exact nature of the contact area with the normal load is essential to the following research on friction.

Topological reaction coordinates to explore the structure of atomic clusters and organic molecule isomers from first principles

NASA Astrophysics Data System (ADS)

Pietrucci, Fabio; Andreoni, Wanda

2011-03-01

We introduce a simple reaction coordinate based on spectral graph theory which describes the topology of the network of chemical bonds around a given atom. We employ the reaction coordinate in combination with DFT-based first-principles metadynamics to systematically explore the possible structures of silicon and carbon clusters (including fullerene-like cages) for sizes of tens of atoms. From our extensive exploration we are able to estimate the fractal dimension of the configuration space, which both for silicon and carbon clusters turns out to be quite low. Using the same approach we simulate the interconversion among a large number of chemically relevant organic molecules which are isomers of the C4 H5 N formula unit, and we demonstrate the possibility of automatically exploring isomerisation, association, and decomposition reactions without prior knowledge of the products involved.

The role of charge transfer in the oxidation state change of Ce atoms in the TM13-CeO2(111) systems (TM = Pd, Ag, Pt, Au): a DFT + U investigation.

PubMed

Tereshchuk, Polina; Freire, Rafael L H; Ungureanu, Crina G; Seminovski, Yohanna; Kiejna, Adam; Da Silva, Juarez L F

2015-05-28

Despite extensive studies of transition metal (TM) clusters supported on ceria (CeO2), fundamental issues such as the role of the TM atoms in the change in the oxidation state of Ce atoms are still not well understood. In this work, we report a theoretical investigation based on static and ab initio molecular dynamics density functional theory calculations of the interaction of 13-atom TM clusters (TM = Pd, Ag, Pt, Au) with the unreduced CeO2(111) surface represented by a large surface unit cell and employing Hubbard corrections for the strong on-site Coulomb correlation in the Ce f-electrons. We found that the TM13 clusters form pyramidal-like structures on CeO2(111) in the lowest energy configurations with the following stacking sequence, TM/TM4/TM8/CeO2(111), while TM13 adopts two-dimensional structures at high energy structures. TM13 induces a change in the oxidation state of few Ce atoms (3 of 16) located in the topmost Ce layer from Ce(IV) (itinerant Ce f-states) to Ce(III) (localized Ce f-states). There is a charge flow from the TM atoms to the CeO2(111) surface, which can be explained by the electronegativity difference between the TM (Pd, Ag, Pt, Au) and O atoms, however, the charge is not uniformly distributed on the topmost O layer due to the pressure induced by the TM13 clusters on the underlying O ions, which yields a decrease in the ionic charge of the O ions located below the cluster and an increase in the remaining O ions. Due to the charge flow mainly from the TM8-layer to the topmost O-layer, the charge cannot flow from the Ce(IV) atoms to the O atoms with the same magnitude as in the clean CeO2(111) surface. Consequently, the effective cationic charge decreases mainly for the Ce atoms that have a bond with the O atoms not located below the cluster, and hence, those Ce atoms change their oxidation state from IV to III. This increases the size of the Ce(III) compared with the Ce(IV) cations, which builds-in a strain within the topmost Ce layer, and hence, also affecting the location of the Ce(III) cations and the structure of the TM13 clusters.

Behaviors of transmutation elements Re and Os and their effects on energetics and clustering of vacancy and self-interstitial atoms in W

NASA Astrophysics Data System (ADS)

Li, Yu-Hao; Zhou, Hong-Bo; Jin, Shuo; Zhang, Ying; Deng, Huiqiu; Lu, Guang-Hong

2017-04-01

We investigate the behaviors of rhenium (Re) and osmium (Os) and their interactions with point defects in tungsten (W) using a first-principles method. We show that Re atoms are energetically favorable to disperse separately in bulk W due to the Re-Re repulsive interaction. Despite the attractive interaction between Os atoms, there is still a large activation energy barrier of 1.10 eV at the critical number of 10 for the formation of Os clusters in bulk W based on the results of the total nucleation free energy change. Interestingly, the presence of vacancy can significantly reduce the total nucleation free energy change of Re/Os clusters, suggesting that vacancy can facilitate the nucleation of Re/Os in W. Re/Os in turn has an effect on the stability of the vacancy clusters (V n ) in W, especially for small vacancy clusters. A single Re/Os atom can raise the total binding energies of V2 and V3 obviously, thus enhancing their formation. Further, we demonstrate that there is a strong attractive interaction between Re/Os and self-interstitial atoms (SIAs). Re/Os could increase the diffusion barrier of SIAs and decrease their rotation barrier, while the interstitial-mediated path may be the optimal diffusion path of Re/Os in W. Consequently, the synergistic effect between Re/Os and point defects plays a key role in Re/Os precipitation and the evolution of defects in irradiated W.

Curved-line search algorithm for ab initio atomic structure relaxation

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

2017-09-01

Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al6Pd

PubMed Central

Pauling, Linus

1989-01-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al6Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 Å, b = 37.6 Å, and c = 33.24 Å, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction. Images PMID:16594092

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al(6)Pd.

PubMed

Pauling, L

1989-12-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al(6)Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 A, b = 37.6 A, and c = 33.24 A, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction.

Structural, electronic and vibrational properties of GexCy (x+y=2-5) nanoclusters: A B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Goswami, Sohini; Saha, Sushmita; Yadav, R. K.

2015-11-01

An ab-initio study of the stability, structural and electronic properties has been made for 84 germanium carbide nanoclusters, GexCy (x+y=2-5). The configuration possessing the maximum value of final binding energy (FBE), among the various configurations corresponding to a fixed x+y=n value, is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize fully the geometries of the nanoclusters. The binding energies (BE), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps have been obtained for all the clusters and the bond lengths have been reported for the most stable clusters. We have considered the zero point energy (ZPE) corrections. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have also been investigated for the most stable structures. The configurations containing the carbon atoms in majority are seen to be the most stable structures. The strong C-C bond has important role in stabilizing the clusters. For the clusters containing one germanium atom and all the other as carbon atoms, the BE increases monotonically with the number of the carbon atoms. The HOMO-LUMO gap, IPs and EAs fluctuates with increase in the number of atoms. The nanoclusters containing even number of carbon atoms have large HOMO-LUMO gaps and IPs, whereas the nanoclusters containing even number of carbon atoms have small EAs. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA). The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in the experiments.

Density functional theory and surface reactivity study of bimetallic AgnYm (n+m = 10) clusters

NASA Astrophysics Data System (ADS)

Hussain, Riaz; Hussain, Abdullah Ijaz; Chatha, Shahzad Ali Shahid; Hussain, Riaz; Hanif, Usman; Ayub, Khurshid

2018-06-01

Density functional theory calculations have been performed on pure silver (Agn), yttrium (Ym) and bimetallic silver yttrium clusters AgnYm (n + m = 2-10) for reactivity descriptors in order to realize sites for nucleophilic and electrophilic attack. The reactivity descriptors of the clusters, studied as a function of cluster size and shape, reveal the presence of different type of reactive sites in a cluster. The size and shape of the pure silver, yttrium and bimetallic silver yttrium cluster (n = 2-10) strongly influences the number and position of active sites for an electrophilic and/or nucleophilic attack. The trends of reactivities through reactivity descriptors are confirmed through comparison with experimental data for CO binding with silver clusters. Moreover, the adsorption of CO on bimetallic silver yttrium clusters is also evaluated. The trends of binding energies support the reactivity descriptors values. Doping of pure cluster with the other element also influence the hardness, softness and chemical reactivity of the clusters. The softness increases as we increase the number of silver atoms in the cluster, whereas the hardness decreases. The chemical reactivity increases with silver doping whereas it decreases by increasing yttrium concentration. Silver atoms are nucleophilic in small clusters but changed to electrophilic in large clusters.

Probing the Structures and Electronic Properties of Dual-Phosphorus-Doped Gold Cluster Anions (AunP-2, n = 1–8): A Density functional Theory Investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Kang-Ming; Huang, Teng; Liu, Yi-Rong

2015-07-29

The geometries of gold clusters doped with two phosphorus atoms, (AunP-2, n = 1–8) were investigated using density functional theory (DFT) methods. Various two-dimensional (2D) and three-dimensional (3D) structures of the doped clusters were studied. The results indicate that the structures of dual-phosphorus-doped gold clusters exhibit large differences from those of pure gold clusters with small cluster sizes. In our study, as for Au6P-2, two cis–trans isomers were found. The global minimum of Au8P-2 presents a similar configuration to that of Au-20, a pyramid-shaped unit, and the potential novel optical and catalytic properties of this structure warrant further attention. Themore » higher stability of AunP-2 clusters relative to Au-n+2 (n = 1–8) clusters was verified based on various energy parameters, and the results indicate that the phosphorus atom can improve the stabilities of the gold clusters. We then explored the evolutionary path of (n = 1–8) clusters. We found that AunP-2 clusters exhibit the 2D–3D structural transition at n = 6, which is much clearer and faster than that of pure gold clusters and single-phosphorus-doped clusters. The electronic properties of AunP-2 (n = 1–8) were then investigated. The photoelectron spectra provide additional fundamental information on the structures and molecular orbitals shed light on the evolution of AunP-2 (n = 1–8). Natural bond orbital (NBO) described the charge distribution in stabilizing structures and revealed the strong relativistic effects of the gold atoms.« less

Single Platinum Atoms Electrocatalysts: Oxygen Reduction and Hydrogen Oxidation Reactions

DOE PAGES

Vukmirovic, Miomir B.; Teeluck, Krishani M.; Liu, Ping; ...

2017-08-08

We prepared atomically dispersed catalyst consisting of Pt atoms arranged in a c(2 × 2) array on RuO2(110) substrate. A large interatomic distance of Pt atoms in a c(2 × 2) phase precludes the reactants to interact with more than one Pt atoms. A strong bond of Pt atoms with RuO2 prevents agglomeration of Pt atoms to form 2D-islands or 3D-clusters. The activities of single Pt atom catalyst for the oxygen reduction and hydrogen oxidation reactions were determined and compared with those of bulk Pt. It has lower catalytic activity for the oxygen reduction reaction and similar activity for hydrogenmore » oxidation reaction compared to Pt(111). This was explained by a large calculated up-shift of the dband center of Pt atoms and larger Pt-Pt interatomic distance than that of Pt(111). Our information is of considerable interest for further development of electrocatalysis.« less

Creating fractional quantum Hall states with atomic clusters using light-assisted insertion of angular momentum

NASA Astrophysics Data System (ADS)

Zhang, Junyi; Beugnon, Jerome; Nascimbene, Sylvain

We describe a protocol to prepare clusters of ultracold bosonic atoms in strongly interacting states reminiscent of fractional quantum Hall states. Our scheme consists in injecting a controlled amount of angular momentum to an atomic gas using Raman transitions carrying orbital angular momentum. By injecting one unit of angular momentum per atom, one realizes a single-vortex state, which is well described by mean-field theory for large enough particle numbers. We also present schemes to realize fractional quantum Hall states, namely, the bosonic Laughlin and Moore-Read states. We investigate the requirements for adiabatic nucleation of such topological states, in particular comparing linear Landau-Zener ramps and arbitrary ramps obtained from optimized control methods. We also show that this protocol requires excellent control over the isotropic character of the trapping potential. ERC-Synergy Grant UQUAM, ANR-10-IDEX-0001-02, DIM NanoK Atocirc project.

Nature's polyoxometalate chemistry: X-ray structure of the Mo storage protein loaded with discrete polynuclear Mo-O clusters.

PubMed

Kowalewski, Björn; Poppe, Juliane; Demmer, Ulrike; Warkentin, Eberhard; Dierks, Thomas; Ermler, Ulrich; Schneider, Klaus

2012-06-13

Some N(2)-fixing bacteria prolong the functionality of nitrogenase in molybdenum starvation by a special Mo storage protein (MoSto) that can store more than 100 Mo atoms. The presented 1.6 Å X-ray structure of MoSto from Azotobacter vinelandii reveals various discrete polyoxomolybdate clusters, three covalently and three noncovalently bound Mo(8), three Mo(5-7), and one Mo(3) clusters, and several low occupied, so far undefinable clusters, which are embedded in specific pockets inside a locked cage-shaped (αβ)(3) protein complex. The structurally identical Mo(8) clusters (three layers of two, four, and two MoO(n) octahedra) are distinguishable from the [Mo(8)O(26)](4-) cluster formed in acidic solutions by two displaced MoO(n) octahedra implicating three kinetically labile terminal ligands. Stabilization in the covalent Mo(8) cluster is achieved by Mo bonding to Hisα156-N(ε2) and Gluα129-O(ε1). The absence of covalent protein interactions in the noncovalent Mo(8) cluster is compensated by a more extended hydrogen-bond network involving three pronounced histidines. One displaced MoO(n) octahedron might serve as nucleation site for an inhomogeneous Mo(5-7) cluster largely surrounded by bulk solvent. In the Mo(3) cluster located on the 3-fold axis, the three accurately positioned His140-N(ε2) atoms of the α subunits coordinate to the Mo atoms. The formed polyoxomolybdate clusters of MoSto, not detectable in bulk solvent, are the result of an interplay between self- and protein-driven assembly processes that unite inorganic supramolecular and protein chemistry in a host-guest system. Template, nucleation/protection, and catalyst functions of the polypeptide as well as perspectives for designing new clusters are discussed.

Melting and Freezing of Metal Clusters

NASA Astrophysics Data System (ADS)

Aguado, Andrés; Jarrold, Martin F.

2011-05-01

Recent developments allow heat capacities to be measured for size-selected clusters isolated in the gas phase. For clusters with tens to hundreds of atoms, the heat capacities determined as a function of temperature usually have a single peak attributed to a melting transition. The melting temperatures and latent heats show large size-dependent fluctuations. In some cases, the melting temperatures change by hundreds of degrees with the addition of a single atom. Theory has played a critical role in understanding the origin of the size-dependent fluctuations, and in understanding the properties of the liquid-like and solid-like states. In some cases, the heat capacities have extra features (an additional peak or a dip) that reveal a more complex behavior than simple melting. In this article we provide a description of the methods used to measure the heat capacities and provide an overview of the experimental and theoretical results obtained for sodium and aluminum clusters.

Orbital magnetism: pros and cons for enhancing the cluster magnetism.

PubMed

Andriotis, Antonis N; Menon, Madhu

2004-07-09

The discrepancy seen in the experimental and theoretical results on the magnetic moment of a small magnetic cluster has been attributed to the contribution arising from orbital magnetism. In this Letter we show that the magnetic states with large orbital magnetic moment are not always energetically favorable; they could, however, be realizable by coating the cluster or deposing it on appropriate substrates. More importantly, our work shows that the crucial factors that determine the cluster magnetism are found to be the intrinsic, and consequently, the extrinsic properties of the constituent atoms of the cluster.

Displacement cascades and defects annealing in tungsten, Part I: Defect database from molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Nandipati, Giridhar; Roche, Kenneth J.

Molecular dynamics simulations have been used to generate a comprehensive database of surviving defects due to displacement cascades in bulk tungsten. Twenty-one data points of primary knock-on atom (PKA) energies ranging from 100 eV (sub-threshold energy) to 100 keV (~780 × Ed, where Ed = 128 eV is the average displacement threshold energy) have been completed at 300 K, 1025 K and 2050 K. Within this range of PKA energies, two regimes of power-law energy-dependence of the defect production are observed. A distinct power-law exponent characterizes the number of Frenkel pairs produced within each regime. The two regimes intersect atmore » a transition energy which occurs at approximately 250 × Ed. The transition energy also marks the onset of the formation of large self-interstitial atom (SIA) clusters (size 14 or more). The observed defect clustering behavior is asymmetric, with SIA clustering increasing with temperature, while the vacancy clustering decreases. This asymmetry increases with temperature such that at 2050 K (~0.5 Tm) practically no large vacancy clusters are formed, meanwhile large SIA clusters appear in all simulations. The implication of such asymmetry on the long-term defect survival and damage accumulation is discussed. In addition, <100> {110} SIA loops are observed to form directly in the highest energy cascades, while vacancy <100> loops are observed to form at the lowest temperature and highest PKA energies, although the appearance of both the vacancy and SIA loops with Burgers vector of <100> type is relatively rare.« less

Experimental and theoretical study on Raman spectra of magnesium fluoride clusters and solids.

PubMed

Neelamraju, S; Bach, A; Schön, J C; Fischer, D; Jansen, M

2012-11-21

In this study, the Raman and IR spectra of a large number of isomers of MgF(2) clusters and of possible bulk polymorphs of MgF(2) are calculated and compared with experimental data observed using a low-temperature atom beam deposition. The bulk polymorphs were taken from earlier work, while the cluster modifications for the neutral (MgF(2))(n) (n = 1-10) clusters and charged clusters (up to the trimer anion and cation, (Mg(3)F(7))(-) and (Mg(3)F(5))(+), respectively) are determined in the present work by global energy landscape explorations using simulated annealing. These theoretical calculations are complemented by an experimental study on both the vapor phase and the deposited films of MgF(2), which are generated in a low-temperature atom beam deposition setup for the synthesis of MgF(2) bulk phases. The MgF(2) vapor and film are characterized via Raman spectroscopy of the MgF(2) gas phase species embedded in an Ar-matrix and of the MgF(2)-films deposited onto a cooled substrate, respectively. We find that, in the vapor phase, there are monomers and dimers and charged species to be present in our experimental setup. Furthermore, the results suggest that in the amorphous bulk MgF(2), rutile-like domains are present and MgF(2) clusters similar to those in the matrix. Finally, peaks at about 800 cm(-1), which are in the same range as the A(g) modes of clusters with dangling fluorine atoms connected to three-coordinated Mg atoms, indicate that such dangling bonds are also present in amorphous MgF(2).

Oriented xenon hydride molecules in the gas phase

NASA Astrophysics Data System (ADS)

Buck, Udo; Fárník, Michal

The production of the xenon hydride molecules HXeX with X = I and Cl in the gas phase is reviewed. These molecules are generated by the photolysis of the hydrogen halide HI and HCl molecules on the surface of large xenon Xen clusters. Molecular dynamics simulations show that the flexible H atoms react with the heavy XeX moiety and form the desired molecules with nearly no rotational motion. They are observed by photodissociation with subsequent detection of the kinetic energy of the H atom fragment. During the generating process, the cluster starts to evaporate and the hydride molecule is left essentially free. For further discrimination against the H atom fragments from HX, the HXeX molecules are oriented in a combined pulsed laser field and a weak electrostatic field. The three topics which represent the background of our experiments are briefly reviewed: the nature and generation of rare gas hydrides, the alignment and orientation of molecules in electric fields, and the photodissociation of selected molecules in rare gas clusters. The conditions for detecting them in the gas phase are discussed. This is the trade off between the stability, which requires high electron affinity, and the conditions for orientation, which necessitate large polarizability anisotropies and dipole moments. Finally the prospects of detecting other classes of molecules are discussed.

Ab initio molecular dynamics simulations of short-range order in Zr 50Cu 45Al 5 and Cu 50Zr 45Al 5 metallic glasses

DOE PAGES

Huang, Yuxiang; Huang, Li; Wang, C. Z.; ...

2016-02-01

Comparative analysis between Zr-rich Zr 50Cu 45Al 5 and Cu-rich Cu 50Zr 45Al 5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr 50Cu 45Al 5 and Cu 50Zr 45Al 5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0 > is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2 > and , are prominent. And the < 0,2,8,2 > polyhedra in Cu 50Zr 45Al 5 MG mainly originate from Al-centered clusters, while the < 0,0,12,0 > in Zr 50Cu 45Al 5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. Lastly, the relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr 50Cu 45Al 5.« less

Ab initio molecular dynamics simulations of short-range order in Zr50Cu45Al5 and Cu50Zr45Al5 metallic glasses

NASA Astrophysics Data System (ADS)

Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

2016-03-01

Comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0> is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2> and < 0,2,8,1> , are prominent. And the < 0,2,8,2> polyhedra in Cu50Zr45Al5 MG mainly originate from Al-centered clusters, while the < 0,0,12,0> in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. The relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.

Super-reduced polyoxometalates: excellent molecular cluster battery components and semipermeable molecular capacitors.

PubMed

Nishimoto, Yoshio; Yokogawa, Daisuke; Yoshikawa, Hirofumi; Awaga, Kunio; Irle, Stephan

2014-06-25

Theoretical investigations are presented on the molecular and electronic structure changes that occur as α-Keggin-type polyoxometalate (POM(3-)) clusters [PM12O40](3-) (M = Mo, W) are converted toward their super-reduced POM(27-) state during the discharging process in lithium-based molecular cluster batteries. Density functional theory was employed in geometry optimization, and first-principles molecular dynamics simulations were used to explore local minima on the potential energy surface of neutral POM clusters adorned with randomly placed Li atoms as electron donors around the cluster surface. On the basis of structural, electron density, and molecular orbital studies, we present evidence that the super-reduction is accompanied by metal-metal bond formation, beginning from the 12th to 14th excess electron transferred to the cluster. Afterward, the number of metal-metal bonds increases nearly linearly with the number of additionally transferred excess electrons. In α-Keggin-type POMs, metal triangles are a prominently emerging structural feature. The origin of the metal triangle formation during super-reduction stems from the formation of characteristic three-center two-electron bonds in triangular metal atom sites, created under preservation of the POM skeleton via "squeezing out" of oxygen atoms bridging two metal atoms when the underlying metal atoms form covalent bonds. The driving force for this unusual geometrical and electronic structure change is a local Jahn-Teller distortion at individual transition-metal octahedral sites, where the triply degenerate t2 d orbitals become partially filled during reduction and gain energy by distortion of the octahedron in such a way that metal-metal bonds are formed. The bonding orbitals show strong contributions from mixing with metal-oxygen antibonding orbitals, thereby "shuffling away" excess electrons from the cluster center to the outside of the cage. The high density of negatively charged yet largely separated oxygen atoms on the surface of the super-reduced POM(27-) polyanion allows the huge Coulombic repulsion due to the presence of the excess electrons to be counterbalanced by the presence of Li countercations, which partially penetrate into the outer oxygen shell. This "semiporous molecular capacitor" structure is likely the reason for the effective electron uptake in POMs.

Stability chart of small mixed 4He-3He clusters

NASA Astrophysics Data System (ADS)

Guardiola, R.; Navarro, J.

2003-11-01

A stability chart of mixed 4He and 3He clusters has been obtained by means of the diffusion Monte Carlo method, using both the Aziz HFD-B and the Tang-Toennies-Yiu atom-atom interaction. The investigated clusters contain up to eight 4He atoms and up to 20 3He atoms. One single 4He binds 20 3He atoms, and two 4He bind 1, 2, 8, and more than 14 3He atoms. All clusters with three or more 4He atoms are bound, although the combinations 4He33He9,10,11 and 4He34He9 are metastable. Clusters with 2, 8, and 20 3He atoms are particularly stable and define magic 3He numbers.

Atomic clusters and atomic surfaces in icosahedral quasicrystals.

PubMed

Quiquandon, Marianne; Portier, Richard; Gratias, Denis

2014-05-01

This paper presents the basic tools commonly used to describe the atomic structures of quasicrystals with a specific focus on the icosahedral phases. After a brief recall of the main properties of quasiperiodic objects, two simple physical rules are discussed that lead one to eventually obtain a surprisingly small number of atomic structures as ideal quasiperiodic models for real quasicrystals. This is due to the fact that the atomic surfaces (ASs) used to describe all known icosahedral phases are located on high-symmetry special points in six-dimensional space. The first rule is maximizing the density using simple polyhedral ASs that leads to two possible sets of ASs according to the value of the six-dimensional lattice parameter A between 0.63 and 0.79 nm. The second rule is maximizing the number of complete orbits of high symmetry to construct as large as possible atomic clusters similar to those observed in complex intermetallic structures and approximant phases. The practical use of these two rules together is demonstrated on two typical examples of icosahedral phases, i-AlMnSi and i-CdRE (RE = Gd, Ho, Tm).

Formation of Exotic Networks of Water Clusters in Helium Droplets Facilitated by the Presence of Neon Atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Douberly, Gary E.; Miller, Roger E.; Xantheas, Sotiris S.

Water clusters are formed in helium droplets via the sequential capture of monomers. One or two neon atoms are added to each droplet prior to the addition of water. The infrared spectrum of the droplet ensemble reveals several signatures of polar, water tetramer clusters having dipole moments between 2D and 3D. Comparison with ab initio computations supports the assignment of the cluster networks to noncyclic “3+1” clusters, which are ~5.3 kcal/mol less stable than the global minimum nonpolar cyclic tetramer. The (H2O)3Ne + H2O ring insertion barrier is sufficiently large, such that evaporative helium cooling is capable of kinetically quenchingmore » the nonequilibrium tetramer system prior to its rearrangement to the lower energy cyclic species. To this end, the reported process results in the formation of exotic water cluster networks that are either higher in energy than the most stable gas-phase analogs or not even stable in the gas phase.« less

Structure and formation of highly luminescent protein-stabilized gold clusters† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc05086k

PubMed Central

Chevrier, D. M.; Thanthirige, V. D.; Luo, Z.; Driscoll, S.; Cho, P.; MacDonald, M. A.; Yao, Q.; Guda, R.; Xie, J.; Johnson, E. R.; Chatt, A.; Zheng, N.

2018-01-01

Highly luminescent gold clusters simultaneously synthesized and stabilized by protein molecules represent a remarkable category of nanoscale materials with promising applications in bionanotechnology as sensors. Nevertheless, the atomic structure and luminescence mechanism of these gold clusters are still unknown after several years of developments. Herein, we report findings on the structure, luminescence and biomolecular self-assembly of gold clusters stabilized by the large globular protein, bovine serum albumin. We highlight the surprising identification of interlocked gold-thiolate rings as the main gold structural unit. Importantly, such gold clusters are in a rigidified state within the protein scaffold, offering an explanation for their highly luminescent character. Combined free-standing cluster synthesis (without protecting protein scaffold) with rigidifying and un-rigidifying experiments, were designed to further verify the luminescence mechanism and gold atomic structure within the protein. Finally, the biomolecular self-assembly process of the protein-stabilized gold clusters was elucidated by time-dependent X-ray absorption spectroscopy measurements and density functional theory calculations. PMID:29732064

Geometrical, electronic, and magnetic properties of CunFe (n=1-12) clusters: A density functional study

NASA Astrophysics Data System (ADS)

Ling, Wang; Dong, Die; Shi-Jian, Wang; Zheng-Quan, Zhao

2015-01-01

The geometrical, electronic, and magnetic properties of small CunFe (n=1-12) clusters have been investigated by using density functional method B3LYP and LanL2DZ basis set. The structural search reveals that Fe atoms in low-energy CunFe isomers tend to occupy the position with the maximum coordination number. The ground state CunFe clusters possess planar structure for n=2-5 and three-dimensional (3D) structure for n=6-12. The electronic properties of CunFe clusters are analyzed through the averaged binding energy, the second-order energy difference and HOMO-LUMO energy gap. It is found that the magic numbers of stability are 1, 3, 7 and 9 for the ground state CunFe clusters. The energy gap of Fe-encapsulated cage clusters is smaller than that of other configurations. The Cu5Fe and Cu7Fe clusters have a very large energy gap (>2.4 eV). The vertical ionization potential (VIP), electron affinity (EA) and photoelectron spectra are also calculated and simulated theoretically for all the ground-state clusters. The magnetic moment analyses for the ground-state CunFe clusters show that Fe atom can enhance the magnetic moment of the host cluster and carries most of the total magnetic moment.

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

DOE PAGES

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

2018-04-24

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-Molecular Dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients; we use this approach to examine atomic condensation onto 6-56 atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity ( v) between atom and cluster andmore » the initial impact parameter ( b). In all cases there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms, and for 14 atom and 28 atom Mg clusters, as cluster equilibration temperature increases the condensation rate coefficient drops to values below the hard sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (> 1000 m s -1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). In conclusion, the presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.« less

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-Molecular Dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients; we use this approach to examine atomic condensation onto 6-56 atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity ( v) between atom and cluster andmore » the initial impact parameter ( b). In all cases there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms, and for 14 atom and 28 atom Mg clusters, as cluster equilibration temperature increases the condensation rate coefficient drops to values below the hard sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (> 1000 m s -1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). In conclusion, the presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.« less

Gd@Au15: A magic magnetic gold cluster for cancer therapy and bioimaging

NASA Astrophysics Data System (ADS)

Yadav, Brahm Deo; Kumar, Vijay

2010-09-01

We report from ab initio calculations a magic magnetic cage cluster of gold, Gd@Au15, obtained by doping of a Gd atom in gold clusters. It has a highest occupied molecular orbital-lowest unoccupied molecular orbital gap of 1.31 eV within the generalized gradient approximation that makes it a potential candidate for cancer therapy with an additional attractive feature that its large magnetic moment of 7 μB could be beneficial for magnetic resonance imaging.

Irradiation-induced microchemical changes in highly irradiated 316 stainless steel

NASA Astrophysics Data System (ADS)

Fujii, K.; Fukuya, K.

2016-02-01

Cold-worked 316 stainless steel specimens irradiated to 74 dpa in a pressurized water reactor (PWR) were analyzed by atom probe tomography (APT) to extend knowledge of solute clusters and segregation at higher doses. The analyses confirmed that those clusters mainly enriched in Ni-Si or Ni-Si-Mn were formed at high number density. The clusters were divided into three types based on their size and Mn content; small Ni-Si clusters (3-4 nm in diameter), and large Ni-Si and Ni-Si-Mn clusters (8-10 nm in diameter). The total cluster number density was 7.7 × 1023 m-3. The fraction of large clusters was almost 1/10 of the total density. The average composition (in at%) for small clusters was: Fe, 54; Cr, 12; Mn, 1; Ni, 22; Si, 11; Mo, 1, and for large clusters it was: Fe, 44; Cr, 9; Mn, 2; Ni, 29; Si, 14; Mo,1. It was likely that some of the Ni-Si clusters correspond to γ‧ phase precipitates while the Ni-Si-Mn clusters were precursors of G phase precipitates. The APT analyses at grain boundaries confirmed enrichment of Ni, Si, P and Cu and depletion of Fe, Cr, Mo and Mn. The segregation behavior was consistent with previous knowledge of radiation induced segregation.

Structures of small Pd Pt bimetallic clusters by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Cheng, Daojian; Huang, Shiping; Wang, Wenchuan

2006-11-01

Segregation phenomena of Pd-Pt bimetallic clusters with icosahedral and decahedral structures are investigated by using Monte Carlo method based on the second-moment approximation of the tight-binding (TB-SMA) potentials. The simulation results indicate that the Pd atoms generally lie on the surface of the smaller clusters. The three-shell onion-like structures are observed in 55-atom Pd-Pt bimetallic clusters, in which a single Pd atom is located in the center, and the Pt atoms are in the middle shell, while the Pd atoms are enriched on the surface. With the increase of Pd mole fraction in 55-atom Pd-Pt bimetallic clusters, the Pd atoms occupy the vertices of clusters first, then edge and center sites, and finally the interior shell. It is noticed that some decahedral structures can be transformed into the icosahedron-like structure at 300 and 500 K. Comparisons are made with previous experiments and theoretical studies of Pd-Pt bimetallic clusters.

Mechanical gate control for atom-by-atom cluster assembly with scanning probe microscopy.

PubMed

Sugimoto, Yoshiaki; Yurtsever, Ayhan; Hirayama, Naoki; Abe, Masayuki; Morita, Seizo

2014-07-11

Nanoclusters supported on substrates are of great importance in physics and chemistry as well as in technical applications, such as single-electron transistors and nanocatalysts. The properties of nanoclusters differ significantly from those of either the constituent atoms or the bulk solid, and are highly sensitive to size and chemical composition. Here we propose a novel atom gating technique to assemble various atom clusters composed of a defined number of atoms at room temperature. The present gating operation is based on the transfer of single diffusing atoms among nanospaces governed by gates, which can be opened in response to the chemical interaction force with a scanning probe microscope tip. This method provides an alternative way to create pre-designed atom clusters with different chemical compositions and to evaluate their chemical stabilities, thus enabling investigation into the influence that a single dopant atom incorporated into the host clusters has on a given cluster stability.

Structures of 38-atom gold-platinum nanoalloy clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atomsmore » are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.« less

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations.

PubMed

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J

2018-04-28

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard-sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-molecular dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients. We use this approach to examine atomic condensation onto 6-56-atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity (v) between atom and cluster and the initial impact parameter (b). In all cases, there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard-sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms and for 14- and 28-atom Mg clusters, as cluster equilibration temperature increases, the condensation rate coefficient drops to values below the hard-sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (>1000 m s -1 ) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). The presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

NASA Astrophysics Data System (ADS)

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

2018-04-01

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard-sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-molecular dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients. We use this approach to examine atomic condensation onto 6-56-atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity (v) between atom and cluster and the initial impact parameter (b). In all cases, there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard-sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms and for 14- and 28-atom Mg clusters, as cluster equilibration temperature increases, the condensation rate coefficient drops to values below the hard-sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (>1000 m s-1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). The presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.

Multiscale structural changes of atomic order in severely deformed industrial aluminum

NASA Astrophysics Data System (ADS)

Samoilenko, Z. A.; Ivakhnenko, N. N.; Pushenko, E. I.; Pashinskaya, E. G.; Varyukhin, V. N.

2016-02-01

The regularities of multiscale structural changes in the atomic order of the aluminum alloy AD-1 after a severe cold plastic deformation by conventional rolling in smooth rolls or in rolls with relief recesses favorable for shear deformation have been investigated. It has been found that there are four types of structural fractions that differ in scale and perfection of atomic order: crystallographic planes with a long-range order; nanoscale fragments of the planes ( D = 100-300 Å) with an incipient long-range order; smaller groups of atoms ( D = 20-30 Å) of amorphized structure; and the least ordered structural fraction of intercluster medium, keeping only a short-range atomic order (2-3 interatomic distances, 10 Å). The presence of diffuse halo bands in the region of intense Debye lines indicates phase transitions of the order → disorder type with the formation of one to three groups of amorphous clusters with the dominance, in the nanometer scale, of the atomic order characteristic of the family of planes (111), (220), and (311) of crystalline aluminum. We have found a dynamic phase transition with the changing crystallographic order of aluminum, with the matrix structure of a face-centered cubic (FCC) lattice, in the form of nanosized local groups of atoms, that is, the deformation clusters of aluminum with a simple cubic K6 lattice. In the case of conventional rolling, the development of large clusters 50-500 Å in size is observed; however, in the use of rolls with relief recesses, the difference in the sizes of the clusters is one half as much: 50-250 Å. Based on the analysis of the integrated intensity of incoherent X-ray scattering by the samples, we have elucidated the nature of the lowest measured density for the sample subjected to conventional rolling, which consists in the volume concentration of disorderly arranged atoms, the highest of the compared structures, which indicates the formation therein of the greatest amount of fluctuation "voids."

Molecular Dynamics Studies of Thermal Induced Chemistry in TATB

NASA Astrophysics Data System (ADS)

Quenneville, Jason; Germann, Timothy

2007-06-01

A reactive force field (ReaxFF^2) is used with molecular dynamics to probe the chemistry induced by intense heating (accelerated `cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 800-atom, simulations, we will show the reaction rate as a function of temperature and density as well as the time evolution of reaction products. A larger simulation (with 14,000 atoms) will illustrate the effect of system size on both carbon clustering and reaction rate. Insight into the mechanisms of product formation will be given, as well as the chemical structure (graphitic or diamond-like) of the carbon clusters obtained. ^2 A. C. T. Van Duin, et al, J. Phys. Chem. A, 1005, 9396 (2001).

Theoretical characterization on the size-dependent electron and hole trapping activity of chloride-passivated CdSe nanoclusters

NASA Astrophysics Data System (ADS)

Cui, Yingqi; Cui, Xianhui; Zhang, Li; Xie, Yujuan; Yang, Mingli

2018-04-01

Ligand passivation is often used to suppress the surface trap states of semiconductor quantum dots (QDs) for their continuous photoluminescence output. The suppression process is related to the electrophilic/nucleophilic activity of surface atoms that varies with the structure and size of QD and the electron donating/accepting nature of ligand. Based on first-principles-based descriptors and cluster models, the electrophilic/nucleophilic activities of bare and chloride-coated CdSe clusters were studied to reveal the suppression mechanism of Cl-passivated QDs and compared to experimental observations. The surface atoms of bare clusters have higher activity than inner atoms and their activity decreases with cluster size. In the ligand-coated clusters, the Cd atom remains as the electrophilic site, while the nucleophilic site of Se atoms is replaced by Cl atoms. The activities of Cd and Cl atoms in the coated clusters are, however, remarkably weaker than those in bare clusters. Cluster size, dangling atoms, ligand coverage, electronegativity of ligand atoms, and solvent (water) were found to have considerable influence on the activity of surface atoms. The suppression of surface trap states in Cl-passivated QDs was attributed to the reduction of electrophilic/nucleophilic activity of Cd/Se/Cl atoms. Both saturation to under-coordinated surface atoms and proper selection for the electron donating/accepting strength of ligands are crucial for eliminating the charge carrier traps. Our calculations predicted a similar suppressing effect of chloride ligands with experiments and provided a simple but effective approach to assess the charge carrier trapping behaviors of semiconductor QDs.

Melting of size-selected gallium clusters with 60-183 atoms.

PubMed

Pyfer, Katheryne L; Kafader, Jared O; Yalamanchali, Anirudh; Jarrold, Martin F

2014-07-10

Heat capacities have been measured as a function of temperature for size-selected gallium cluster cations with between 60 and 183 atoms. Almost all clusters studied show a single peak in the heat capacity that is attributed to a melting transition. The peaks can be fit by a two-state model incorporating only fully solid-like and fully liquid-like species, and hence no partially melted intermediates. The exceptions are Ga90(+), which does not show a peak, and Ga80(+) and Ga81(+), which show two peaks. For the clusters with two peaks, the lower temperature peak is attributed to a structural transition. The melting temperatures for clusters with less than 50 atoms have previously been shown to be hundreds of degrees above the bulk melting point. For clusters with more than 60 atoms the melting temperatures decrease, approaching the bulk value (303 K) at around 95 atoms, and then show several small upward excursions with increasing cluster size. A plot of the latent heat against the entropy change for melting reveals two groups of clusters: the latent heats and entropy changes for clusters with less than 94 atoms are distinct from those for clusters with more than 93 atoms. This observation suggests that a significant change in the nature of the bonding or the structure of the clusters occurs at 93-94 atoms. Even though the melting temperatures are close to the bulk value for the larger clusters studied here, the latent heats and entropies of melting are still far from the bulk values.

Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.

PubMed

Šipr, O; Ebert, H; Minár, J

2015-02-11

A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.

Reactivity Control of Rhodium Cluster Ions by Alloying with Tantalum Atoms.

PubMed

Mafuné, Fumitaka; Tawaraya, Yuki; Kudoh, Satoshi

2016-02-18

Gas phase, bielement rhodium and tantalum clusters, RhnTam(+) (n + m = 6), were prepared by the double laser ablation of Rh and Ta rods in He carrier gas. The clusters were introduced into a reaction gas cell filled with nitric oxide (NO) diluted with He and were subjected to collisions with NO and He at room temperature. The product species were observed by mass spectrometry, demonstrating that the NO molecules were sequentially adsorbed on the RhnTam(+) clusters to form RhnTam(+)NxOx (x = 1, 2, 3, ...) species. In addition, oxide clusters, RhnTam(+)O2, were also observed, suggesting that the NO molecules were dissociatively adsorbed on the cluster, the N atoms migrated on the surface to form N2, and the N2 molecules were released from RhnTam(+)N2O2. The reactivity, leading to oxide formation, was composition dependent: oxide clusters were dominantly formed for the bielement clusters containing both Rh and Ta atoms, whereas such clusters were hardly formed for the single-element Rhn(+) and Tam(+) clusters. DFT calculations indicated that the Ta atoms induce dissociation of NO on the clusters by lowering the dissociation energy, whereas the Rh atoms enable release of N2 by lowering the binding energy of the N atoms on the clusters.

Hund’s rule in superatoms with transition metal impurities

PubMed Central

Medel, Victor M.; Reveles, Jose Ulises; Khanna, Shiv N.; Chauhan, Vikas; Sen, Prasenjit; Castleman, A. Welford

2011-01-01

The quantum states in metal clusters bunch into supershells with associated orbitals having shapes resembling those in atoms, giving rise to the concept that selected clusters could mimic the characteristics of atoms and be classified as superatoms. Unlike atoms, the superatom orbitals span over multiple atoms and the filling of orbitals does not usually exhibit Hund’s rule seen in atoms. Here, we demonstrate the possibility of enhancing exchange splitting in superatom shells via a composite cluster of a central transition metal and surrounding nearly free electron metal atoms. The transition metal d states hybridize with superatom D states and result in enhanced splitting between the majority and minority sets where the moment and the splitting can be controlled by the nature of the central atom. We demonstrate these findings through studies on TMMgn clusters where TM is a 3d atom. The clusters exhibit Hund’s filling, opening the pathway to superatoms with magnetic shells. PMID:21646542

Hund's rule in superatoms with transition metal impurities.

PubMed

Medel, Victor M; Reveles, Jose Ulises; Khanna, Shiv N; Chauhan, Vikas; Sen, Prasenjit; Castleman, A Welford

2011-06-21

The quantum states in metal clusters bunch into supershells with associated orbitals having shapes resembling those in atoms, giving rise to the concept that selected clusters could mimic the characteristics of atoms and be classified as superatoms. Unlike atoms, the superatom orbitals span over multiple atoms and the filling of orbitals does not usually exhibit Hund's rule seen in atoms. Here, we demonstrate the possibility of enhancing exchange splitting in superatom shells via a composite cluster of a central transition metal and surrounding nearly free electron metal atoms. The transition metal d states hybridize with superatom D states and result in enhanced splitting between the majority and minority sets where the moment and the splitting can be controlled by the nature of the central atom. We demonstrate these findings through studies on TMMg(n) clusters where TM is a 3d atom. The clusters exhibit Hund's filling, opening the pathway to superatoms with magnetic shells.

Paramagnetic Attraction of Impurity-Helium Solids

NASA Technical Reports Server (NTRS)

Bernard, E. P.; Boltnev, R. E.; Khmelenko, V. V.; Lee, D. M.

2003-01-01

Impurity-helium solids are formed when a mixture of impurity and helium gases enters a volume of superfluid helium. Typical choices of impurity gas are hydrogen deuteride, deuterium, nitrogen, neon and argon, or a mixture of these. These solids consist of individual impurity atoms and molecules as well as clusters of impurity atoms and molecules covered with layers of solidified helium. The clusters have an imperfect crystalline structure and diameters ranging up to 90 angstroms, depending somewhat on the choice of impurity. Immediately following formation the clusters aggregate into loosely connected porous solids that are submerged in and completely permeated by the liquid helium. Im-He solids are extremely effective at stabilizing high concentrations of free radicals, which can be introduced by applying a high power RF dis- charge to the impurity gas mixture just before it strikes the super fluid helium. Average concentrations of 10(exp 19) nitrogen atoms/cc and 5 x 10(exp 18) deuterium atoms/cc can be achieved this way. It shows a typical sample formed from a mixture of atomic and molecular hydrogen and deuterium. It shows typical sample formed from atomic and molecular nitrogen. Much of the stability of Im-He solids is attributed to their very large surface area to volume ratio and their permeation by super fluid helium. Heat resulting from a chance meeting and recombination of free radicals is quickly dissipated by the super fluid helium instead of thermally promoting the diffusion of other nearby free radicals.

Energetic ion bombardment of Ag surfaces by C60+ and Ga+ projectiles.

PubMed

Sun, Shixin; Szakal, Christopher; Winograd, Nicholas; Wucher, Andreas

2005-10-01

The ion bombardment-induced release of particles from a metal surface is investigated using energetic fullerene cluster ions as projectiles. The total sputter yield as well as partial yields of neutral and charged monomers and clusters leaving the surface are measured and compared with corresponding data obtained with atomic projectile ions of similar impact kinetic energy. It is found that all yields are enhanced by about one order of magnitude under bombardment with the C60+ cluster projectiles compared with Ga+ ions. In contrast, the electronic excitation processes determining the secondary ion formation probability are unaffected. The kinetic energy spectra of sputtered particles exhibit characteristic differences which reflect the largely different nature of the sputtering process for both types of projectiles. In particular, it is found that under C60+ impact (1) the energy spectrum of sputtered atoms peaks at significantly lower kinetic energies than for Ga+ bombardment and (2) the velocity spectra of monomers and dimers are virtually identical, a finding which is in pronounced contrast to all published data obtained for atomic projectiles. The experimental findings are in reasonable agreement with recent molecular dynamics simulations.

Photoionization of rare gas clusters

NASA Astrophysics Data System (ADS)

Zhang, Huaizhen

This thesis concentrates on the study of photoionization of van der Waals clusters with different cluster sizes. The goal of the experimental investigation is to understand the electronic structure of van der Waals clusters and the electronic dynamics. These studies are fundamental to understand the interaction between UV-X rays and clusters. The experiments were performed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The experimental method employs angle-resolved time-of-flight photoelectron spectrometry, one of the most powerful methods for probing the electronic structure of atoms, molecules, clusters and solids. The van der Waals cluster photoionization studies are focused on probing the evolution of the photoelectron angular distribution parameter as a function of photon energy and cluster size. The angular distribution has been known to be a sensitive probe of the electronic structure in atoms and molecules. However, it has not been used in the case of van der Waals clusters. We carried out outer-valence levels, inner-valence levels and core-levels cluster photoionization experiments. Specifically, this work reports on the first quantitative measurements of the angular distribution parameters of rare gas clusters as a function of average cluster sizes. Our findings for xenon clusters is that the overall photon-energy-dependent behavior of the photoelectrons from the clusters is very similar to that of the corresponding free atoms. However, distinct differences in the angular distribution point at cluster-size-dependent effects were found. For krypton clusters, in the photon energy range where atomic photoelectrons have a high angular anisotropy, our measurements show considerably more isotropic angular distributions for the cluster photoelectrons, especially right above the 3d and 4p thresholds. For the valence electrons, a surprising difference between the two spin-orbit components was found. For argon clusters, we found that the angular distribution parameter values of the two-spin-orbit components from Ar 2p clusters are slightly different. When comparing the beta values for Ar between atoms and clusters, we found different results between Ar 3s atoms and clusters, and between Ar 3p atoms and clusters. Argon cluster resonance from surface and bulk were also measured. Furthermore, the angular distribution parameters of Ar cluster photoelectrons and Ar atom photoelectrons in the 3s → np ionization region were obtained.

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.

PubMed

Nawrocki, Grzegorz; Wang, Po-Hung; Yu, Isseki; Sugita, Yuji; Feig, Michael

2017-12-14

For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. Although internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.

Atomically precise cluster catalysis towards quantum controlled catalysts

PubMed Central

Watanabe, Yoshihide

2014-01-01

Catalysis of atomically precise clusters supported on a substrate is reviewed in relation to the type of reactions. The catalytic activity of supported clusters has generally been discussed in terms of electronic structure. Several lines of evidence have indicated that the electronic structure of clusters and the geometry of clusters on a support, including the accompanying cluster-support interaction, are strongly correlated with catalytic activity. The electronic states of small clusters would be easily affected by cluster–support interactions. Several studies have suggested that it is possible to tune the electronic structure through atomic control of the cluster size. It is promising to tune not only the number of cluster atoms, but also the hybridization between the electronic states of the adsorbed reactant molecules and clusters in order to realize a quantum-controlled catalyst. PMID:27877723

Central Doping of a Foreign Atom into the Silver Cluster for Catalytic Conversion of CO2 toward C-C Bond Formation.

PubMed

Liu, Yuanyuan; Chai, Xiaoqi; Cai, Xiao; Chen, Mingyang; Jin, Rongchao; Ding, Weiping; Zhu, Yan

2018-06-19

Clusters with an exact number of atoms are of particular research interest in catalysis. Their catalytic behaviors can be potentially altered with the addition or removal of a single atom. Herein we explore the effects of the single-foreign-atom (Au, Pd and Pt) doping into the core of an Ag cluster with 25-atoms on the catalytic properties, where the foreign atom is protected by 24 Ag atoms (i.e., Au@Ag24, Pd@Ag24, and Pt@Ag24). The central doping of a single atom into the Ag25 cluster is found to have a substantial influence on the catalytic performance in the carboxylation reaction of CO2 with terminal alkyne through C-C bond formation to produce propiolic acid. Our studies reveal that the catalytic properties of the cluster catalysts can be dramatically changed with the subtle alteration by a single atom away from the active sites. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiple valence superatoms.

PubMed

Reveles, J U; Khanna, S N; Roach, P J; Castleman, A W

2006-12-05

We recently demonstrated that, in gas phase clusters containing aluminum and iodine atoms, an Al(13) cluster behaves like a halogen atom, whereas an Al(14) cluster exhibits properties analogous to an alkaline earth atom. These observations, together with our findings that Al(13)(-) is inert like a rare gas atom, have reinforced the idea that chosen clusters can exhibit chemical behaviors reminiscent of atoms in the periodic table, offering the exciting prospect of a new dimension of the periodic table formed by cluster elements, called superatoms. As the behavior of clusters can be controlled by size and composition, the superatoms offer the potential to create unique compounds with tailored properties. In this article, we provide evidence of an additional class of superatoms, namely Al(7)(-), that exhibit multiple valences, like some of the elements in the periodic table, and hence have the potential to form stable compounds when combined with other atoms. These findings support the contention that there should be no limitation in finding clusters, which mimic virtually all members of the periodic table.

Preparation of Gelatin Layer Film with Gold Clusters in Using Photographic Film

NASA Astrophysics Data System (ADS)

Kuge, Ken'ichi; Arisawa, Michiko; Aoki, Naokazu; Hasegawa, Akira

2000-12-01

A gelatin layer film with gold clusters is produced by taking advantage of the photosensitivity of silver halide photography. Through exposure silver specks, which are called latent-image specks and are composed of several reduced silver atoms, are formed on the surface of silver halide grains in the photographic film. As the latent-image specks act as a catalyst for redox reaction, reduced gold atoms are deposited on the latent-image specks when the exposed film is immersed in a gold (I) thiocyanate complex solution for 5-20 days. Subsequently, when the silver halide grains are dissolved and removed, the gelatin layer film with gold clusters remains. The film produced by this method is purple and showed an absorption spectrum having a maximum of approximately 560 nm as a result of plasmon absorption. The clusters continued to grow with immersion time, and the growth rate increased as the concentration of the gold complex solution was increased. The cluster diameter changed from 20 nm to 100 nm. By this method, it is possible to produce a gelatin film of a large area with evenly dispersed gold clusters, and since it is produced only on the exposed area, pattern forming is also possible.

Meta-atom cluster acoustic metamaterial with broadband negative effective mass density

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Huaijun; Zhai, Shilong; Ding, Changlin

2014-02-07

We design a resonant meta-atom cluster, via which a two-dimensional (2D) acoustic metamaterial (AM) with broadband negative effective mass density from 1560 Hz to 5580 Hz is fabricated. Experimental results confirm that there is only weak interaction among the meta-atoms in the cluster. And then the meta-atoms in the cluster independently resonate, resulting in the cluster becoming equivalent to a broadband resonance unit. Extracted effective refractive indices from reflection and transmission measurements of the 2D AM appear to be negative from 1500 Hz to 5480 Hz. The broadband negative refraction has also been demonstrated by our further experiments. We expectmore » that this meta-atom cluster AM will significantly contribute to the design of broadband negative effective mass density AM.« less

Extending DFT-based genetic algorithms by atom-to-place re-assignment via perturbation theory: A systematic and unbiased approach to structures of mixed-metallic clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weigend, Florian, E-mail: florian.weigend@kit.edu

2014-10-07

Energy surfaces of metal clusters usually show a large variety of local minima. For homo-metallic species the energetically lowest can be found reliably with genetic algorithms, in combination with density functional theory without system-specific parameters. For mixed-metallic clusters this is much more difficult, as for a given arrangement of nuclei one has to find additionally the best of many possibilities of assigning different metal types to the individual positions. In the framework of electronic structure methods this second issue is treatable at comparably low cost at least for elements with similar atomic number by means of first-order perturbation theory, asmore » shown previously [F. Weigend, C. Schrodt, and R. Ahlrichs, J. Chem. Phys. 121, 10380 (2004)]. In the present contribution the extension of a genetic algorithm with the re-assignment of atom types to atom sites is proposed and tested for the search of the global minima of PtHf{sub 12} and [LaPb{sub 7}Bi{sub 7}]{sup 4−}. For both cases the (putative) global minimum is reliably found with the extended technique, which is not the case for the “pure” genetic algorithm.« less

Formation of multiply charged ions from large molecules using massive-cluster impact.

PubMed

Mahoney, J F; Cornett, D S; Lee, T D

1994-05-01

Massive-cluster impact is demonstrated to be an effective ionization technique for the mass analysis of proteins as large as 17 kDa. The design of the cluster source permits coupling to both magnetic-sector and quadrupole mass spectrometers. Mass spectra are characterized by the almost total absence of chemical background and a predominance of multiply charged ions formed from 100% glycerol matrix. The number of charge states produced by the technique is observed to range from +3 to +9 for chicken egg lysozyme (14,310 Da). The lower m/z values provided by higher charge states increase the effective mass range of analyses performed with conventional ionization by fast-atom bombardment or liquid secondary ion mass spectrometry.

Change of Energy of the Cubic Subnanocluster of Iron Under Influence of Interstitial and Substitutional Atoms.

PubMed

Nedolya, Anatoliy V; Bondarenko, Natalya V

2016-12-01

Energy change of an iron face-centred cubic subnanocluster was evaluated using molecular mechanics method depending on the position of a carbon interstitial atom and substitutional atoms of nickel. Calculations of all possible positions of impurity atoms show that the energy change of the system are discrete and at certain positions of the atoms are close to continuous.In terms of energy, when all impurity atoms are on the same edge of an atomic cluster, their positions are more advantageous. The presence of nickel atoms on the edge of a cubic cluster resulted in decrease of potential barrier for a carbon atom and decrease in energy in the whole cluster. A similar drift of a carbon atom from central octahedral interstitial site to the surface in the direction <011> occurred under the influence of surface factors.Such configuration corresponds to decreasing symmetry and increasing the number of possible energy states of a subnanocluster, and it corresponds to the condition of spontaneous crystallization process in an isolated system.Taking into account accidental positions of the nickel atom in the iron cluster, such behaviour of the carbon atom can explain the mechanism of growth of a new phase and formation of new clusters in the presence of other kind of atoms because of surface influence.

The study of structures and properties of PdnHm(n=1-10, m=1,2) clusters by density functional theory

NASA Astrophysics Data System (ADS)

Wen, Jun-Qing; Chen, Guo-Xiang; Zhang, Jian-Min; Wu, Hua

2018-04-01

The geometrical evolution, local relative stability, magnetism and charge transfer characteristics of PdnHm(n = 1-10, m = 1,2) have been systematically calculated by using density functional theory. The studied results show that the most stable geometries of PdnH and PdnH2 (n = 1-10) can be got by doping one or two H atoms on the sides of Pdn clusters except Pd6H and Pd6H2. It is found that doping one or two H atoms on Pdn clusters cannot change the basic framework of Pdn. The analysis of stability shows that Pd2H, Pd4H, Pd7H, Pd2H2, Pd4H2 and Pd7H2 clusters have higher local relative stability than neighboring clusters. The analysis of magnetic properties demonstrates that absorption of hydrogen atoms decreases the average atomic magnetic moments compared with pure Pdn clusters. More charges transfer from H atoms to Pd atoms for Pd6H and Pd6H2 clusters, demonstrating the adsorption of hydrogen atoms change from side adsorption to surface adsorption.

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

NASA Astrophysics Data System (ADS)

Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F.; Neese, Frank

2016-01-01

Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate previous implementation.

Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.

PubMed

Han, Kyungreem; Venable, Richard M; Bryant, Anne-Marie; Legacy, Christopher J; Shen, Rong; Li, Hui; Roux, Benoît; Gericke, Arne; Pastor, Richard W

2018-02-01

All-atom molecular dynamics simulations combined with graph-theoretic analysis reveal that clustering of monomethyl phosphate dianion (MMP 2- ) is strongly influenced by the types and combinations of cations in the aqueous solution. Although Ca 2+ promotes the formation of stable and large MMP 2- clusters, K + alone does not. Nonetheless, clusters are larger and their link lifetimes are longer in mixtures of K + and Ca 2+ . This "synergistic" effect depends sensitively on the Lennard-Jones interaction parameters between Ca 2+ and the phosphorus oxygen and correlates with the hydration of the clusters. The pronounced MMP 2- clustering effect of Ca 2+ in the presence of K + is confirmed by Fourier transform infrared spectroscopy. The characterization of the cation-dependent clustering of MMP 2- provides a starting point for understanding cation-dependent clustering of phosphoinositides in cell membranes.

Structure and Stability of GeAu{sub n}, n = 1-10 clusters: A Density Functional Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Priyanka,; Dharamvir, Keya; Sharma, Hitesh

2011-12-12

The structures of Germanium doped gold clusters GeAu{sub n} (n = 1-10) have been investigated using ab initio calculations based on density functional theory (DFT). We have obtained ground state geometries of GeAu{sub n} clusters and have it compared with Silicon doped gold clusters and pure gold clusters. The ground state geometries of the GeAu{sub n} clusters show patterns similar to silicon doped gold clusters except for n = 5, 6 and 9. The introduction of germanium atom increases the binding energy of gold clusters. The binding energy per atom of germanium doped cluster is smaller than the corresponding siliconmore » doped gold cluster. The HUMO-LOMO gap for Au{sub n}Ge clusters have been found to vary between 0.46 eV-2.09 eV. The mullikan charge analysis indicates that charge of order of 0.1e always transfers from germanium atom to gold atom.« less

Measurement of the spectral signature of small carbon clusters at near and far infrared wavelengths

NASA Technical Reports Server (NTRS)

Tarter, J.; Saykally, R.

1991-01-01

A significant percentage of the carbon inventory of the circumstellar and interstellar media may be in the form of large refractory molecules (or small grains) referred to as carbon clusters. At the small end, uneven numbers of carbon atoms seem to be preferred, whereas above 12 atoms, clusters containing an even number of carbon atoms appear to be preferred in laboratory chemistry. In the lab, the cluster C-60 appears to be a particularly stable form and has been nicknamed Bucky Balls because of its resemblance to a soccer ball and to geodesic domes designed by Buckminster Fuller. In order to investigate the prevalence of these clusters, and their relationship to the polycyclic aromatic hydrocarbons (PAHs) that have become the newest focus of IR astronomy, it is necessary to determine the spectroscopic characteristics of these clusters at near and far infrared wavelengths. Described here is the construction of a near to far IR laser magnetic resonance spectrometer that has been built at the University of California Berkeley in order to detect and characterize these spectra. The equipment produces carbon clusters by laser evaporation of a graphitic target. The clusters are then cooled in a supersonic expansion beam in order to simulate conditions in the interstellar medium (ISM). The expansion beam feeds into the spectrometer chamber and permits concentrations of clusters sufficiently high as to permit ultra-high resolution spectroscopy at near and far IR wavelengths. The first successful demonstration of this apparatus occurred last year when the laboratory studies permitted the observational detection of C-5 in the stellar outflow surrounding IRC+10216 in the near-IR. Current efforts focus on reducing the temperature of the supersonic expansion beam that transport the C clusters evaporated from a graphite target into the spectrometer down to temperatures as low as 1 K.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

Molecular dynamics simulations with electronic stopping can reproduce experimental sputtering yields of metals impacted by large cluster ions

NASA Astrophysics Data System (ADS)

Tian, Jiting; Zhou, Wei; Feng, Qijie; Zheng, Jian

2018-03-01

An unsolved problem in research of sputtering from metals induced by energetic large cluster ions is that molecular dynamics (MD) simulations often produce sputtering yields much higher than experimental results. Different from the previous simulations considering only elastic atomic interactions (nuclear stopping), here we incorporate inelastic electrons-atoms interactions (electronic stopping, ES) into MD simulations using a friction model. In this way we have simulated continuous 45° impacts of 10-20 keV C60 on a Ag(111) surface, and found that the calculated sputtering yields can be very close to the experimental results when the model parameter is appropriately assigned. Conversely, when we ignore the effect of ES, the yields are much higher, just like the previous studies. We further expand our research to the sputtering of Au induced by continuous keV C60 or Ar100 bombardments, and obtain quite similar results. Our study indicates that the gap between the experimental and the simulated sputtering yields is probably induced by the ignorance of ES in the simulations, and that a careful treatment of this issue is important for simulations of cluster-ion-induced sputtering, especially for those aiming to compare with experiments.

Engineering quantum hyperentangled states in atomic systems

NASA Astrophysics Data System (ADS)

Nawaz, Mehwish; -Islam, Rameez-ul; Abbas, Tasawar; Ikram, Manzoor

2017-11-01

Hyperentangled states have boosted many quantum informatics tasks tremendously due to their high information content per quantum entity. Until now, however, the engineering and manipulation of such states were limited to photonic systems only. In present article, we propose generating atomic hyperentanglement involving atomic internal states as well as atomic external momenta states. Hypersuperposition, hyperentangled cluster, Bell and Greenberger-Horne-Zeilinger states are engineered deterministically through resonant and off-resonant Bragg diffraction of neutral two-level atoms. Based on the characteristic parameters of the atomic Bragg diffraction, such as comparatively large interaction times and spatially well-separated outputs, such decoherence resistant states are expected to exhibit good overall fidelities and offer the evident benefits of full controllability, along with extremely high detection efficiency, over the counterpart photonic states comprised entirely of flying qubits.

Many particle spectroscopy of atoms, molecules, clusters and surfaces: international conference MPS-2016

NASA Astrophysics Data System (ADS)

Grum-Grzhimailo, Alexei N.; Popov, Yuri V.; Gryzlova, Elena V.; Solov'yov, Andrey V.

2017-07-01

The conference on Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces (MPS-2016) brought together near to a hundred scientists in the field of electronic, photonic, atomic and molecular collisions, and spectroscopy from around the world. We deliver an Editorial of a topical issue presenting original research results from some of the participants on both experimental and theoretical studies involving many particle spectroscopy of atoms, molecules, clusters and surfaces. Contribution to the Topical Issue "Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces", edited by A.N. Grum-Grzhimailo, E.V. Gryzlova, Yu.V. Popov, and A.V. Solov'yov.

Nonlocal screening effects on core-level photoemission spectra investigated by large-cluster models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okada, K.; Kotani, A.

1995-08-15

The copper 2{ital p} core-level x-ray photoemission spectrum in CuO{sub 2} plane systems is calculated by means of large-cluster models to investigate in detail the nonlocal screening effects, which were pointed out by van Veenendaal {ital et} {ital al}. [Phys. Rev. B 47, 11 462 (1993)]. Calculating the hole distributions for the initial and final states of photoemission, we show that the atomic coordination in a cluster strongly affects accessible final states. Accordingly, we point out that the interpretation for Cu{sub 3}O{sub 10} given by van Veenendaal {ital et} {ital al}. is not always general. Moreover, it is shown thatmore » the spectrum can be remarkably affected by whether or not the O 2{ital p}{sub {pi}} orbits are taken into account in the calculations. We also introduce a Hartree-Fock approximation in order to treat much larger-cluster models.« less

Cluster adsorption on amorphous and crystalline surfaces - A molecular dynamics study of model Pt on Cu and model Pd on Pt

NASA Technical Reports Server (NTRS)

Garofalini, S. H.; Halicioglu, T.; Pound, G. M.

1981-01-01

Molecular dynamics was used to study the structure, dispersion and short-time behavior of ten-atom clusters adsorbed onto amorphous and crystalline substrates, in which the cluster atoms differed from the substrate atoms. Two adatom-substrate model systems were chosen; one, in which the interaction energy between adatom pairs was greater than that between substrate pairs, and the other, in which the reverse was true. At relatively low temperature ranges, increased dispersion of cluster atoms occurred: (a) on the amorphous substrate as compared to the FCC(100) surface, (b) with increasing reduced temperature, and (c) with adatom-substrate interaction energy stronger than adatom-adatom interaction. Two-dimensional clusters (rafts) on the FCC(100) surface displayed migration of edge atoms only, indicating a mechanism for the cluster rotation and shape changes found in experimental studies.

Probing the Structural, Electronic, and Magnetic Properties of Ag n V (n = 1-12) Clusters.

PubMed

Xiong, Ran; Die, Dong; Xiao, Lu; Xu, Yong-Gen; Shen, Xu-Ying

2017-12-16

The structural, electronic, and magnetic properties of Ag n V (n = 1-12) clusters have been studied using density functional theory and CALYPSO structure searching method. Geometry optimizations manifest that a vanadium atom in low-energy Ag n V clusters favors the most highly coordinated location. The substitution of one V atom for an Ag atom in Ag n + 1 (n ≥ 5) cluster modifies the lowest energy structure of the host cluster. The infrared spectra, Raman spectra, and photoelectron spectra of Ag n V (n = 1-12) clusters are simulated and can be used to determine the most stable structure in the future. The relative stability, dissociation channel, and chemical activity of the ground states are analyzed through atomic averaged binding energy, dissociation energy, and energy gap. It is found that V atom can improve the stability of the host cluster, Ag 2 excepted. The most possible dissociation channels are Ag n V = Ag + Ag n - 1 V for n = 1 and 4-12 and Ag n V = Ag 2  + Ag n - 2 V for n = 2 and 3. The energy gap of Ag n V cluster with odd n is much smaller than that of Ag n + 1 cluster. Analyses of magnetic property indicate that the total magnetic moment of Ag n V cluster mostly comes from V atom and varies from 1 to 5 μ B . The charge transfer between V and Ag atoms should be responsible for the change of magnetic moment.

Site-specific polarizabilities as descriptors of metallic behavior in atomic clusters

NASA Astrophysics Data System (ADS)

Jackson, Koblar; Jellinek, Julius

The electric dipole polarizability of a cluster is a measure of its response to an applied electric field. The site specific polarizability method decomposes the total cluster polarizability into contributions from individual atoms and also allows it to be partitioned into charge transfer and electric dipole contributions. By systematically examining the trends in these quantities for several types of metal atom clusters over a wide range of cluster sizes, we find common characteristics that uniquely link the behavior of the clusters to that of the corresponding bulk metals for clusters as small as 10 atoms. We discuss these trends and compare and contrast them with results for non-metal clusters. This work was supported by the Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences, U.S. Department of Energy under Grant SC0001330 (KAJ) and Contract No. DE-AC02-06CH11357 (JJ).

Is the interaction between Ti atoms and fullerenes the origin of the 21-μ m feature?

NASA Astrophysics Data System (ADS)

Kimura, Y.; Nuth, J. A., III; Ferguson, F. T.

2005-12-01

A 21-μ m-emission feature has been observed in the shells of carbon-rich post-asymptotic giant branch (AGB) stars. The carrier of the 21-μ m feature remains unidentified, although many candidate materials have been proposed, including nanodiamond, SiS2, a derivative of SiC and nanometer-sized TiC. In particular, TiC grains were extensively discussed after the report by von Helden (2000). Gas-phase TiC clusters less than 1 nm in diameter have been suggested as the source of the 21-μ m dust feature. The spectrum of TiC clusters recorded in the laboratory provides a good fit with the observational data. However, only negative results have been reported for both theoretical and laboratory experimental studies concerning TiC since the discovery by von Helden. Recent measurements of fullerenes and Ti atoms recorded in our laboratory have demonstrated the presence of an infrared feature near 21 μ m. The feature observed has nearly the same shape and position as is observed for one of the most enigmatic features in post-AGB stars. In our experimental system, large-cage carbon particles, such as large fullerenes, were produced from CO gas by the Boudouard reaction. Large-cage carbon particles intermixed with Ti atoms were produced by the evaporation of a Ti-metal-wrapped carbon electrode in CO gas. The infrared spectra of large fullerenes interacting with Ti atoms show a characteristic feature at 20.3 μ m that closely corresponds to the 20.1-μ m feature observed in post-AGB stars. Both the laboratory and stellar spectra also show a small but significant peak at 19.0 μ m, which is attributed to fullerenes. We propose that the interaction between fullerenes and Ti atoms may be a plausible explanation for the 21-μ m feature seen in some post-AGB stars.

Hybrid quantum and molecular mechanics embedded cluster models for chemistry on silicon and silicon carbide surfaces

NASA Astrophysics Data System (ADS)

Shoemaker, James Richard

Fabrication of silicon carbide (SiC) semiconductor devices are of interest for aerospace applications because of their high-temperature tolerance. Growth of an insulating SiO2 layer on SiC by oxidation is a poorly understood process, and sometimes produces interface defects that degrade device performance. Accurate theoretical models of surface chemistry, using quantum mechanics (QM), do not exist because of the huge computational cost of solving Schrodinger's equation for a molecular cluster large enough to represent a surface. Molecular mechanics (MM), which describes a molecule as a collection of atoms interacting through classical potentials, is a fast computational method, good at predicting molecular structure, but cannot accurately model chemical reactions. A new hybrid QM/MM computational method for surface chemistry was developed and applied to silicon and SiC surfaces. The addition of MM steric constraints was shown to have a large effect on the energetics of O atom adsorption on SiC. Adsorption of O atoms on Si-terminated SiC(111) favors above surface sites, in contrast to Si(111), but favors subsurface adsorption sites on C- terminated SiC(111). This difference, and the energetics of C atom etching via CO2 desorption, can explain the observed poor performance of SiC devices in which insulating layers were grown on C-terminated surfaces.

Iron-carbide cluster thermal dynamics for catalyzed carbon nanotube growth

NASA Astrophysics Data System (ADS)

Ding, Feng; Bolton, Kim; Rosén, Arne

2004-07-01

Molecular dynamics simulations have been used to study the thermal behavior of FeN-mCm clusters where N, the total number of atoms, extends up to 2400. Comparison of the computed results with experimental data shows that the simulations yield the correct trends for the liquid-solid region of the iron-carbide phase diagram as well as the correct dependence of cluster melting point as a function of cluster size. The calculation indicates that, when carbon nanotubes (CNTs) are grown on large (>3-4 nm) catalyst particles at low temperatures (<1200 K), the catalyst particles are not completely molten. It is argued that the mechanism of CNT growth under these conditions may be governed by the surface melting of the cluster. .

Correlated electronic decay in expanding clusters triggered by intense XUV pulses from a Free-Electron-Laser

PubMed Central

Oelze, Tim; Schütte, Bernd; Müller, Maria; Müller, Jan P.; Wieland, Marek; Frühling, Ulrike; Drescher, Markus; Al-Shemmary, Alaa; Golz, Torsten; Stojanovic, Nikola; Krikunova, Maria

2017-01-01

Irradiation of nanoscale clusters and large molecules with intense laser pulses transforms them into highly-excited non- equilibrium states. The dynamics of intense laser-cluster interaction is encoded in electron kinetic energy spectra, which contain signatures of direct photoelectron emission as well as emission of thermalized nanoplasma electrons. In this work we report on a so far not observed spectrally narrow bound state signature in the electron kinetic energy spectra from mixed Xe core - Ar shell clusters ionized by intense extreme-ultraviolet (XUV) pulses from a free-electron-laser. This signature is attributed to the correlated electronic decay (CED) process, in which an excited atom relaxes and the excess energy is used to ionize the same or another excited atom or a nanoplasma electron. By applying the terahertz field streaking principle we demonstrate that CED-electrons are emitted at least a few picoseconds after the ionizing XUV pulse has ended. Following the recent finding of CED in clusters ionized by intense near-infrared laser pulses, our observation of CED in the XUV range suggests that this process is of general relevance for the relaxation dynamics in laser produced nanoplasmas. PMID:28098175

Remarkable Second-Order Optical Nonlinearity of Nano-Sized Au Cluster: A TDDFT Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Kechen; Li, Jun; Lin, Chensheng

2004-04-21

The dipole polarizability, static first hyperpolarizability, and UV-vis spectrum of the recently identified nano-sized tetrahedral cluster of Au have been investigated by using time-dependent density functional response theory. We have discovered that the Au cluster possesses remarkably large molecular second-order optical nonlinearity with the first hyperpolarizabilty (xyz) calculated to be 14.3 x 10 electrostatic unit (esu). The analysis of the low-energy absorption band suggests that the charge transfer from the edged gold atoms to the vertex ones plays the key role in nonlinear optical (NLO) response of Au.

Quasi-planar elemental clusters in pair interactions approximation

NASA Astrophysics Data System (ADS)

Chkhartishvili, Levan

2016-01-01

The pair-interactions approximation, when applied to describe elemental clusters, only takes into account bonding between neighboring atoms. According to this approach, isomers of wrapped forms of 2D clusters - nanotubular and fullerene-like structures - and truly 3D clusters, are generally expected to be more stable than their quasi-planar counterparts. This is because quasi-planar clusters contain more peripheral atoms with dangling bonds and, correspondingly, fewer atoms with saturated bonds. However, the differences in coordination numbers between central and peripheral atoms lead to the polarization of bonds. The related corrections to the molar binding energy can make small, quasi-planar clusters more stable than their 2D wrapped allotropes and 3D isomers. The present work provides a general theoretical frame for studying the relative stability of small elemental clusters within the pair interactions approximation.

Basic Equations Interrelate Atomic and Nuclear Properties to Patterns at the Size Scales of the Cosmos, Extended Clusters of Galaxies, Galaxies, and Nebulae

NASA Astrophysics Data System (ADS)

Allen, Rob

2016-09-01

Structures within molecules and nuclei have relationships to astronomical patterns. The COBE cosmic scale plots, and large scale surveys of galaxy clusters have patterns also repeating and well known at atomic scales. The Induction, Strong Force, and Nuclear Binding Energy Periods within the Big Bang are revealed to have played roles in the formation of these large scale distributions. Equations related to the enormous patterns also model chemical bonds and likely nucleus and nucleon substructures. ratios of the forces that include gravity are accurately calculated from the distributions and shapes. In addition, particle masses and a great many physical constants can be derived with precision and accuracy from astrophysical shapes. A few very basic numbers can do modelling from nucleon internals to molecules to super novae, and up to the Visible Universe. Equations are also provided along with possible structural configurations for some Cold Dark Matter and Dark Energy.

Structure and vibrational spectra of low-energy silicon clusters

NASA Astrophysics Data System (ADS)

Sieck, A.; Porezag, D.; Frauenheim, Th.; Pederson, M. R.; Jackson, K.

1997-12-01

We have identified low-energy structures of silicon clusters with 9 to 14 atoms using a nonorthogonal tight-binding method (TB) based on density-functional theory (DF). We have further investigated the resulting structures with an accurate all-electron first-principles technique. The results for cohesive energies, cluster geometries, and highest occupied to lowest unoccupied molecular orbital (HOMO-LUMO) gaps show an overall good agreement between DF-TB and self-consistent-field (SCF) DF theory. For Si9 and Si14, we have found equilibrium structures, whereas for Si11, Si12, and Si13, we present clusters with energies close to that of the corresponding ground-state structure recently proposed in the literature. The bonding scheme of clusters in this size range is different from the bulk tetrahedral symmetry. The most stable structures, characterized by low energies and large HOMO-LUMO gaps, have similar common subunits. To aid in their experimental identification, we have computed the full vibrational spectra of the structures, along with the Raman activities, IR intensities, and static polarizabilities, using SCF-DF theory within the local-density approximation (LDA). This method has already been successfully applied to the determination of Raman and IR spectra of silicon clusters with 3-8, 10, 13, 20, and 21 atoms.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kira, M., E-mail: mackillo.kira@physik.uni-marburg.de

Atomic Bose–Einstein condensates (BECs) can be viewed as macroscopic objects where atoms form correlated atom clusters to all orders. Therefore, the presence of a BEC makes the direct use of the cluster-expansion approach–lucrative e.g. in semiconductor quantum optics–inefficient when solving the many-body kinetics of a strongly interacting Bose. An excitation picture is introduced with a nonunitary transformation that describes the system in terms of atom clusters within the normal component alone. The nontrivial properties of this transformation are systematically studied, which yields a cluster-expansion friendly formalism for a strongly interacting Bose gas. Its connections and corrections to the standard Hartree–Fock–Bogoliubov approachmore » are discussed and the role of the order parameter and the Bogoliubov excitations are identified. The resulting interaction effects are shown to visibly modify number fluctuations of the BEC. Even when the BEC has a nearly perfect second-order coherence, the BEC number fluctuations can still resolve interaction-generated non-Poissonian fluctuations. - Highlights: • Excitation picture expresses interacting Bose gas with few atom clusters. • Semiconductor and BEC many-body investigations are connected with cluster expansion. • Quantum statistics of BEC is identified in terms of atom clusters. • BEC number fluctuations show extreme sensitivity to many-body correlations. • Cluster-expansion friendly framework is established for an interacting Bose gas.« less

Structural evolutions and hereditary characteristics of icosahedral nano-clusters formed in Mg70Zn30 alloys during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liang, Yong-Chao; Liu, Rang-Su; Xie, Quan; Tian, Ze-An; Mo, Yun-Fei; Zhang, Hai-Tao; Liu, Hai-Rong; Hou, Zhao-Yang; Zhou, Li-Li; Peng, Ping

2017-02-01

To investigate the structural evolution and hereditary mechanism of icosahedral nano-clusters formed during rapid solidification, a molecular dynamics (MD) simulation study has been performed for a system consisting of 107 atoms of liquid Mg70Zn30 alloy. Adopting Honeycutt-Anderson (HA) bond-type index method and cluster type index method (CTIM-3) to analyse the microstructures in the system it is found that for all the nano-clusters including 2~8 icosahedral clusters in the system, there are 62 kinds of geometrical structures, and those can be classified, by the configurations of the central atoms of basic clusters they contained, into four types: chain-like, triangle-tailed, quadrilateral-tailed and pyramidal-tailed. The evolution of icosahedral nano-clusters can be conducted by perfect heredity and replacement heredity, and the perfect heredity emerges when temperature is slightly less than Tm then increase rapidly and far exceeds the replacement heredity at Tg; while for the replacement heredity, there are three major modes: replaced by triangle (3-atoms), quadrangle (4-atoms) and pentagonal pyramid (6-atoms), rather than by single atom step by step during rapid solidification processes.

On the Surface Mapping using Individual Cluster Impacts

PubMed Central

Fernandez-Lima, F.A.; Eller, M.J.; DeBord, J.D.; Verkhoturov, S.V.; Della-Negra, S.; Schweikert, E.A.

2011-01-01

This paper describes the advantages of using single impacts of large cluster projectiles (e.g. C60 and Au400) for surface mapping and characterization. The analysis of co-emitted time-resolved photon spectra, electron distributions and characteristic secondary ions shows that they can be used as surface fingerprints for target composition, morphology and structure. Photon, electron and secondary ion emission increases with the projectile cluster size and energy. The observed, high abundant secondary ion emission makes cluster projectiles good candidates for surface mapping of atomic and fragment ions (e.g., yield >1 per nominal mass) and molecular ions (e.g., few tens of percent in the 500 < m/z < 1500 range). PMID:22393269

Report on simulation of fission gas and fission product diffusion in UO 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersson, Anders David; Perriot, Romain Thibault; Pastore, Giovanni

2016-07-22

In UO 2 nuclear fuel, the retention and release of fission gas atoms such as xenon (Xe) are important for nuclear fuel performance by, for example, reducing the fuel thermal conductivity, causing fuel swelling that leads to mechanical interaction with the clad, increasing the plenum pressure and reducing the fuel–clad gap thermal conductivity. We use multi-­scale simulations to determine fission gas diffusion mechanisms as well as the corresponding rates in UO 2 under both intrinsic and irradiation conditions. In addition to Xe and Kr, the fission products Zr, Ru, Ce, Y, La, Sr and Ba have been investigated. Density functionalmore » theory (DFT) calculations are used to study formation, binding and migration energies of small clusters of Xe atoms and vacancies. Empirical potential calculations enable us to determine the corresponding entropies and attempt frequencies for migration as well as investigate the properties of large clusters or small fission gas bubbles. A continuum reaction-­diffusion model is developed for Xe and point defects based on the mechanisms and rates obtained from atomistic simulations. Effective fission gas diffusivities are then obtained by solving this set of equations for different chemical and irradiation conditions using the MARMOT phase field code. The predictions are compared to available experimental data. The importance of the large Xe U3O cluster (a Xe atom in a uranium + oxygen vacancy trap site with two bound uranium vacancies) is emphasized, which is a consequence of its high mobility and high binding energy. We find that the Xe U3O cluster gives Xe diffusion coefficients that are higher for intrinsic conditions than under irradiation over a wide range of temperatures. Under irradiation the fast-­moving Xe U3O cluster recombines quickly with irradiation-induced interstitial U ions, while this mechanism is less important for intrinsic conditions. The net result is higher concentration of the Xe U3O cluster for intrinsic conditions than under irradiation. We speculate that differences in the irradiation conditions and their impact on the Xe U3O cluster can explain the wide range of diffusivities reported in experimental studies. However, all vacancy-­mediated mechanisms underestimate the Xe diffusivity compared to the empirical radiation-­enhanced rate used in most fission gas release models. We investigate the possibility that diffusion of small fission gas bubbles or extended Xe-­vacancy clusters may give rise to the observed radiation-­enhanced diffusion coefficient. These studies highlight the importance of U divacancies and an octahedron coordination of uranium vacancies encompassing a Xe fission gas atom. The latter cluster can migrate via a multistep mechanism with a rather low effective barrier, which together with irradiation-induced clusters of uranium vacancies, gives rise to the irradiation-enhanced diffusion coefficient observed in experiments.« less

Patterned growth of p-type MoS 2 atomic layers using sol-gel as precursor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Wei; Lin, Junhao; Feng, Wei

2D layered MoS 2 has drawn intense attention for its applications in flexible electronic, optoelectronic, and spintronic devices. Most of the MoS 2 atomic layers grown by conventional chemical vapor deposition techniques are n-type due to the abundant sulfur vacancies. Facile production of MoS 2 atomic layers with p-type behavior, however, remains challenging. Here, a novel one-step growth has been developed to attain p-type MoS 2 layers in large scale by using Mo-containing sol–gel, including 1% tungsten (W). Atomic-resolution electron microscopy characterization reveals that small tungsten oxide clusters are commonly present on the as-grown MoS 2 film due to themore » incomplete reduction of W precursor at the reaction temperature. These omnipresent small tungsten oxide clusters contribute to the p-type behavior, as verified by density functional theory calculations, while preserving the crystallinity of the MoS 2 atomic layers. The Mo containing sol–gel precursor is compatible with the soft-lithography techniques, which enables patterned growth of p-type MoS 2 atomic layers into regular arrays with different shapes, holding great promise for highly integrated device applications. Lastly, an atomically thin p–n junction is fabricated by the as-prepared MoS 2, which shows strong rectifying behavior.« less

Patterned growth of p-type MoS 2 atomic layers using sol-gel as precursor

DOE PAGES

Zheng, Wei; Lin, Junhao; Feng, Wei; ...

2016-07-19

2D layered MoS 2 has drawn intense attention for its applications in flexible electronic, optoelectronic, and spintronic devices. Most of the MoS 2 atomic layers grown by conventional chemical vapor deposition techniques are n-type due to the abundant sulfur vacancies. Facile production of MoS 2 atomic layers with p-type behavior, however, remains challenging. Here, a novel one-step growth has been developed to attain p-type MoS 2 layers in large scale by using Mo-containing sol–gel, including 1% tungsten (W). Atomic-resolution electron microscopy characterization reveals that small tungsten oxide clusters are commonly present on the as-grown MoS 2 film due to themore » incomplete reduction of W precursor at the reaction temperature. These omnipresent small tungsten oxide clusters contribute to the p-type behavior, as verified by density functional theory calculations, while preserving the crystallinity of the MoS 2 atomic layers. The Mo containing sol–gel precursor is compatible with the soft-lithography techniques, which enables patterned growth of p-type MoS 2 atomic layers into regular arrays with different shapes, holding great promise for highly integrated device applications. Lastly, an atomically thin p–n junction is fabricated by the as-prepared MoS 2, which shows strong rectifying behavior.« less

Reactivity and Catalytic Activity of Hydrogen Atom Chemisorbed Silver Clusters.

PubMed

Manzoor, Dar; Pal, Sourav

2015-06-18

Metal clusters of silver have attracted recent interest of researchers as a result of their potential in different catalytic applications and low cost. However, due to the completely filled d orbital and very high first ionization potential of the silver atom, the silver-based catalysts interact very weakly with the reacting molecules. In the current work, density functional theory calculations were carried out to investigate the effect of hydrogen atom chemisorption on the reactivity and catalytic properties of inert silver clusters. Our results affirm that the hydrogen atom chemisorption leads to enhancement in the binding energy of the adsorbed O2 molecule on the inert silver clusters. The increase in the binding energy is also characterized by the decrease in the Ag-O and increase in the O-O bond lengths in the case of the AgnH silver clusters. Pertinent to the increase in the O-O bond length, a significant red shift in the O-O stretching frequency is also noted in the case of the AgnH silver clusters. Moreover, the hydrogen atom chemisorbed silver clusters show low reaction barriers and high heat of formation of the final products for the environmentally important CO oxidation reaction as compared to the parent catalytically inactive clusters. The obtained results were compared with those of the corresponding gold and hydrogen atom chemisorbed gold clusters obtained at the same level of theory. It is expected the current computational study will provide key insights for future advances in the design of efficient nanosilver-based catalysts through the adsorption of a small atom or a ligand.

Does Each Atom Count in the Reactivity of Vanadia Nanoclusters?

PubMed

Zhang, Mei-Qi; Zhao, Yan-Xia; Liu, Qing-Yu; Li, Xiao-Na; He, Sheng-Gui

2017-01-11

Vanadium oxide cluster anions (V 2 O 5 ) n V x O y - (n = 1-31; x = 0, 1; and x + y ≤ 5) with different oxygen deficiencies (Δ = 2y-1-5x = 0, ± 1, and ±2) have been prepared by laser ablation and reacted to abstract hydrogen atoms from alkane molecules (n-butane) in a fast flow reactor. When the cluster size n is less than 25, the Δ = 1 series [(V 2 O 5 ) n O - clusters] that can contain atomic oxygen radical anions (O •- ) generally have much higher reactivity than the other four cluster series (Δ = -2, -1, 0, and 2), indicating that each atom counts in the hydrogen-atom abstraction (HAA) reactivity. Unexpectedly, all of the five cluster series have similar HAA reactivity when the cluster size is greater than 25. The critical dimension of vanadia particles separating the cluster behavior (each atom counts) from the bulk behavior (each atom contributes a little part) is thus about 1.6 nm (∼V 50 O 125 ). The strong electron-phonon coupling of the vanadia particles has been proposed to create the O •- radicals (V 5+ = O 2- + heat → V 4+ -O •- ) for the n > 25 clusters with Δ = -2, -1, 0, and 2. Such a mechanism is supported by a comparative study with the scandium system [(Sc 2 O 3 ) n Sc x O y - (n = 1-29; x = 0, 1; and x + y ≤ 4)] for which the Δ = 1 series [(Sc 2 O 3 ) n O - clusters] always have much higher HAA reactivity than the other cluster series.

Stability and migration of large oxygen clusters in UO(2+x): density functional theory calculations.

PubMed

Andersson, D A; Espinosa-Faller, F J; Uberuaga, B P; Conradson, S D

2012-06-21

Using ab initio molecular dynamics simulations and nudged elastic band calculations we examine the finite temperature stability, transition pathways, and migration mechanisms of large oxygen clusters in UO(2+x). Here we specifically consider the recently proposed split quad-interstitial and cuboctahedral oxygen clusters. It is shown that isolated cuboctahedral clusters may transform into more stable configurations that are closely linked to the split quad-interstitial. The split quad-interstitial is stable with respect to single interstitials occupying the empty octahedral holes of the UO(2) lattice. In order to better understand discrepancies between theory and experiments, the simulated atomic pair distribution functions for the split quad-interstitial structures are analyzed with respect to the distribution function for U(4)O(9) previously obtained from neutron diffraction data. Our nudged elastic band calculations suggest that the split quad-interstitial may migrate by translating one of its constituent di-interstitial clusters via a barrier that is lower than the corresponding barrier for individual interstitials, but higher than the barrier for the most stable di-interstitial cluster.

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

PubMed Central

Faria, José P.; Davis, James J.; Edirisinghe, Janaka N.; Taylor, Ronald C.; Weisenhorn, Pamela; Olson, Robert D.; Stevens, Rick L.; Rocha, Miguel; Rocha, Isabel; Best, Aaron A.; DeJongh, Matthew; Tintle, Nathan L.; Parrello, Bruce; Overbeek, Ross; Henry, Christopher S.

2016-01-01

Understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets, Atomic Regulons (ARs), represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes and to enable rational genetic engineering of cellular systems. Here, we describe an approach for inferring ARs that leverages large-scale expression data sets, gene context, and functional relationships among genes. We computed ARs for Escherichia coli based on 907 gene expression experiments and compared our results with gene clusters produced by two prevalent data-driven methods: Hierarchical clustering and k-means clustering. We compared ARs and purely data-driven gene clusters to the curated set of regulatory interactions for E. coli found in RegulonDB, showing that ARs are more consistent with gold standard regulons than are data-driven gene clusters. We further examined the consistency of ARs and data-driven gene clusters in the context of gene interactions predicted by Context Likelihood of Relatedness (CLR) analysis, finding that the ARs show better agreement with CLR predicted interactions. We determined the impact of increasing amounts of expression data on AR construction and find that while more data improve ARs, it is not necessary to use the full set of gene expression experiments available for E. coli to produce high quality ARs. In order to explore the conservation of co-regulated gene sets across different organisms, we computed ARs for Shewanella oneidensis, Pseudomonas aeruginosa, Thermus thermophilus, and Staphylococcus aureus, each of which represents increasing degrees of phylogenetic distance from E. coli. Comparison of the organism-specific ARs showed that the consistency of AR gene membership correlates with phylogenetic distance, but there is clear variability in the regulatory networks of closely related organisms. As large scale expression data sets become increasingly common for model and non-model organisms, comparative analyses of atomic regulons will provide valuable insights into fundamental regulatory modules used across the bacterial domain. PMID:27933038

Icosahedral quasicrystals of intermetallic compounds are icosahedral twins of cubic crystals of three kinds, consisting of large (about 5000 atoms) icosahedral complexes in either a cubic body-centered or a cubic face-centered arrangement or smaller (about 1350 atoms) icosahedral complexes in the β-tungsten arrangement

PubMed Central

Pauling, Linus

1989-01-01

The twofold-axis electron-diffraction photographs of icosahedral quasicrystals are of three kinds, reflecting three different structures of the cubic crystals that by icosahedral twinning form the quasicrystals. The first kind, represented by Al13Cu4Fe3, contains two very large icosahedral complexes, each of about 4680 atoms, in the body-centered arrangement, with six smaller icosahedral complexes (104 atoms each) in the principal interstices. The second kind, represented by Al5Mn, contains four of the very large complexes in the face-centered arrangement (cubic close packing), with four of the smaller clusters in the interstices. The third kind, represented by Al6CuLi3, contains eight icosahedral complexes, each of about 1350 atoms, in the β-W arrangement. The supporting evidence for these cubic structures is discussed as well as other evidence showing that the simple quasicrystal theory, which states that quasicrystals do not involve any translational identity operations, has to be modified. Images PMID:16594078

Silver clusters encapsulated in C{sub 60}: A density functional study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dhiman, Shobhna; Kumar, Ranjan; Dharamvir, Keya

2015-08-28

We explore the possibility of formation of endohedral complexes of Ag{sub n} atoms (n=1-9) inside C{sub 60} molecule using density functional theory and molecular dynamics. The obtained results reveal that Ag{sub n} (n=8) atoms can form stable complexes with the C{sub 60} molecule. Encapsulation of large number of Ag{sub n} atoms (n>8) make C{sub 60} cage instable, showing distortion of cage. Binding energy/atom increases with the number of Ag atoms up to n=4, after that it increases. Ionization potential decreases till n=4 and then increases, electron affinity increases till n=4 and then shows oscillatory nature as a function of Agmore » atoms inside the cage. Homo –Lumo gap shows no systematic pattern. Our results agreed well with the data available.« less

Composition formulas of binary eutectics

PubMed Central

Ma, Y. P.; Dong, D. D.; Dong, C.; Luo, L. J.; Wang, Q.; Qiang, J. B.; Wang, Y. M.

2015-01-01

The present paper addresses the long-standing composition puzzle of eutectic points by introducing a new structural tool for the description of short-range-order structural unit, the cluster-plus-glue-atom model. In this model, any structure is dissociated into a 1st-neighbor cluster and a few glue atoms between the clusters, expressed by a cluster formula [cluster]gluex. This model is applied here to establish the structural model for eutectic liquids, assuming that a eutectic liquid consist of two subunits issued from the relevant eutectic phases, each being expressed by the cluster formula for ideal metallic glasses, i.e., [cluster](glue atom)1 or 3. A structural unit is then composed of two clusters from the relevant eutectic phases plus 2, 4, or 6 glue atoms. Such a dual cluster formulism is well validated in all boron-containing (except those located by the extreme phase diagram ends) and in some commonly-encountered binary eutectics, within accuracies below 1 at.%. The dual cluster formulas vary extensively and are rarely identical even for eutectics of close compositions. They are generally formed with two distinctly different cluster types, with special cluster matching rules such as cuboctahedron plus capped trigonal prism and rhombidodecahedron plus octahedral antiprism. PMID:26658618

Geometric, electronic, and bonding properties of AuNM (N = 1-7, M = Ni, Pd, Pt) clusters.

PubMed

Yuan, D W; Wang, Yang; Zeng, Zhi

2005-03-15

Employing first-principles methods, based on density functional theory, we report the ground state geometric and electronic structures of gold clusters doped with platinum group atoms, Au(N)M (N = 1-7, M = Ni, Pd, Pt). The stability and electronic properties of Ni-doped gold clusters are similar to that of pure gold clusters with an enhancement of bond strength. Due to the strong d-d or s-d interplay between impurities and gold atoms originating in the relativistic effects and unique properties of dopant delocalized s-electrons in Pd- and Pt-doped gold clusters, the dopant atoms markedly change the geometric and electronic properties of gold clusters, and stronger bond energies are found in Pt-doped clusters. The Mulliken populations analysis of impurities and detailed decompositions of bond energies as well as a variety of density of states of the most stable dopant gold clusters are given to understand the different effects of individual dopant atom on bonding and electronic properties of dopant gold clusters. From the electronic properties of dopant gold clusters, the different chemical reactivity toward O(2), CO, or NO molecule is predicted in transition metal-doped gold clusters compared to pure gold clusters.

Bimetallic cages

NASA Astrophysics Data System (ADS)

Fournier, René; Afzal-Hussain, Sabeen

2013-02-01

We report the results of density functional theory for 39 clusters AxBy (x + y = 10 or 12) where A and B are metals from group 1, 2, 11, 12, 13, or 14 of the periodic table. The chemical compositions were chosen to satisfy an electronic shell closing criterion. We performed an unbiased search for the global minimum (GM) by taboo search in descriptor space in each case. Eight of the 39 putative GM are cages even though none of the clusters contains gold, a metal with a well known propensity to form cages. These cages are large enough to accommodate a dopant atom with an atomic radius varying between 0.7 Å and 1.2 Å. The chemical compositions most likely to produce cages have an element of group 11 alloyed with an element of group 2, 12, or 13.

Interplay between atomic disorder, lattice swelling and defect energy in ion-irradiation-induced amorphization of SiC

DOE PAGES

Debelle, Aurelien; Boulle, Alexandre; Chartier, Alain; ...

2014-11-25

We present a combination of experimental and computational evaluations of disorder level and lattice swelling in ion-irradiated materials. Information obtained from X-ray diffraction experiments is compared to X-ray diffraction data generated using atomic-scale simulations. The proposed methodology, which can be applied to a wide range of crystalline materials, is used to study the amorphization process in irradiated SiC. Results show that this process can be divided into two steps. In the first step, point defects and small defect clusters are produced and generate both large lattice swelling and high elastic energy. In the second step, enhanced coalescence of defects andmore » defect clusters occurs to limit this increase in energy, which rapidly leads to complete amorphization.« less

MicroED Structure of Au146(p-MBA)57 at Subatomic Resolution Reveals a Twinned FCC Cluster.

PubMed

Vergara, Sandra; Lukes, Dylan A; Martynowycz, Michael W; Santiago, Ulises; Plascencia-Villa, Germán; Weiss, Simon C; de la Cruz, M Jason; Black, David M; Alvarez, Marcos M; López-Lozano, Xochitl; Barnes, Christopher O; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L; Gonen, Tamir; Yacaman, Miguel Jose; Calero, Guillermo

2017-11-16

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au 146 (p-MBA) 57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C 2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au 146 (p-MBA) 57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.

MicroED structure of Au146(p-MBA)57 at subatomic resolution reveals a twinned FCC cluster

PubMed Central

Vergara, Sandra; Lukes, Dylan A.; Martynowycz, Michael W.; Santiago, Ulises; Plascencia-Villa, German; Weiss, Simon C.; de la Cruz, M. Jason; Black, David M.; Alvarez, Marcos M.; Lopez-Lozano, Xochitl; Barnes, Christopher O.; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L.; Gonen, Tamir; Jose-Yacaman, Miguel; Calero, Guillermo

2018-01-01

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault. PMID:29072840

Selective Nanoscale Mass Transport across Atomically Thin Single Crystalline Graphene Membranes.

PubMed

Kidambi, Piran R; Boutilier, Michael S H; Wang, Luda; Jang, Doojoon; Kim, Jeehwan; Karnik, Rohit

2017-05-01

Atomically thin single crystals, without grain boundaries and associated defect clusters, represent ideal systems to study and understand intrinsic defects in materials, but probing them collectively over large area remains nontrivial. In this study, the authors probe nanoscale mass transport across large-area (≈0.2 cm 2 ) single-crystalline graphene membranes. A novel, polymer-free picture frame assisted technique, coupled with a stress-inducing nickel layer is used to transfer single crystalline graphene grown on silicon carbide substrates to flexible polycarbonate track etched supports with well-defined cylindrical ≈200 nm pores. Diffusion-driven flow shows selective transport of ≈0.66 nm hydrated K + and Cl - ions over ≈1 nm sized small molecules, indicating the presence of selective sub-nanometer to nanometer sized defects. This work presents a framework to test the barrier properties and intrinsic quality of atomically thin materials at the sub-nanometer to nanometer scale over technologically relevant large areas, and suggests the potential use of intrinsic defects in atomically thin materials for molecular separations or desalting. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of helium-vacancy complexes in He-ions implanted Fe9Cr by using positron annihilation spectroscopy

NASA Astrophysics Data System (ADS)

Zhu, Te; Jin, Shuoxue; Zhang, Peng; Song, Ligang; Lian, Xiangyu; Fan, Ping; Zhang, Qiaoli; Yuan, Daqing; Wu, Haibiao; Yu, Runsheng; Cao, Xingzhong; Xu, Qiu; Wang, Baoyi

2018-07-01

The formation of helium bubble precursors, i.e., helium-vacancy complexes, was investigated for Fe9Cr alloy, which was uniformly irradiated by using 100 keV helium ions with fluences up to 5 × 1016 ions/cm2 at RT, 523, 623, 723, and 873 K. Helium-irradiation-induced microstructures in the alloy were probed by positron annihilation technique. The results show that the ratio of helium atom to vacancy (m/n) in the irradiation induced HemVn clusters is affected by the irradiation temperature. Irradiated at room temperature, there is a coexistence of large amounts of HemV1 and mono-vacancies in the sample. However, the overpressured HemVn (m > n) clusters or helium bubbles are easily formed by the helium-filled vacancy clusters (HemV1 and HemVn (m ≈ n)) absorbing helium atoms when irradiated at 523 K and 823 K. The results also show that void swelling of the alloy is the largest under 723 K irradiation.

Field evaporation of ZnO: A first-principles study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Yu, E-mail: yuxia@dal.ca; Karahka, Markus; Kreuzer, H. J.

2015-07-14

With recent advances in atom probe tomography of insulators and semiconductors, there is a need to understand high electrostatic field effects in these materials as well as the details of field evaporation. We use density functional theory to study field effects in ZnO clusters calculating the potential energy curves, the local field distribution, the polarizability, and the dielectric constant as a function of field strength. We confirm that, as in MgO, the HOMO-LUMO gap of a ZnO cluster closes at the evaporation field strength signaling field-induced metallization of the insulator. Following the structural changes in the cluster at the evaporationmore » field strength, we can identify the field evaporated species, in particular, we show that the most abundant ion, Zn{sup 2+}, is NOT post-ionized but leaves the surface as 2+ largely confirming the experimental observations. Our results also help to explain problems related to stoichiometry in the mass spectra measured in atom probe tomography.« less

A Density Functional Theory Investigation of Nin , Pdn , and Ptn Clusters (n=1-4) Adsorbed on Buckminsterfullerene.

PubMed

Pham, Nguyet N T; Le, Hung M

2017-05-19

In this study, we examine the adsorptions of Ni, Pd, and Pt clusters on C 60 by using a computational approach. Our calculation results show that the base structure of C 60 can host Ni n /Pd n /Pt n (n=1-4) clusters with good adsorption stability and the complexes establish either two or no unpaired electrons. The binding energy of Pd and Pt clusters increases as the number of metal atoms increases, implying that the coverage of C 60 with Pd or Pt preferentially establishes a large-size metal cluster. A single metal atom favorably occupies the C-C bridge site. For dimer clusters, the three metals of interest share a similar binding fashion, in which two metal atoms establish direct interactions with the C-C bridge sites. For trimer adsorptions, the formation of linear and triangular structures is observed. Both Pt 3 and Ni 3 preferably constitute isosceles triangles on C 60 , whilst Pd 3 favorably establishes a linear shape. Finally, for each of the Ni 4 and Pd 4 adsorption cases, we observed three stable binding configurations: rhombus, tetrahedron, and Y-form. Whereas Ni 4 establishes a tetrahedral form, Pd 4 attains the most stable form with the Y-shape geometry on C 60 . Overall, we observe that the trend of Pd binding to C 60 tends to go beyond the fashion of Ni and Pt. In terms of magnetic alignment, the Pd n -C 60 systems seem to be non-magnetic in most cases, unlike the Ni and Pt cases, the structures of which possess magnetic moments of 2 μB in their most stable forms. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relaxation channels of multi-photon excited xenon clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serdobintsev, P. Yu.; Melnikov, A. S.; Department of Physics, St. Petersburg State University, Saint Petersburg 198904

2015-09-21

The relaxation processes of the xenon clusters subjected to multi-photon excitation by laser radiation with quantum energies significantly lower than the thresholds of excitation of atoms and ionization of clusters were studied. Results obtained by means of the photoelectron spectroscopy method showed that desorption processes of excited atoms play a significant role in the decay of two-photon excited xenon clusters. A number of excited states of xenon atoms formed during this process were discovered and identified.

Average and local atomic-scale structure in BaZrxTi(1-x)O3 (x = 0. 10, 0.20, 0.40) ceramics by high-energy x-ray diffraction and Raman spectroscopy.

PubMed

Buscaglia, Vincenzo; Tripathi, Saurabh; Petkov, Valeri; Dapiaggi, Monica; Deluca, Marco; Gajović, Andreja; Ren, Yang

2014-02-12

High-resolution x-ray diffraction (XRD), Raman spectroscopy and total scattering XRD coupled to atomic pair distribution function (PDF) analysis studies of the atomic-scale structure of archetypal BaZrxTi(1-x)O3 (x = 0.10, 0.20, 0.40) ceramics are presented over a wide temperature range (100-450 K). For x = 0.1 and 0.2 the results reveal, well above the Curie temperature, the presence of Ti-rich polar clusters which are precursors of a long-range ferroelectric order observed below TC. Polar nanoregions (PNRs) and relaxor behaviour are observed over the whole temperature range for x = 0.4. Irrespective of ceramic composition, the polar clusters are due to locally correlated off-centre displacement of Zr/Ti cations compatible with local rhombohedral symmetry. Formation of Zr-rich clusters is indicated by Raman spectroscopy for all compositions. Considering the isovalent substitution of Ti with Zr in BaZrxTi1-xO3, the mechanism of formation and growth of the PNRs is not due to charge ordering and random fields, but rather to a reduction of the local strain promoted by the large difference in ion size between Zr(4+) and Ti(4+). As a result, non-polar or weakly polar Zr-rich clusters and polar Ti-rich clusters are randomly distributed in a paraelectric lattice and the long-range ferroelectric order is disrupted with increasing Zr concentration.

Density functional study of structural and electronic properties of bimetallic silver-gold clusters: Comparison with pure gold and silver clusters

NASA Astrophysics Data System (ADS)

Bonacic-Koutecky, Vlasta; Burda, Jaroslav; Mitric, Roland; Ge, Maofa; Zampella, Giuseppe; Fantucci, Piercarlo

2002-08-01

Bimetallic silver-gold clusters offer an excellent opportunity to study changes in metallic versus "ionic" properties involving charge transfer as a function of the size and the composition, particularly when compared to pure silver and gold clusters. We have determined structures, ionization potentials, and vertical detachment energies for neutral and charged bimetallic AgmAun 3[less-than-or-equal](m+n)[less-than-or-equal]5 clusters. Calculated VDE values compare well with available experimental data. In the stable structures of these clusters Au atoms assume positions which favor the charge transfer from Ag atoms. Heteronuclear bonding is usually preferred to homonuclear bonding in clusters with equal numbers of hetero atoms. In fact, stable structures of neutral Ag2Au2, Ag3Au3, and Ag4Au4 clusters are characterized by the maximum number of hetero bonds and peripheral positions of Au atoms. Bimetallic tetramer as well as hexamer are planar and have common structural properties with corresponding one-component systems, while Ag4Au4 and Ag8 have 3D forms in contrast to Au8 which assumes planar structure. At the density functional level of theory we have shown that this is due to participation of d electrons in bonding of pure Aun clusters while s electrons dominate bonding in pure Agm as well as in bimetallic clusters. In fact, Aun clusters remain planar for larger sizes than Agm and AgnAun clusters. Segregation between two components in bimetallic systems is not favorable, as shown in the example of Ag5Au5 cluster. We have found that the structures of bimetallic clusters with 20 atoms Ag10Au10 and Ag12Au8 are characterized by negatively charged Au subunits embedded in Ag environment. In the latter case, the shape of Au8 is related to a pentagonal bipyramid capped by one atom and contains three exposed negatively charged Au atoms. They might be suitable for activating reactions relevant to catalysis. According to our findings the charge transfer in bimetallic clusters is responsible for formation of negatively charged gold subunits which are expected to be reactive, a situation similar to that of gold clusters supported on metal oxides.

Atomic cluster collisions

NASA Astrophysics Data System (ADS)

Korol, Andrey V.; Solov'yov, Andrey

2013-01-01

Atomic cluster collisions are a field of rapidly emerging research interest by both experimentalists and theorists. The international symposium on atomic cluster collisions (ISSAC) is the premier forum to present cutting-edge research in this field. It was established in 2003 and the most recent conference was held in Berlin, Germany in July of 2011. This Topical Issue presents original research results from some of the participants, who attended this conference. This issues specifically focuses on two research areas, namely Clusters and Fullerenes in External Fields and Nanoscale Insights in Radiation Biodamage.

Interaction of intense laser pulses with hydrogen atomic clusters

NASA Astrophysics Data System (ADS)

Du, Hong-Chuan; Wang, Hui-Qiao; Liu, Zuo-Ye; Sun, Shao-Hua; Li, Lu; Ma, Ling-Ling; Hu, Bi-Tao

2010-03-01

The interaction between intense femtosecond laser pulses and hydrogen atomic clusters is studied by a simplified Coulomb explosion model. The dependences of average proton kinetic energy on cluster size, pulse duration, laser intensity and wavelength are studied respectively. The calculated results indicate that the irradiation of a femtosecond laser of longer wavelength on hydrogen atomic clusters may be a simple, economical way to produce highly kinetic hydrogen ions. The phenomenon suggests that the irradiation of femtosecond laser of longer wavelength on deuterium atomic clusters may be easier than that of shorter wavelength to drive nuclear fusion reactions. The product of the laser intensity and the squared laser wavelength needed to make proton energy saturated as a function of the squared cluster radius is also investigated. The proton energy distribution calculated is also shown and compared with the experimental data. Our results are in agreement with the experimental results fairly well.

The stability of vacancy clusters and their effect on helium behaviors in 3C-SiC

NASA Astrophysics Data System (ADS)

Sun, Jingjing; Li, B. S.; You, Yu-Wei; Hou, Jie; Xu, Yichun; Liu, C. S.; Fang, Q. F.; Wang, Z. G.

2018-05-01

We have carried out systematical ab initio calculations to study the stability of vacancy clusters and their effect on helium behaviors in 3C-SiC. It is found that the formation energies of vacancy clusters containing only carbon vacancies are the lowest although the vacancies are not closest to each other, while the binding energies of vacancy clusters composed of both silicon and carbon vacancies in the closest neighbors to each other are the highest. Vacancy clusters can provide with free space for helium atoms to aggregate, while interstitial sites are not favorable for helium atoms to accumulate. The binding energies of vacancy clusters with helium atoms increase almost linearly with the ratio of helium to vacancy, n/m. The binding strength of vacancy cluster having the participation of the silicon vacancy with helium is relatively stronger than that without silicon vacancy. The vacancy clusters with more vacancies can trap helium atoms more tightly. With the presence of vacancy clusters in the material, the diffusivity of helium will be significantly reduced. Moreover, the three-dimension electron density is calculated to analyze the interplay of vacancy clusters with helium.

Electronic levels and charge distribution near the interface of nickel

NASA Technical Reports Server (NTRS)

Waber, J. T.

1982-01-01

The energy levels in clusters of nickel atoms were investigated by means of a series of cluster calculations using both the multiple scattering and computational techniques (designated SSO) which avoids the muffin-tin approximation. The point group symmetry of the cluster has significant effect on the energy of levels nominally not occupied. This influences the electron transfer process during chemisorption. The SSO technique permits the approaching atom or molecule plus a small number of nickel atoms to be treated as a cluster. Specifically, molecular levels become more negative in the O atom, as well as in a CO molecule, as the metal atoms are approached. Thus, electron transfer from the nickel and bond formation is facilitated. This result is of importance in understanding chemisorption and catalytic processes.

Study of MoNbO(y) (y = 2-5) anion and neutral clusters using photoelectron spectroscopy and density functional theory calculations: impact of spin contamination on single point calculations.

PubMed

Waller, Sarah E; Mann, Jennifer E; Rothgeb, David W; Jarrold, Caroline C

2012-10-04

Results of a study combining anion photoelectron spectroscopy and density functional theory calculations on the heteronuclear MoNbO(y)(-) (y = 2-5) transition metal suboxide cluster series are reported and analyzed. The photoelectron spectra, which exhibit broad electronic bands with partially resolved vibrational structure, were compared to spectral simulations generated from calculated spectroscopic parameters for all computationally determined energetically competitive structures. Although computational results on the less oxidized clusters could not be satisfactorily reconciled with experimental spectra, possibly because of heavy spin contamination found in a large portion of the computational results, the results suggest that (1) neutral cluster electron affinity is a strong indicator of whether O-atoms are bound in M-O-M bridge positions or M═O terminal positions, (2) MoNbO(y) anions and neutrals have structures that can be described as intermediate with respect to the unary (homonuclear) Mo(2)O(y) and Nb(2)O(y) clusters, and (3) structures in which O-atoms preferentially bind to the Nb center are slightly more stable than alternative structures. Several challenges associated with the calculations are considered, including spin contamination, which appears to cause spurious single point calculations used to determine vertical detachment energies.

Point defect induced segregation of alloying solutes in α-Fe

NASA Astrophysics Data System (ADS)

You, Yu-Wei; Zhang, Yange; Li, Xiangyan; Xu, Yichun; Liu, C. S.; Chen, J. L.; Luo, G.-N.

2016-10-01

Segregation of alloying solute toward clusters and precipitates can result in hardening and embrittlement of ferritic and ferritic/martensitic steels in aging nuclear power plants. Thus, it is essential to study the segregation of solute in α-Fe. In this study, the segregation of eight kinds of alloying solutes (Al, Si, P, S, Ga, Ge, As, Se) in defect-free system and at vacancy, divacancy, and self-interstitial atom in α-Fe has been systematically studied by first-principles calculations. We find that it is energetically favorable for multiple solute S or Se atoms to segregate in defect-free system to form solute clusters, whereas it is very difficult for the other solute atoms to form the similar clusters. With the presence of vacancy and divacancy, the segregation of all the solutes are significantly promoted to form vacancy-solute and divacancy-solute clusters. The divacancy-solute cluster is more stable than the vacancy-solute cluster. The most-stable self-interstitial atom 〈110〉 dumbbell is also found to tightly bind with multiple solute atoms. The 〈110〉-S is even more stable than divacancy-S cluster. Meanwhile, the law of mass action is employed to predict the concentration evolution of vacancy-Si, vacancy-P, and vacancy-S clusters versus temperature and vacancy concentration.

About the atomic structures of icosahedral quasicrystals

NASA Astrophysics Data System (ADS)

Quiquandon, Marianne; Gratias, Denis

2014-01-01

This paper is a survey of the crystallographic methods that have been developed these last twenty five years to decipher the atomic structures of the icosahedral stable quasicrystals since their discovery in 1982 by D. Shechtman. After a brief recall of the notion of quasiperiodicity and the natural description of Z-modules in 3-dim as projection of regular lattices in N>3-dim spaces, we give the basic geometrical ingredients useful to describe icosahedral quasicrystals as irrational 3-dim cuts of ordinary crystals in 6-dim space. Atoms are described by atomic surfaces (ASs) that are bounded volumes in the internal (or perpendicular) 3-dim space and the intersections of which with the physical space are the actual atomic positions. The main part of the paper is devoted to finding the major properties of quasicrystalline icosahedral structures. As experimentally demonstrated, they can be described with a surprisingly few high symmetry ASs located at high symmetry special points in 6-dim space. The atomic structures are best described by aggregations and intersections of high symmetry compact interpenetrating atomic clusters. We show here that the experimentally relevant clusters are derived from one generic cluster made of two concentric triacontahedra scaled by τ and an external icosidodecahedron. Depending on which ones of the orbits of this cluster are eventually occupied by atoms, the actual atomic clusters are of type Bergman, Mackay, Tsai and others….

Self-organized formation of quantum dots of a material on a substrate

DOEpatents

Zhang, Zhenyu; Wendelken, John F.; Chang, Ming-Che; Pai, Woei Wu

2001-01-01

Systems and methods are described for fabricating arrays of quantum dots. A method for making a quantum dot device, includes: forming clusters of atoms on a substrate; and charging the clusters of atoms such that the clusters of atoms repel one another. The systems and methods provide advantages because the quantum dots can be ordered with regard to spacing and/or size.

Time-efficient simulations of tight-binding electronic structures with Intel Xeon PhiTM many-core processors

NASA Astrophysics Data System (ADS)

Ryu, Hoon; Jeong, Yosang; Kang, Ji-Hoon; Cho, Kyu Nam

2016-12-01

Modelling of multi-million atomic semiconductor structures is important as it not only predicts properties of physically realizable novel materials, but can accelerate advanced device designs. This work elaborates a new Technology-Computer-Aided-Design (TCAD) tool for nanoelectronics modelling, which uses a sp3d5s∗ tight-binding approach to describe multi-million atomic structures, and simulate electronic structures with high performance computing (HPC), including atomic effects such as alloy and dopant disorders. Being named as Quantum simulation tool for Advanced Nanoscale Devices (Q-AND), the tool shows nice scalability on traditional multi-core HPC clusters implying the strong capability of large-scale electronic structure simulations, particularly with remarkable performance enhancement on latest clusters of Intel Xeon PhiTM coprocessors. A review of the recent modelling study conducted to understand an experimental work of highly phosphorus-doped silicon nanowires, is presented to demonstrate the utility of Q-AND. Having been developed via Intel Parallel Computing Center project, Q-AND will be open to public to establish a sound framework of nanoelectronics modelling with advanced HPC clusters of a many-core base. With details of the development methodology and exemplary study of dopant electronics, this work will present a practical guideline for TCAD development to researchers in the field of computational nanoelectronics.

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

NASA Astrophysics Data System (ADS)

Di Pasquale, Nicodemo; Davie, Stuart J.; Popelier, Paul L. A.

2018-06-01

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Breaking the bottleneck: Use of molecular tailoring approach for the estimation of binding energies at MP2/CBS limit for large water clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Gurmeet; Nandi, Apurba; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in

2016-03-14

A pragmatic method based on the molecular tailoring approach (MTA) for estimating the complete basis set (CBS) limit at Møller-Plesset second order perturbation (MP2) theory accurately for large molecular clusters with limited computational resources is developed. It is applied to water clusters, (H{sub 2}O){sub n} (n = 7, 8, 10, 16, 17, and 25) optimized employing aug-cc-pVDZ (aVDZ) basis-set. Binding energies (BEs) of these clusters are estimated at the MP2/aug-cc-pVNZ (aVNZ) [N = T, Q, and 5 (whenever possible)] levels of theory employing grafted MTA (GMTA) methodology and are found to lie within 0.2 kcal/mol of the corresponding full calculationmore » MP2 BE, wherever available. The results are extrapolated to CBS limit using a three point formula. The GMTA-MP2 calculations are feasible on off-the-shelf hardware and show around 50%–65% saving of computational time. The methodology has a potential for application to molecular clusters containing ∼100 atoms.« less

Electrodeposition of Isolated Platinum Atoms and Clusters on Bismuth-Characterization and Electrocatalysis.

PubMed

Zhou, Min; Dick, Jeffrey E; Bard, Allen J

2017-12-06

We describe a method for the electrodeposition of an isolated single Pt atom or small cluster, up to 9 atoms, on a bismuth ultramicroelectrode (UME). This deposition was immediately followed by electrochemical characterization via the hydrogen evolution reaction (HER) that occurs readily on the electrodeposited Pt but not on Bi. The observed voltammetric current plateau, even for a single atom, which behaves as an electrode, allows the estimation of deposit size. Pt was plated from solutions of femtomolar PtCl 6 2- , which allowed precise control of the arrival of ions and thus the plating rate on the Bi UME, to one ion every few seconds. This allowed the atom-by-atom fabrication of isolated platinum deposits, ranging from single atoms to 9-atom clusters. The limiting currents in voltammetry gave the size and number of atoms of the clusters. Given the stochasticity of the plating process, we show that the number of atoms plated over a given time (10 and 20 s) follows a Poisson distribution. Taking the potential at a certain current density as a measure of the relative rate of the HER, we found that the potential shifted positively as the size increased, with single atoms showing the largest overpotentials compared to bulk Pt.

Quantum chemistry of the minimal CdSe clusters

NASA Astrophysics Data System (ADS)

Yang, Ping; Tretiak, Sergei; Masunov, Artëm E.; Ivanov, Sergei

2008-08-01

Colloidal quantum dots are semiconductor nanocrystals (NCs) which have stimulated a great deal of research and have attracted technical interest in recent years due to their chemical stability and the tunability of photophysical properties. While internal structure of large quantum dots is similar to bulk, their surface structure and passivating role of capping ligands (surfactants) are not fully understood to date. We apply ab initio wavefunction methods, density functional theory, and semiempirical approaches to study the passivation effects of substituted phosphine and amine ligands on the minimal cluster Cd2Se2, which is also used to benchmark different computational methods versus high level ab initio techniques. Full geometry optimization of Cd2Se2 at different theory levels and ligand coverage is used to understand the affinities of various ligands and the impact of ligands on cluster structure. Most possible bonding patterns between ligands and surface Cd/Se atoms are considered, including a ligand coordinated to Se atoms. The degree of passivation of Cd and Se atoms (one or two ligands attached to one atom) is also studied. The results suggest that B3LYP/LANL2DZ level of theory is appropriate for the system modeling, whereas frequently used semiempirical methods (such as AM1 and PM3) produce unphysical results. The use of hydrogen atom for modeling of the cluster passivating ligands is found to yield unphysical results as well. Hence, the surface termination of II-VI semiconductor NCs with hydrogen atoms often used in computational models should probably be avoided. Basis set superposition error, zero-point energy, and thermal corrections, as well as solvent effects simulated with polarized continuum model are found to produce minor variations on the ligand binding energies. The effects of Cd-Se complex structure on both the electronic band gap (highest occupied molecular orbital-lowest unoccupied molecular orbital energy difference) and ligand binding energies are systematically examined. The role played by positive charges on ligand binding is also explored. The calculated binding energies for various ligands L are found to decrease in the order OPMe3>OPH3>NH2Me>=NH3>=NMe3>PMe3>PH3 for neutral clusters and OPMe3>OPH3>PMe3>=NMe3>=NH2Me>=NH3>PH3 and OPMe3>OPH3>NH2Me>=NMe3>=PMe3>=NH3>PH3 for single and double ligations of positively charged Cd2Se22+ cluster, respectively.

Probing the structural and electronic properties of cationic rubidium-gold clusters: [AunRb]+ (n = 1-10)

NASA Astrophysics Data System (ADS)

Zhao, Ya-Ru; Zhang, Hai-Rong; Qian, Yu; Duan, Xu-Chao; Hu, Yan-Fei

2016-03-01

Density functional theory has been applied to study the geometric structures, relative stabilities, and electronic properties of cationic [AunRb]+ and Aun + 1+ (n = 1-10) clusters. For the lowest energy structures of [AunRb]+ clusters, the planar to three-dimensional transformation is found to occur at cluster size n = 4 and the Rb atoms prefer being located at the most highly coordinated position. The trends of the averaged atomic binding energies, fragmentation energies, second-order difference of energies, and energy gaps show pronounced even-odd alternations. It indicated that the clusters containing odd number of atoms maintain greater stability than the clusters in the vicinity. In particular, the [Au6Rb]+ clusters are the most stable isomer for [AunRb]+ clusters in the region of n = 1-10. The charges in [AunRb]+ clusters transfer from the Rb atoms to Aun host. Density of states revealed that the Au-5d, Au-5p, and Rb-4p orbitals hardly participated in bonding. In addition, it is found that the most favourable channel of the [AunRb]+ clusters is Rb+ cation ejection. The electronic localisation function (ELF) analysis of the [AunRb]+ clusters shown that strong interactions are not revealed in this study.

The electron screening puzzle and nuclear clustering

DOE PAGES

Spitaleri, C.; Bertulani, C. A.; Fortunato, L.; ...

2016-02-12

Accurate measurements of nuclear reactions of astrophysical interest within, or close to, the Gamow peak show evidence of an unexpected effect attributed to the presence of atomic electrons in the target. The experiments need to include an effective "screening" potential to explain the enhancement of the cross sections at the lowest measurable energies. Despite various theoretical studies conducted over the past 20 years and numerous experimental measurements, a theory has not yet been found that can explain the cause of the exceedingly high values of the screening potential needed to explain the data. Furthermore, in this letter we show thatmore » instead of an atomic physics solution of the "electron screening puzzle", the reason for the large screening potential values is in fact due to clusterization effects in nuclear reactions, in particular for reaction involving light nuclei.« less

Helium self-trapping and diffusion behaviors in deformed 316L stainless steel exposed to high flux and low energy helium plasma

NASA Astrophysics Data System (ADS)

Gong, Yihao; Jin, Shuoxue; Zhu, Te; Cheng, Long; Cao, Xingzhong; You, Li; Lu, Guanghong; Guo, Liping; Wang, Baoyi

2018-04-01

A large number of dislocation networks were introduced in to 316L stainless steel by cold rolling. Subsequently, low energy (40 eV) helium ions were implanted by exposing the steel to helium plasma. Thermal desorption and positron annihilation spectroscopy were used to study the behavior of helium in the presence of dislocations, with emphasis on helium self-trapping and migration behaviors. Helium desorption behaviour from different helium trapping states was measured by the thermal desorption spectroscopy. Most of the helium desorbed from the He m V n clusters, and the corresponding desorption peak is located at ~650 K. The desorption peak from helium-dislocation clusters (He m D) is at approximately 805 K. The effect of annealing on the defect evolution was investigated by positron annihilation spectroscopy. For the specimen exposed to helium plasma without displacement damage, the increment of S parameter meant the existence of helium self-trapping behavior (He m V n ). Helium atoms could diffuse two to three orders of magnitude deeper than the implantation depth calculated by SRIM. The diffusing helium atoms were gradually trapped by dislocation lines and formed He m D. Elevated temperatures enhance the self-trapping behavior and cause helium atoms to dissociate/desorb from the He m V n clusters, increasing the S parameters at 473-673 K. The gradual recovery of vacancies in the He m V n clusters decreased the S parameter above 673 K.

Effective scheme for partitioning covalent bonds in density-functional embedding theory: From molecules to extended covalent systems.

PubMed

Huang, Chen; Muñoz-García, Ana Belén; Pavone, Michele

2016-12-28

Density-functional embedding theory provides a general way to perform multi-physics quantum mechanics simulations of large-scale materials by dividing the total system's electron density into a cluster's density and its environment's density. It is then possible to compute the accurate local electronic structures and energetics of the embedded cluster with high-level methods, meanwhile retaining a low-level description of the environment. The prerequisite step in the density-functional embedding theory is the cluster definition. In covalent systems, cutting across the covalent bonds that connect the cluster and its environment leads to dangling bonds (unpaired electrons). These represent a major obstacle for the application of density-functional embedding theory to study extended covalent systems. In this work, we developed a simple scheme to define the cluster in covalent systems. Instead of cutting covalent bonds, we directly split the boundary atoms for maintaining the valency of the cluster. With this new covalent embedding scheme, we compute the dehydrogenation energies of several different molecules, as well as the binding energy of a cobalt atom on graphene. Well localized cluster densities are observed, which can facilitate the use of localized basis sets in high-level calculations. The results are found to converge faster with the embedding method than the other multi-physics approach ONIOM. This work paves the way to perform the density-functional embedding simulations of heterogeneous systems in which different types of chemical bonds are present.

Interaction of scandium and titanium atoms with a carbon surface containing five- and seven-membered rings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krasnov, P. O., E-mail: kpo1980@gmail.com; Eliseeva, N. S.; Kuzubov, A. A., E-mail: alex_xx@rambler.ru

2012-01-15

The use of carbon nanotubes coated by atoms of transition metals to store molecular hydrogen is associated with the problem of the aggregation of these atoms, which leads to the formation of metal clusters. The quantum-chemical simulation of cluster models of the carbon surface of a graphene type with scandium and titanium atoms has been performed. It has been shown that the presence of five- and seven-membered rings, in addition to six-membered rings, in these structures makes it possible to strongly suppress the processes of the migration of metal atoms over the surface, preventing their clustering.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mannix, A. J.; Zhou, X. -F.; Kiraly, B.

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework.

PubMed

Kim, In Soo; Li, Zhanyong; Zheng, Jian; Platero-Prats, Ana E; Mavrandonakis, Andreas; Pellizzeri, Steven; Ferrandon, Magali; Vjunov, Aleksei; Gallington, Leighanne C; Webber, Thomas E; Vermeulen, Nicolaas A; Penn, R Lee; Getman, Rachel B; Cramer, Christopher J; Chapman, Karena W; Camaioni, Donald M; Fulton, John L; Lercher, Johannes A; Farha, Omar K; Hupp, Joseph T; Martinson, Alex B F

2018-01-22

Single atoms and few-atom clusters of platinum are uniformly installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 °C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and X-ray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novel catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lin -Lin; Johnson, Duane D.; Tringides, Michael C.

Density functional theory is used to study structural energetics of Pb vacancy cluster formation on C 60/Pb/Si(111) to explain the unusually fast and error-free transformations between the “Devil's Staircase” (DS) phases on the Pb/Si(111) wetting layer at low temperature (~110K). The formation energies of vacancy clusters are calculated in C 60/Pb/Si(111) as Pb atoms are progressively ejected from the initial dense Pb wetting layer. Vacancy clusters larger than five Pb atoms are found to be stable with seven being the most stable, while vacancy clusters smaller than five are highly unstable, which agrees well with the observed ejection rate ofmore » ~5 Pb atoms per C 60. Furthermore, the high energy cost (~0.8 eV) for the small vacancy clusters to form indicates convincingly that the unusually fast transformation observed experimentally between the DS phases, upon C 60 adsorption at low temperature, cannot be the result of single-atom random walk diffusion but of correlated multi-atom processes.« less

Supersonic Bare Metal Cluster Beams. Final Report

DOE R&D Accomplishments Database

Smalley, R. E.

1997-10-14

A major portion of the project involved elucidating the relation between reactivity and the electronic structure of transition-metal (TM) clusters of 2--200 atoms, which required the construction and continuous development of two principal apparati; the Fourier Transform-Ion Cyclotron Resonance (FT-ICR) apparatus, and Ultraviolet Photoelectron Spectroscopy (UPS). Together, these machines have enabled the most detailed probing of the structure and chemical reactivity of TM clusters. Clusters of all the transition metals were included in these studies. Fundamental aspects in chemisorption, reactivity, and heterogeneous catalysis have also become better understood as a result of these experiments for important classes of systems such as H{sub 2}, CO, and CO{sub 2} adsorbed onto clusters of many of the metals listed above. In particular, a correlation was found between reactivity of H{sub 2} with Fe, Co, and Ni clusters and differences between the cluster IP and EA. As recounted in a previous technical report, the DOE`s role in the initial discovery of fullerenes at Rice was central, and from the start investigations were made into metal atoms trapped in the fullerenes cage. More recently, the authors have discovered that 2--4 atoms of La, Y, or Sc can be produced by laser vaporization of composite graphite/metal-oxide disks. This work was largely motivated by the prospects of using such endohedral TM metals for their catalytic activity without the well-known difficulties of effective support media and lack of control over particle size. Thus, while it will certainly be important to discover ways to efficiently scale up production (e.g., the solar generation method explored with DOE support), the efforts have concentrated more on characterization, purification, and manipulation of doped fullerenes. For the past two years, much of the group`s effort has involved the production, purification, and characterization of carbon nanotubes.

A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: Theory and application to microfilaments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Tong; Gu, YuanTong, E-mail: yuantong.gu@qut.edu.au

As all-atom molecular dynamics method is limited by its enormous computational cost, various coarse-grained strategies have been developed to extend the length scale of soft matters in the modeling of mechanical behaviors. However, the classical thermostat algorithm in highly coarse-grained molecular dynamics method would underestimate the thermodynamic behaviors of soft matters (e.g. microfilaments in cells), which can weaken the ability of materials to overcome local energy traps in granular modeling. Based on all-atom molecular dynamics modeling of microfilament fragments (G-actin clusters), a new stochastic thermostat algorithm is developed to retain the representation of thermodynamic properties of microfilaments at extra coarse-grainedmore » level. The accuracy of this stochastic thermostat algorithm is validated by all-atom MD simulation. This new stochastic thermostat algorithm provides an efficient way to investigate the thermomechanical properties of large-scale soft matters.« less

Ligand-protected gold clusters: the structure, synthesis and applications

NASA Astrophysics Data System (ADS)

Pichugina, D. A.; Kuz'menko, N. E.; Shestakov, A. F.

2015-11-01

Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Aun with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au15 and Au25) and on anchorage to a support surface (Au25/SiO2, Au20/C, Au10/FeOx) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR)n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters MxAunLm (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR)x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active sites. The bibliography includes 345 references.

Catalysis applications of size-selected cluster deposition

DOE PAGES

Vajda, Stefan; White, Michael G.

2015-10-23

In this Perspective, we review recent studies of size-selected cluster deposition for catalysis applications performed at the U.S. DOE National Laboratories, with emphasis on work at Argonne National Laboratory (ANL) and Brookhaven National Laboratory (BNL). The focus is on the preparation of model supported catalysts in which the number of atoms in the deposited clusters is precisely controlled using a combination of gas-phase cluster ion sources, mass spectrometry, and soft-landing techniques. This approach is particularly effective for investigations of small nanoclusters, 0.5-2 nm (<200 atoms), where the rapid evolution of the atomic and electronic structure makes it essential to havemore » precise control over cluster size. Cluster deposition allows for independent control of cluster size, coverage, and stoichiometry (e.g., the metal-to-oxygen ratio in an oxide cluster) and can be used to deposit on any substrate without constraints of nucleation and growth. Examples are presented for metal, metal oxide, and metal sulfide cluster deposition on a variety of supports (metals, oxides, carbon/diamond) where the reactivity, cluster-support electronic interactions, and cluster stability and morphology are investigated. Both UHV and in situ/operando studies are presented that also make use of surface-sensitive X-ray characterization tools from synchrotron radiation facilities. Novel applications of cluster deposition to electrochemistry and batteries are also presented. This review also highlights the application of modern ab initio electronic structure calculations (density functional theory), which can essentially model the exact experimental system used in the laboratory (i.e., cluster and support) to provide insight on atomic and electronic structure, reaction energetics, and mechanisms. As amply demonstrated in this review, the powerful combination of atomically precise cluster deposition and theory is able to address fundamental aspects of size-effects, cluster-support interactions, and reaction mechanisms of cluster materials that are central to how catalysts function. Lastly, the insight gained from such studies can be used to further the development of novel nanostructured catalysts with high activity and selectivity.« less

Endohedral beryllium atoms in germanium clusters with eight and fewer vertices: how small can a cluster be and still encapsulate a central atom?

PubMed

Uţă, M M; King, R B

2012-05-31

Structures of the beryllium-centered germanium clusters Be@Ge(n)(z) (n = 8, 7, 6; z = -4, -2, 0, +2) have been investigated by density functional theory to provide some insight regarding the smallest metal cluster that can encapsulate an interstitial atom. The lowest energy structures of the eight-vertex Be@Ge(8)(z) clusters (z = -4, -2, 0, +2) all have the Be atom at the center of a closed polyhedron, namely, a D(4d) square antiprism for Be@Ge(8)(4-), a D(2d) bisdisphenoid for Be@Ge(8)(2-), an ideal O(h) cube for Be@Ge(8), and a C(2v) distorted cube for Be@Ge(8)(2+). The Be-centered cubic structures predicted for Be@Ge(8) and Be@Ge(8)(2+) differ from the previously predicted lowest energy structures for the isoelectronic Ge(8)(2-) and Ge(8). This appears to be related to the larger internal volume of the cube relative to other closed eight-vertex polyhedra. The lowest energy structures for the smaller seven- and six-vertex clusters Be@Ge(n)(z) (n = 7, 6; z = -4, -2, 0, +2) no longer have the Be atom at the center of a closed Ge(n) polyhedron. Instead, either the Ge(n) polyhedron has opened up to provide a larger volume for the Be atom or the Be atom has migrated to the surface of the polyhedron. However, higher energy structures are found in which the Be atom is located at the center of a Ge(n) (n = 7, 6) polyhedron. Examples of such structures are a centered C(2v) capped trigonal prismatic structure for Be@Ge(7)(2-), a centered D(5h) pentagonal bipyramidal structure for Be@Ge(7), a centered D(3h) trigonal prismatic structure for Be@Ge(6)(4-), and a centered octahedral structure for Be@Ge(6). Cluster buildup reactions of the type Be@Ge(n)(z) + Ge(2) → Be@Ge(n+2)(z) (n = 6, 8; z = -4, -2, 0, +2) are all predicted to be highly exothermic. This suggests that interstitial clusters having an endohedral atom inside a bare post transition element polyhedron with eight or fewer vertices are less than the optimum size. This is consistent with the experimental observation of several types of 10-vertex polyhedral bare post transition element clusters with interstitial atoms but the failure to observe such clusters with external polyhedra having eight or fewer vertices.

Doubly charged coronene clusters—Much smaller than previously observed

NASA Astrophysics Data System (ADS)

Mahmoodi-Darian, Masoomeh; Raggl, Stefan; Renzler, Michael; Goulart, Marcelo; Huber, Stefan E.; Mauracher, Andreas; Scheier, Paul; Echt, Olof

2018-05-01

The smallest doubly charged coronene cluster ions reported so far, Cor152+, were produced by charge exchange between bare coronene clusters and He2+ [H. A. B. Johansson et al., Phys. Rev. A 84, 043201 (2011)]. These dications are at least five times larger than the estimated Rayleigh limit, i.e., the size at which the activation barrier for charge separation vanishes. Such a large discrepancy is unheard of for doubly charged atomic or molecular clusters. Here we report the mass spectrometric observation of doubly charged coronene trimers, produced by electron ionization of helium nanodroplets doped with coronene. The observation implies that Cor32+ features a non-zero fission barrier too large to overcome under the present experimental conditions. The height of the barriers for the dimer and trimer has been estimated by means of density functional theory calculations. A sizeable barrier for the trimer has been revealed in agreement with the experimental findings.

High Intensity Femtosecond XUV Pulse Interactions with Atomic Clusters: Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ditmire, Todd

We propose to expand our recent studies on the interactions of intense extreme ultraviolet (XUV) femtosecond pulses with atomic and molecular clusters. The work described follows directly from work performed under BES support for the past grant period. During this period we upgraded the THOR laser at UT Austin by replacing the regenerative amplifier with optical parametric amplification (OPA) using BBO crystals. This increased the contrast of the laser, the total laser energy to ~1.2 J , and decreased the pulse width to below 30 fs. We built a new all reflective XUV harmonic beam line into expanded lab space. This enabled an increase influence by a factor ofmore » 25 and an increase in the intensity by a factor of 50. The goal of the program proposed in this renewal is to extend this class of experiments to available higher XUV intensity and a greater range of wavelengths. In particular we plan to perform experiments to confirm our hypothesis about the origin of the high charge states in these exploding clusters, an effect which we ascribe to plasma continuum lowering (ionization potential depression) in a cluster nano-­plasma. To do this we will perform experiments in which XUV pulses of carefully chosen wavelength irradiate clusters composed of only low-Z atoms and clusters with a mixture of this low-­Z atom with higher Z atoms. The latter clusters will exhibit higher electron densities and will serve to lower the ionization potential further than in the clusters composed only of low Z atoms. This should have a significant effect on the charge states produced in the exploding cluster. We will also explore the transition of explosions in these XUV irradiated clusters from hydrodynamic expansion to Coulomb explosion. The work proposed here will explore clusters of a wider range of constituents, including clusters from solids. Experiments on clusters from solids will be enabled by development we performed during the past grant period in which we constructed and tested a cluster generator based on the Laser Ablation of Microparticles (LAM) method.« less

Image reconstruction of muon tomographic data using a density-based clustering method

NASA Astrophysics Data System (ADS)

Perry, Kimberly B.

Muons are subatomic particles capable of reaching the Earth's surface before decaying. When these particles collide with an object that has a high atomic number (Z), their path of travel changes substantially. Tracking muon movement through shielded containers can indicate what types of materials lie inside. This thesis proposes using a density-based clustering algorithm called OPTICS to perform image reconstructions using muon tomographic data. The results show that this method is capable of detecting high-Z materials quickly, and can also produce detailed reconstructions with large amounts of data.

Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamiya, Muneaki; Hirata, So; Valiev, Marat

2008-02-19

Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly-interacting molecular clusters [Hirata et al. Mol. Phys. 103, 2255 (2005)] have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine–water clusters with an excellent result for an initial performance assessment. Our original method included up to two- or three-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the dipole–dipole approximation. In this work, the dipole moments are replaced by atom-centered point charges determined so that they reproduce the electrostatic potentials of themore » cluster subunits as closely as possible and also self-consistently with one another in the cluster environment. They have been shown to lead to dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits like zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSE) known to plague direct evaluation of weak interactions have been eliminated by com-bining the Valiron–Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method in an economical fashion (quadratic scaling n2 with respect to the number of subunits n when n is small and linear scaling when n is large). A new variant of VMFC has also been proposed in which three-body and all higher-order Coulomb effects on BSSE are estimated approximately. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results of conventional electron correlation calculations within 0.1 kcal/mol. The proposed method is significantly more accurate and also efficient than conventional correlation methods uncorrected of BSSE.« less

Addition of a thallium vertex to empty and centered nine-atom deltahedral zintl ions of germanium and tin.

PubMed

Rios, Daniel; Gillett-Kunnath, Miriam M; Taylor, Jacob D; Oliver, Allen G; Sevov, Slavi C

2011-03-21

Nickel atoms were inserted into nine-atom deltahedral Zintl ions of E(9)(4-) (E = Ge, Sn) via reactions with Ni(cod)(2) (cod = cyclooctadiene), and [Ni@Sn(9)](3-) was structurally characterized. Both the empty and the Ni-centered clusters react with TlCp (Cp = cyclopentadienyl anion) and add a thallium vertex to form the deltahedral ten-atom closo-species [E(9)Tl](3-) and [Ni@E(9)Tl](3-), respectively. The structures of [Ge(9)Tl](3-) and [Ni@Sn(9)Tl](3-) showed that, as expected, the geometry of the ten-atom clusters is that of a bicapped square antiprism where the Tl-atom occupies one of the two capping vertices. This illustrates that centering a nine-atom cluster with a nickel atom does not change its reactivity toward TlCp. All compounds were characterized by electrospray mass spectrometry.

First-principles melting of gallium clusters down to nine atoms: structural and electronic contributions to melting.

PubMed

Steenbergen, Krista G; Gaston, Nicola

2013-10-07

First-principles Born-Oppenheimer molecular dynamics simulations of small gallium clusters, including parallel tempering, probe the distinction between cluster and molecule in the size range of 7-12 atoms. In contrast to the larger sizes, dynamic measures of structural change at finite temperature demonstrate that Ga7 and Ga8 do not melt, suggesting a size limit to melting in gallium exists at 9 atoms. Analysis of electronic structure further supports this size limit, additionally demonstrating that a covalent nature cannot be identified for clusters larger than the gallium dimer. Ga9, Ga10 and Ga11 melt at greater-than-bulk temperatures, with no evident covalent character. As Ga12 represents the first small gallium cluster to melt at a lower-than-bulk temperature, we examine the structural properties of each cluster at finite temperature in order to probe both the origins of greater-than-bulk melting, as well as the significant differences in melting temperatures induced by a single atom addition. Size-sensitive melting temperatures can be explained by both energetic and entropic differences between the solid and liquid phases for each cluster. We show that the lower-than-bulk melting temperature of the 12-atom cluster can be attributed to persistent pair bonding, reminiscent of the pairing observed in α-gallium. This result supports the attribution of greater-than-bulk melting in gallium clusters to the anomalously low melting temperature of the bulk, due to its dimeric structure.

Accelerating atomic structure search with cluster regularization

NASA Astrophysics Data System (ADS)

Sørensen, K. H.; Jørgensen, M. S.; Bruix, A.; Hammer, B.

2018-06-01

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

Melting phenomena: effect of composition for 55-atom Ag-Pd bimetallic clusters.

PubMed

Cheng, Daojian; Wang, Wenchuan; Huang, Shiping

2008-05-14

Understanding the composition effect on the melting processes of bimetallic clusters is important for their applications. Here, we report the relationship between the melting point and the metal composition for the 55-atom icosahedral Ag-Pd bimetallic clusters by canonical Monte Carlo simulations, using the second-moment approximation of the tight-binding potentials (TB-SMA) for the metal-metal interactions. Abnormal melting phenomena for the systems of interest are found. Our simulation results reveal that the dependence of the melting point on the composition is not a monotonic change, but experiences three different stages. The melting temperatures of the Ag-Pd bimetallic clusters increase monotonically with the concentration of the Ag atoms first. Then, they reach a plateau presenting almost a constant value. Finally, they decrease sharply at a specific composition. The main reason for this change can be explained in terms of the relative stability of the Ag-Pd bimetallic clusters at different compositions. The results suggest that the more stable the cluster, the higher the melting point for the 55-atom icosahedral Ag-Pd bimetallic clusters at different compositions.

Study of diffusion and local structure of sodium-silicate liquid: the molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Hung, Pham Khac; Noritake, Fumiya; San, Luyen Thi; Van, To Ba; Vinh, Le The

2017-10-01

A systematic analysis on sodium-silicate melt with various silica contents was carried out. The simulation revealed two diffusion mechanisms occurred in the melt: the bond-breaking and hopping between sites. The local structure was analyzed through T-simplexes. It was revealed that T-clusters have a non-spherical shape and represent the diffusion channel, in which Na atoms are dominant, but no any O atoms are located. The SiO2-poor melt acquires a long channel. In contrast, the SiO2-rich melt consists of unconnected short channels. The simulation also revealed the immobile and mobile regions which differ in local structure and constituent composition. We propose a new CL-function to characterizing the spatial distribution of different atom component. The spatial distribution of mobile and immobile atoms is found quite different. In particular, the immobile atoms are concentrated in high-density regions possessing very large density of immobile atoms. The spatial distribution of mobile atoms in contrast is more homogeneous.

Theoretical studies of large water clusters: (H2O)28, (H2O)29, (H2O)30, and (H2O)31 hexakaidecahedral structures

NASA Astrophysics Data System (ADS)

Khan, Arshad

1997-04-01

The 28, 29, 30, and 31 mer hexakaidecahedral water clusters were studied by applying the intermediate neglect of differential overlap self-consistent field restricted Hartree-Fock method (INDO SCF RHF) after parametrization for H and O atoms. The most stable 29 and 30 mer clusters have one and two water molecules, respectively within the cavity of the distorted hexakaidecahedral cage with stabilization energy/monomer values of around 10.9 and 11.0 kcal, respectively. The 31 mer cluster with three water molecules within the cavity is less stable than the isomer with two molecules within the cavity and the third one bonded outside of the cage by around 3 kcal/mol.

Correlation between the resistivity and the atomic clusters in liquid Cu-Sn alloys

NASA Astrophysics Data System (ADS)

Jia, Peng; Zhang, Jinyang; Hu, Xun; Li, Cancan; Zhao, Degang; Teng, XinYing; Yang, Cheng

2018-05-01

The liquid structure of CuxSn100-x (x = 0, 10, 20, 33, 40, 50, 60, 75, 80 and 100) alloys with atom percentage were investigated with resistivity and viscosity methods. It can be found from the resistivity data that the liquid Cu75Sn25 and Cu80Sn20 alloys had a negative temperature coefficient of resistivity (TCR), and liquid Cu75Sn25 alloy had a minimum value of -9.24 μΩ cm K-1. While the rest of liquid Cu-Sn alloys had a positive TCR. The results indicated that the Cu75Sn25 atomic clusters existed in Cu-Sn alloys. In addition, the method of calculating the percentage of Cu75Sn25 atomic clusters was established on the basis of resistivity theory and the law of conservation of mass. The Cu75Sn25 alloy had a maximum volume of the atomic clusters and a highest activation energy. The results further proved the existence of Cu75Sn25 atomic clusters. Furthermore, the correlation between the liquid structure and the resistivity was established. These results provide a useful reference for the investigation of liquid structure via the sensitive physical properties to the liquid structure.

Impact-parameter dependence of the energy loss of fast molecular clusters in hydrogen

NASA Astrophysics Data System (ADS)

Fadanelli, R. C.; Grande, P. L.; Schiwietz, G.

2008-03-01

The electronic energy loss of molecular clusters as a function of impact parameter is far less understood than atomic energy losses. For instance, there are no analytical expressions for the energy loss as a function of impact parameter for cluster ions. In this work, we describe two procedures to evaluate the combined energy loss of molecules: Ab initio calculations within the semiclassical approximation and the coupled-channels method using atomic orbitals; and simplified models for the electronic cluster energy loss as a function of the impact parameter, namely the molecular perturbative convolution approximation (MPCA, an extension of the corresponding atomic model PCA) and the molecular unitary convolution approximation (MUCA, a molecular extension of the previous unitary convolution approximation UCA). In this work, an improved ansatz for MPCA is proposed, extending its validity for very compact clusters. For the simplified models, the physical inputs are the oscillators strengths of the target atoms and the target-electron density. The results from these models applied to an atomic hydrogen target yield remarkable agreement with their corresponding ab initio counterparts for different angles between cluster axis and velocity direction at specific energies of 150 and 300 keV/u.

Autoionization following nanoplasma formation in atomic and molecular clusters

NASA Astrophysics Data System (ADS)

Schütte, Bernd; Lahl, Jan; Oelze, Tim; Krikunova, Maria; Vrakking, Marc J. J.; Rouzée, Arnaud

2016-05-01

Nanoplasmas resulting from the ionization of nano-scale particles by intense laser pulses are typically described by quasiclassical models, where electron emission is understood to take place via thermal processes. Recently, we discovered that, following the interaction of intense near-infrared (NIR) laser pulses with molecular oxygen clusters, electron emission from nanoplasmas can also occur from atomic bound states via autoionization [Schütte et al., Phys. Rev. Lett. 114, 123002 (2015)]. Here we extend these studies and demonstrate that the formation and decay of doubly-excited atoms and ions is a very common phenomenon in nanoplasmas. We report on the observation of autoionization involving spin-orbit excited states in molecular oxygen and carbon dioxide clusters as well as in atomic krypton and xenon clusters ionized by intense NIR pulses, for which we find clear bound-state signatures in the electron kinetic energy spectra. By applying terahertz (THz) streaking, we show that the observed autoionization processes take place on a picosecond to nanosecond timescale after the interaction of the NIR laser pulse with the clusters. Contribution to the Topical Issue "Atomic Cluster Collisions (7th International Symposium)", edited by Gerardo Delgado Barrio, Andrey Solov'Yov, Pablo Villarreal, Rita Prosmiti.

Phase stability and electronic structure of UMo2Al20: A first-principles study

NASA Astrophysics Data System (ADS)

Liu, Peng-Chuang; Xian, Ya-Jiang; Wang, Xin; Zhang, Yu-Ting; Zhang, Peng-Cheng

2017-09-01

In this paper, the phase stability of UMo2Al20 was explored using cluster formula in combination with first-principles calculations. Cluster formula analysis uncovered that the compound was composed of two principal clusters, i.e. [Mo-Al12] and [U-Al16]. The electronic interactions between U, Mo and Al atoms in this compound were discussed using elastic property, Bader charges and energy-resolved local bonding analysis, as well as the electronic interactions between Mo and Al atoms in [Mo-Al12] cluster and between U and Al atoms in [U-Al16] cluster. It revealed that UMo2Al20 satisfied the mechanical stability criterion for cubic system, and exhibited near ionic bonding character with weak bonding directionality. The calculations within both standard DFT and HSE frameworks demonstrated that U and Al atoms acted as an electron donor while Mo atoms acted as electron acceptor. The intrinsic stability of UMo2Al20 mainly stemmed from the bonding states of Mo-Al bonds and Al-Al bonds in [Mo-Al12] cluster. These calculations provide a further insight on the CeCr2Al20-type ternary compounds.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs.

PubMed

Mannix, Andrew J; Zhou, Xiang-Feng; Kiraly, Brian; Wood, Joshua D; Alducin, Diego; Myers, Benjamin D; Liu, Xiaolong; Fisher, Brandon L; Santiago, Ulises; Guest, Jeffrey R; Yacaman, Miguel Jose; Ponce, Arturo; Oganov, Artem R; Hersam, Mark C; Guisinger, Nathan P

2015-12-18

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal. Copyright © 2015, American Association for the Advancement of Science.

Growth of Ni nanoclusters on irradiated graphene: a molecular dynamics study.

PubMed

Valencia, F J; Hernandez-Vazquez, E E; Bringa, E M; Moran-Lopez, J L; Rogan, J; Gonzalez, R I; Munoz, F

2018-04-23

We studied the soft landing of Ni atoms on a previously damaged graphene sheet by means of molecular dynamics simulations. We found a monotonic decrease of the cluster frequency as a function of its size, but few big clusters comprise an appreciable fraction of the total number of Ni atoms. The aggregation of Ni atoms is also modeled by means of a simple phenomenological model. The results are in clear contrast with the case of hard or energetic landing of metal atoms, where there is a tendency to form mono-disperse metal clusters. This behavior is attributed to the high diffusion of unattached Ni atoms, together with vacancies acting as capture centers. The findings of this work show that a simple study of the energetics of the system is not enough in the soft landing regime, where it is unavoidable to also consider the growth process of metal clusters.

Derivatized gold clusters and antibody-gold cluster conjugates

DOEpatents

Hainfeld, James F.; Furuya, Frederic R.

1994-11-01

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab').sub.2 fragments thereof are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy.

Degradation of Perfluorinated Ether Lubricants on Pure Aluminum Surfaces: Semiempirical Quantum Chemical Modeling

NASA Technical Reports Server (NTRS)

Slaby, Scott M.; Ewing, David W.; Zehe, Michael J.

1997-01-01

The AM1 semiempirical quantum chemical method was used to model the interaction of perfluoroethers with aluminum surfaces. Perfluorodimethoxymethane and perfluorodimethyl ether were studied interacting with aluminum surfaces, which were modeled by a five-atom cluster and a nine-atom cluster. Interactions were studied for edge (high index) sites and top (low index) sites of the clusters. Both dissociative binding and nondissociative binding were found, with dissociative binding being stronger. The two different ethers bound and dissociated on the clusters in different ways: perfluorodimethoxymethane through its oxygen atoms, but perfluorodimethyl ether through its fluorine atoms. The acetal linkage of perfluorodimeth-oxymethane was the key structural feature of this molecule in its binding and dissociation on the aluminum surface models. The high-index sites of the clusters caused the dissociation of both ethers. These results are consistent with the experimental observation that perfluorinated ethers decompose in contact with sputtered aluminum surfaces.

Sequential desorption energy of hydrogen from nickel clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deepika,; Kumar, Rakesh, E-mail: rakesh@iitrpr.ac.in; R, Kamal Raj.

2015-06-24

We report reversible Hydrogen adsorption on Nickel clusters, which act as a catalyst for solid state storage of Hydrogen on a substrate. First-principles technique is employed to investigate the maximum number of chemically adsorbed Hydrogen molecules on Nickel cluster. We observe a maximum of four Hydrogen molecules adsorbed per Nickel atom, but the average Hydrogen molecules adsorbed per Nickel atom decrease with cluster size. The dissociative chemisorption energy per Hydrogen molecule and sequential desorption energy per Hydrogen atom on Nickel cluster is found to decrease with number of adsorbed Hydrogen molecules, which on optimization may help in economical storage andmore » regeneration of Hydrogen as a clean energy carrier.« less

Helium segregation on surfaces of plasma-exposed tungsten

DOE PAGES

Maroudas, Dimitrios; Blondel, Sophie; Hu, Lin; ...

2016-01-21

Here we report a hierarchical multi-scale modeling study of implanted helium segregation on surfaces of tungsten, considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations based on a reliable interatomic interaction potential, including molecular-statics simulations to understand the origin of helium surface segregation, targeted molecular-dynamics (MD) simulations of near-surface cluster reactions, and large-scale MD simulations of implanted helium evolution in plasma-exposed tungsten. We find that small, mobile He-n (1 <= n <= 7) clusters in the near-surface region are attracted to the surface due to an elastic interaction force that provides themore » thermodynamic driving force for surface segregation. Elastic interaction force induces drift fluxes of these mobile Hen clusters, which increase substantially as the migrating clusters approach the surface, facilitating helium segregation on the surface. Moreover, the clusters' drift toward the surface enables cluster reactions, most importantly trap mutation, in the near-surface region at rates much higher than in the bulk material. Moreover, these near-surface cluster dynamics have significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure. We integrate the findings of such atomic-scale simulations into a properly parameterized and validated spatially dependent, continuum-scale reaction-diffusion cluster dynamics model, capable of predicting implanted helium evolution, surface segregation, and its near-surface effects in tungsten. This cluster-dynamics model sets the stage for development of fully atomistically informed coarse-grained models for computationally efficient simulation predictions of helium surface segregation, as well as helium retention and surface morphological evolution, toward optimal design of plasma facing components.« less

Barrierless growth of precursor-free, ultrafast laser-fragmented noble metal nanoparticles by colloidal atom clusters - A kinetic in situ study.

PubMed

Jendrzej, Sandra; Gökce, Bilal; Amendola, Vincenzo; Barcikowski, Stephan

2016-02-01

Unintended post-synthesis growth of noble metal colloids caused by excess amounts of reactants or highly reactive atom clusters represents a fundamental problem in colloidal chemistry, affecting product stability or purity. Hence, quantified kinetics could allow defining nanoparticle size determination in dependence of the time. Here, we investigate in situ the growth kinetics of ps pulsed laser-fragmented platinum nanoparticles in presence of naked atom clusters in water without any influence of reducing agents or surfactants. The nanoparticle growth is investigated for platinum covering a time scale of minutes to 50days after nanoparticle generation, it is also supplemented by results obtained from gold and palladium. Since a minimum atom cluster concentration is exceeded, a significant growth is determined by time resolved UV/Vis spectroscopy, analytical disc centrifugation, zeta potential measurement and transmission electron microscopy. We suggest a decrease of atom cluster concentration over time, since nanoparticles grow at the expense of atom clusters. The growth mechanism during early phase (<1day) of laser-synthesized colloid is kinetically modeled by rapid barrierless coalescence. The prolonged slow nanoparticle growth is kinetically modeled by a combination of coalescence and Lifshitz-Slyozov-Wagner kinetic for Ostwald ripening, validated experimentally by the temperature dependence of Pt nanoparticle size and growth quenching by Iodide anions. Copyright © 2015. Published by Elsevier Inc.

Nanophase materials assembled from clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siegel, R.W.

1992-02-01

The preparation of metal and ceramic atom clusters by means of the gas-condensation method, followed by their in situ collection and consolidation under high-vacuum conditions, has recently led to the synthesis of a new class of ultrafine-grained materials. These nanophase materials, with typical average grain sizes of 5 to 50 nm and, hence, a large fraction of their atoms in interfaces, exhibit properties that are often considerably improved relative to those of conventional materials. Furthermore, their synthesis and processing characteristics should enable the design of new materials with unique properties. Some examples are ductile ceramics that can be formed andmore » sintered to full density at low temperatures without the need for binding or sintering aids, and metals with dramatically increased strength. The synthesis of these materials is briefly described along with what is presently known of their structure and properties. Their future impact on materials science and technology is also considered.« less

Molecular dynamics simulations investigating consecutive nucleation, solidification and grain growth in a twelve-million-atom Fe-system

NASA Astrophysics Data System (ADS)

Okita, Shin; Verestek, Wolfgang; Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi

2017-09-01

Continuous processes of homogeneous nucleation, solidification and grain growth are spontaneously achieved from an undercooled iron melt without any phenomenological parameter in the molecular dynamics (MD) simulation with 12 million atoms. The nucleation rate at the critical temperature is directly estimated from the atomistic configuration by cluster analysis to be of the order of 1034 m-3 s-1. Moreover, time evolution of grain size distribution during grain growth is obtained by the combination of Voronoi and cluster analyses. The grain growth exponent is estimated to be around 0.3 from the geometric average of the grain size distribution. Comprehensive understanding of kinetic properties during continuous processes is achieved in the large-scale MD simulation by utilizing the high parallel efficiency of a graphics processing unit (GPU), which is shedding light on the fundamental aspects of production processes of materials from the atomistic viewpoint.

C 60 -induced Devil's Staircase transformation on a Pb/Si(111) wetting layer

DOE PAGES

Wang, Lin -Lin; Johnson, Duane D.; Tringides, Michael C.

2015-12-03

Density functional theory is used to study structural energetics of Pb vacancy cluster formation on C 60/Pb/Si(111) to explain the unusually fast and error-free transformations between the “Devil's Staircase” (DS) phases on the Pb/Si(111) wetting layer at low temperature (~110K). The formation energies of vacancy clusters are calculated in C 60/Pb/Si(111) as Pb atoms are progressively ejected from the initial dense Pb wetting layer. Vacancy clusters larger than five Pb atoms are found to be stable with seven being the most stable, while vacancy clusters smaller than five are highly unstable, which agrees well with the observed ejection rate ofmore » ~5 Pb atoms per C 60. Furthermore, the high energy cost (~0.8 eV) for the small vacancy clusters to form indicates convincingly that the unusually fast transformation observed experimentally between the DS phases, upon C 60 adsorption at low temperature, cannot be the result of single-atom random walk diffusion but of correlated multi-atom processes.« less

Theoretical studies on structural, magnetic, and spintronic characteristics of sandwiched Eu(n)COT(n+1) (n = 1-4) clusters.

PubMed

Zhang, Xiuyun; Ng, Man-Fai; Wang, Yanbiao; Wang, Jinlan; Yang, Shuo-Wang

2009-09-22

Europium (Eu)-cyclootetatrene (COT = C(8)H(8)) multidecker clusters (Eu(n)COT(n+1), n = 1-4) are studied by relativistic density functional theory calculations. These clusters are found to be thermodynamically stable with freely rotatable COT rings, and their total magnetic moments (MMs) increase linearly along with the number of Eu atoms. Each Eu atom contributes about 7 mu(B) to the cluster. Meanwhile, the internal COT rings have little MM contribution while the external COT rings have about 1 mu(B) MM aligned in opposite direction to that of the Eu atoms. The total MM of the Eu(n)COT(n+1) clusters can thus be generalized as 7n - 2 mu(B) where n is the number of Eu atoms. Besides, the ground states of these clusters are ferromagnetic and energetically competitive with the antiferromagnetic states, meaning that their spin states are very unstable, especially for larger clusters. More importantly, we uncover an interesting bonding characteristic of these clusters in which the interior ionic structure is capped by two hybrid covalent-ionic terminals. We suggest that such a characteristic makes the Eu(n)COT(n+1) clusters extremely stable. Finally, we reveal that for the positively charged clusters, the hybrid covalent-ionic terminals will tip further toward the interior part of the clusters to form deeper covalent-ionic caps. In contrast, the negatively charged clusters turn to pure ionic structures.

Recombination-enhanced surface expansion of clusters in intense soft x-ray laser pulses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rupp, Daniela; Flückiger, Leonie; Adolph, Marcus

Here, we studied the nanoplasma formation and explosion dynamics of single large xenon clusters in ultrashort, intense x-ray free-electron laser pulses via ion spectroscopy. The simultaneous measurement of single-shot diffraction images enabled a single-cluster analysis that is free from any averaging over the cluster size and laser intensity distributions. The measured charge state-resolved ion energy spectra show narrow distributions with peak positions that scale linearly with final ion charge state. These two distinct signatures are attributed to highly efficient recombination that eventually leads to the dominant formation of neutral atoms in the cluster. The measured mean ion energies exceed themore » value expected without recombination by more than an order of magnitude, indicating that the energy release resulting from electron-ion recombination constitutes a previously unnoticed nanoplasma heating process. This conclusion is supported by results from semiclassical molecular dynamics simulations.« less

Medium-induced change of the optical response of metal clusters in rare-gas matrices

NASA Astrophysics Data System (ADS)

Xuan, Fengyuan; Guet, Claude

2017-10-01

Interaction with the surrounding medium modifies the optical response of embedded metal clusters. For clusters from about ten to a few hundreds of silver atoms, embedded in rare-gas matrices, we study the environment effect within the matrix random phase approximation with exact exchange (RPAE) quantum approach, which has proved successful for free silver clusters. The polarizable surrounding medium screens the residual two-body RPAE interaction, adds a polarization term to the one-body potential, and shifts the vacuum energy of the active delocalized valence electrons. Within this model, we calculate the dipole oscillator strength distribution for Ag clusters embedded in helium droplets, neon, argon, krypton, and xenon matrices. The main contribution to the dipole surface plasmon red shift originates from the rare-gas polarization screening of the two-body interaction. The large size limit of the dipole surface plasmon agrees well with the classical prediction.

Recombination-enhanced surface expansion of clusters in intense soft x-ray laser pulses

DOE PAGES

Rupp, Daniela; Flückiger, Leonie; Adolph, Marcus; ...

2016-10-07

Here, we studied the nanoplasma formation and explosion dynamics of single large xenon clusters in ultrashort, intense x-ray free-electron laser pulses via ion spectroscopy. The simultaneous measurement of single-shot diffraction images enabled a single-cluster analysis that is free from any averaging over the cluster size and laser intensity distributions. The measured charge state-resolved ion energy spectra show narrow distributions with peak positions that scale linearly with final ion charge state. These two distinct signatures are attributed to highly efficient recombination that eventually leads to the dominant formation of neutral atoms in the cluster. The measured mean ion energies exceed themore » value expected without recombination by more than an order of magnitude, indicating that the energy release resulting from electron-ion recombination constitutes a previously unnoticed nanoplasma heating process. This conclusion is supported by results from semiclassical molecular dynamics simulations.« less

Effects of carbonyl bond, metal cluster dissociation, and evaporation rates on predictions of nanotube production in high-pressure carbon monoxide

NASA Technical Reports Server (NTRS)

Scott, Carl D.; Smalley, Richard E.

2003-01-01

The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNTs) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the conformation of CO2. It is shown that the production of CO2 is significantly greater for FeCO because of its lower bond energy as compared with that of NiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

Effects of Carbonyl Bond and Metal Cluster Dissociation and Evaporation Rates on Predictions of Nanotube Production in HiPco

NASA Technical Reports Server (NTRS)

Scott, Carl D.; Smalley, Richard E.

2002-01-01

The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNT) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the co-formation of CO2. It is shown that the production of CO2 is significantly greater for FeCO due to its lower bond energy as compared with that ofNiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

Conformational Properties, Spectroscopy and Structure of ISATIN-(WATER)_{n=1-3} Clusters

NASA Astrophysics Data System (ADS)

Singh, Milind K.; Upadhya, D. M.; Singh, Vipin B.

2009-06-01

The structure, stability and vibrational characteristics of Isatin-(Water)_n clusters with n=1=3 have been investigated using second order Moller-Plesset (MP2) perturbation tehory and Density Functional Theory (with B3LYP) methods employing the basis set 6-31+G(d). The vertical excitation energies for these complexes have been also computed using the time-dependent density functional theory. The three stable conformational isomers, each for Isatin-(Water)_1 and Isatin-(Water)_2 clusters were obtained. It is shown that in the most stable isomer of Isatin-(Water)_1 cluster hydrogen bond between amide hydrogen and oxygen of water is found stronger as compared to the H-bond in Indole-(Water)_1 cluster. For a particular position of complexation of water, between the carbonyl oxygen's, results an unusual increase in the dipole moment due to an electronic charge displacement from the N atom to the C atom of the neighboring carbonyl bond. This causes a large separation between the effective charges forming the dipole. The complexes involving this position of water are expected to show a small charge transfer character. The experimentally observed electronic absorption peaks are reasonably reproduced by the TD-DFT calculations and it is found that the longest wavelength absorption peak of isatin at 406 nm is significantly red shifted after addition of a water molecule.

The role of highly oxygenated molecules (HOMs) in determining the composition of ambient ions in the boreal forest

NASA Astrophysics Data System (ADS)

Bianchi, Federico; Garmash, Olga; He, Xucheng; Yan, Chao; Iyer, Siddharth; Rosendahl, Ida; Xu, Zhengning; Rissanen, Matti P.; Riva, Matthieu; Taipale, Risto; Sarnela, Nina; Petäjä, Tuukka; Worsnop, Douglas R.; Kulmala, Markku; Ehn, Mikael; Junninen, Heikki

2017-11-01

In order to investigate the negative ions in the boreal forest we have performed measurements to chemically characterise the composition of negatively charged clusters containing highly oxygenated molecules (HOMs). Additionally, we compared this information with the chemical composition of the neutral gas-phase molecules detected in the ambient atmosphere during the same period. The chemical composition of the ions was retrieved using an atmospheric pressure interface time-of-flight mass spectrometer (APi-TOF-MS) while the gas-phase neutral molecules (mainly sulfuric acid and HOMs) were characterised using the same mass spectrometer coupled to a nitrate-based chemical ionisation unit (CI-APi-TOF). Overall, we divided the identified HOMs in two classes: HOMs containing only carbon, hydrogen and oxygen and nitrogen-containing HOMs or organonitrates (ONs). During the day, among the ions, in addition to the well-known pure sulfuric acid clusters, we found a large number of HOMs clustered with nitrate (NO3-) or bisulfate (HSO4-), with the first one being more abundant. During the night, the distribution of ions, mainly composed of HOM clustered with NO3-, was very similar to the neutral compounds that are detected in the CI-APi-TOF as adducts with the artificially introduced primary ion (NO3-). For the first time, we identified several clusters containing up to 40 carbon atoms. These ions are formed by up to four oxidised α-pinene units clustered with NO3-. While we know that dimers (16-20 carbon atoms) are probably formed by a covalent bond between two α-pinene oxidised units, it is still unclear what bonding formed larger clusters. Finally, diurnal profiles of the negative ions were consistent with the neutral compounds revealing that ONs peak during the day while HOMs are more abundant at night-time. However, during the day, a large fraction of the negative charge is taken up by the pure sulfuric acid clusters causing differences between ambient ions and neutral compounds (i.e. less available charge for HOM and ON).

Structure determination in 55-atom Li-Na and Na-K nanoalloys.

PubMed

Aguado, Andrés; López, José M

2010-09-07

The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions.

A Hardware-Accelerated Quantum Monte Carlo framework (HAQMC) for N-body systems

NASA Astrophysics Data System (ADS)

Gothandaraman, Akila; Peterson, Gregory D.; Warren, G. Lee; Hinde, Robert J.; Harrison, Robert J.

2009-12-01

Interest in the study of structural and energetic properties of highly quantum clusters, such as inert gas clusters has motivated the development of a hardware-accelerated framework for Quantum Monte Carlo simulations. In the Quantum Monte Carlo method, the properties of a system of atoms, such as the ground-state energies, are averaged over a number of iterations. Our framework is aimed at accelerating the computations in each iteration of the QMC application by offloading the calculation of properties, namely energy and trial wave function, onto reconfigurable hardware. This gives a user the capability to run simulations for a large number of iterations, thereby reducing the statistical uncertainty in the properties, and for larger clusters. This framework is designed to run on the Cray XD1 high performance reconfigurable computing platform, which exploits the coarse-grained parallelism of the processor along with the fine-grained parallelism of the reconfigurable computing devices available in the form of field-programmable gate arrays. In this paper, we illustrate the functioning of the framework, which can be used to calculate the energies for a model cluster of helium atoms. In addition, we present the capabilities of the framework that allow the user to vary the chemical identities of the simulated atoms. Program summaryProgram title: Hardware Accelerated Quantum Monte Carlo (HAQMC) Catalogue identifier: AEEP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 691 537 No. of bytes in distributed program, including test data, etc.: 5 031 226 Distribution format: tar.gz Programming language: C/C++ for the QMC application, VHDL and Xilinx 8.1 ISE/EDK tools for FPGA design and development Computer: Cray XD1 consisting of a dual-core, dualprocessor AMD Opteron 2.2 GHz with a Xilinx Virtex-4 (V4LX160) or Xilinx Virtex-II Pro (XC2VP50) FPGA per node. We use the compute node with the Xilinx Virtex-4 FPGA Operating system: Red Hat Enterprise Linux OS Has the code been vectorised or parallelized?: Yes Classification: 6.1 Nature of problem: Quantum Monte Carlo is a practical method to solve the Schrödinger equation for large many-body systems and obtain the ground-state properties of such systems. This method involves the sampling of a number of configurations of atoms and averaging the properties of the configurations over a number of iterations. We are interested in applying the QMC method to obtain the energy and other properties of highly quantum clusters, such as inert gas clusters. Solution method: The proposed framework provides a combined hardware-software approach, in which the QMC simulation is performed on the host processor, with the computationally intensive functions such as energy and trial wave function computations mapped onto the field-programmable gate array (FPGA) logic device attached as a co-processor to the host processor. We perform the QMC simulation for a number of iterations as in the case of our original software QMC approach, to reduce the statistical uncertainty of the results. However, our proposed HAQMC framework accelerates each iteration of the simulation, by significantly reducing the time taken to calculate the ground-state properties of the configurations of atoms, thereby accelerating the overall QMC simulation. We provide a generic interpolation framework that can be extended to study a variety of pure and doped atomic clusters, irrespective of the chemical identities of the atoms. For the FPGA implementation of the properties, we use a two-region approach for accurately computing the properties over the entire domain, employ deep pipelines and fixed-point for all our calculations guaranteeing the accuracy required for our simulation.

Anion photoelectron spectroscopy of germanium and tin clusters containing a transition- or lanthanide-metal atom; MGe(n)- (n = 8-20) and MSn(n)- (n = 15-17) (M = Sc-V, Y-Nb, and Lu-Ta).

PubMed

Atobe, Junko; Koyasu, Kiichirou; Furuse, Shunsuke; Nakajima, Atsushi

2012-07-14

The electronic properties of germanium and tin clusters containing a transition- or lanthanide-metal atom from group 3, 4, or 5, MGe(n) (M = Sc, Ti, V, Y, Zr, Nb, Lu, Hf, and Ta) and MSn(n) (M = Sc, Ti, Y. Zr, and Hf), were investigated by anion photoelectron spectroscopy at 213 nm. In the case of the group 3 elements Sc, Y, and Lu, the threshold energy of electron detachment of MGe(n)(-) exhibits local maxima at n = 10 and 16, while in the case of the group 4 elements Ti, Zr, and Hf, it exhibits a local minimum only at n = 16, associated with the presence of a small bump in the spectrum. A similar behavior is observed for MSn(n)(-) around n = 16, and these electronic characteristics of MGe(n) and MSn(n) are closely related to those of MSi(n). Compared to MSi(n), however, the larger cavity size of a Ge(n) cage allows metal atom encapsulation at a smaller size n. A cooperative effect between the electronic and geometric structures of clusters with a large cavity of Ge(16) or Sn(16) is discussed together with the results of experiments that probe their geometric stability via their reactivity to H(2)O adsorption.

Al7CX (X=Li-Cs) clusters: Stability and the prospect for cluster materials

NASA Astrophysics Data System (ADS)

Ashman, C.; Khanna, S. N.; Pederson, M. R.; Kortus, J.

2000-12-01

Al7C clusters, recently found to have a high-electron affinity and exceptional stability, are shown to form ionic molecules when combined with alkali-metal atoms. Our studies, based on an ab initio gradient-corrected density-functional scheme, show that Al7CX (X=Li-Cs) clusters have a very low-electron affinity and a high-ionization potential. When combined, the two- and four-atom composite clusters of Al7CLi units leave the Al7C clusters almost intact. Preliminary studies indicate that Al7CLi may be suitable to form cluster-based materials.

Derivatized gold clusters and antibody-gold cluster conjugates

DOEpatents

Hainfeld, J.F.; Furuya, F.R.

1994-11-01

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab')[sub 2] fragments are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy. 7 figs.

Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp, E-mail: philipp.marquetand@univie.ac.at

Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy ismore » constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.« less

Restructuring and Hydrogen Evolution on Pt Nanoparticle† †Electronic supplementary information (ESI) available: Discussions on the structures of Pt clusters and the stability of the subsurface H atoms in Pt cluster, TS structure of H–H coupling on {111} facets of Pt44H80, XYZ coordinate of Pt44 and Pt44H80. Movie of structure evolution at Pt44H50 See DOI: 10.1039/c4sc02806f Click here for additional data file. Click here for additional data file.

PubMed Central

Wei, Guang-Feng

2015-01-01

The restructuring of nanoparticles at the in situ condition is a common but complex phenomenon in nanoscience. Here, we present the first systematic survey on the structure dynamics and its catalytic consequence for hydrogen evolution reaction (HER) on Pt nanoparticles, as represented by a magic number Pt44 octahedron (∼1 nm size). Using a first principles calculation based global structure search method, we stepwise follow the significant nanoparticle restructuring under HER conditions as driven by thermodynamics to expose {100} facets, and reveal the consequent large activity enhancement due to the marked increase of the concentration of the active site, being identified to be apex atoms. The enhanced kinetics is thus a “byproduct” of the thermodynamical restructuring. Based on the results, the best Pt catalyst for HER is predicted to be ultrasmall Pt particles without core atoms, a size below ∼20 atoms. PMID:29560237

Classification Order of Surface-Confined Intermixing at Epitaxial Interface

NASA Astrophysics Data System (ADS)

Michailov, M.

The self-organization phenomena at epitaxial interface hold special attention in contemporary material science. Being relevant to the fundamental physical problem of competing, long-range and short-range atomic interactions in systems with reduced dimensionality, these phenomena have found exacting academic interest. They are also of great technological importance for their ability to bring spontaneous formation of regular nanoscale surface patterns and superlattices with exotic properties. The basic phenomenon involved in this process is surface diffusion. That is the motivation behind the present study which deals with important details of diffusion scenarios that control the fine atomic structure of epitaxial interface. Consisting surface imperfections (terraces, steps, kinks, and vacancies), the interface offers variety of barriers for surface diffusion. Therefore, the adatoms and clusters need a certain critical energy to overcome the corresponding diffusion barriers. In the most general case the critical energies can be attained by variation of the system temperature. Hence, their values define temperature limits of system energy gaps associated with different diffusion scenarios. This systematization imply classification order of surface alloying: blocked, incomplete, and complete. On that background, two diffusion problems, related to the atomic-scale surface morphology, will be discussed. The first problem deals with diffusion of atomic clusters on atomically smooth interface. On flat domains, far from terraces and steps, we analyzed the impact of size, shape, and cluster/substrate lattice misfit on the diffusion behavior of atomic clusters (islands). We found that the lattice constant of small clusters depends on the number N of building atoms at 1 < N ≤ 10. In heteroepitaxy, this effect of variable lattice constant originates from the enhanced charge transfer and the strong influence of the surface potential on cluster atomic arrangement. At constant temperature, the variation of the lattice constant leads to variable misfit which affects the island migration. The cluster/substrate commensurability influences the oscillation behavior of the diffusion coefficient caused by variation in the cluster shape. We discuss the results in a physical model that implies cluster diffusion with size-dependent cluster/substrate misfit. The second problem is devoted to diffusion phenomena in the vicinity of atomic terraces on stepped or vicinal surfaces. Here, we develop a computational model that refines important details of diffusion behavior of adatoms accounting for the energy barriers at specific atomic sites (smooth domains, terraces, and steps) located on the crystal surface. The dynamic competition between energy gained by mixing and substrate strain energy results in diffusion scenario where adatoms form alloyed islands and alloyed stripes in the vicinity of terrace edges. Being in agreement with recent experimental findings, the observed effect of stripe and island alloy formation opens up a way regular surface patterns to be configured at different atomic levels on the crystal surface. The complete surface alloying of the entire interface layer is also briefly discussed with critical analysis and classification of experimental findings and simulation data.

Electronic and magnetic properties of small rhodium clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

We report a theoretical study of the electronic and magnetic properties of rhodium-atomic clusters. The lowest energy structures at the semi-empirical level of rhodium clusters are first obtained from a novel global-minimum search algorithm, known as PTMBHGA, where Gupta potential is used to describe the atomic interaction among the rhodium atoms. The structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof generalized gradient approximation. For the purpose of calculating the magnetic moment of a given cluster, we calculate the optimized structure as a function of the spin multiplicity within the DFT framework.more » The resultant magnetic moments with the lowest energies so obtained allow us to work out the magnetic moment as a function of cluster size. Rhodium atomic clusters are found to display a unique variation in the magnetic moment as the cluster size varies. However, Rh{sub 4} and Rh{sub 6} are found to be nonmagnetic. Electronic structures of the magnetic ground-state structures are also investigated within the DFT framework. The results are compared against those based on different theoretical approaches available in the literature.« less

Structural and magnetic properties of FeGen-/0 (n = 3-12) clusters: Mass-selected anion photoelectron spectroscopy and density functional theory calculations

NASA Astrophysics Data System (ADS)

Deng, Xiao-Jiao; Kong, Xiang-Yu; Liang, Xiaoqing; Yang, Bin; Xu, Hong-Guang; Xu, Xi-Ling; Feng, Gang; Zheng, Wei-Jun

2017-12-01

The structural, electronic, and magnetic properties of FeGen-/0 (n = 3-12) clusters were investigated by using anion photoelectron spectroscopy in combination with density functional theory calculations. For both anionic and neutral FeGen (n = 3-12) clusters with n ≤ 7, the dominant structures are exohedral. The FeGe8-/0 clusters have half-encapsulated boat-shaped structures, and the opening of the boat-shaped structure is gradually covered by the additional Ge atoms to form Gen cage from n = 9 to 11. The structures of FeGe10-/0 can be viewed as two Ge atoms symmetrically capping the opening of the boat-shaped structure of FeGe8, and those of FeGe12-/0 are distorted hexagonal prisms with the Fe atom at the center. Natural population analysis shows that there is an electron transfer from the Ge atoms to the Fe atom at n = 8-12. The total magnetic moment of FeGen-/0 and local magnetic moment of the Fe atom have not been quenched.

Atom-Level Understanding of the Sodiation Process in Silicon Anode Material.

PubMed

Jung, Sung Chul; Jung, Dae Soo; Choi, Jang Wook; Han, Young-Kyu

2014-04-03

Despite the exceptionally large capacities in Li ion batteries, Si has been considered inappropriate for applications in Na ion batteries. We report an atomic-level study on the applicability of a Si anode in Na ion batteries using ab initio molecular dynamics simulations. While crystalline Si is not suitable for alloying with Na atoms, amorphous Si can accommodate 0.76 Na atoms per Si atom, corresponding to a specific capacity of 725 mA h g(-1). Bader charge analyses reveal that the sodiation of an amorphous Si electrode continues until before the local Na-rich clusters containing neutral Na atoms are formed. The amorphous Na0.76Si phase undergoes a volume expansion of 114% and shows a Na diffusivity of 7 × 10(-10) cm(2) s(-1) at room temperature. Overall, the amorphous Si phase turns out quite attractive in performance compared to other alloy-type anode materials. This work suggests that amorphous Si might be a competitive candidate for Na ion battery anodes.

Density functional theory study of small X-doped Mg(n) (X = Fe, Co, Ni, n = 1-9) bimetallic clusters: equilibrium structures, stabilities, electronic and magnetic properties.

PubMed

Kong, Fanjie; Hu, Yanfei

2014-03-01

The geometries, stabilities, and electronic and magnetic properties of Mg(n) X (X = Fe, Co, Ni, n = 1-9) clusters were investigated systematically within the framework of the gradient-corrected density functional theory. The results show that the Mg(n)Fe, Mg(n)Co, and Mg(n)Ni clusters have similar geometric structures and that the X atom in Mg(n)X clusters prefers to be endohedrally doped. The average atomic binding energies, fragmentation energies, second-order differences in energy, and HOMO-LUMO gaps show that Mg₄X (X = Fe, Co, Ni) clusters possess relatively high stability. Natural population analysis was performed and the results showed that the 3s and 4s electrons always transfer to the 3d and 4p orbitals in the bonding atoms, and that electrons also transfer from the Mg atoms to the doped atoms (Fe, Co, Ni). In addition, the spin magnetic moments were analyzed and compared. Several clusters, such as Mg₁,₂,₃,₄,₅,₆,₈,₉Fe, Mg₁,₂,₄,₅,₆,₈,₉Co, and Mg₁,₂,₅,₆,₇,₉Ni, present high magnetic moments (4 μ(B), 3 μ(B), and 2 μ(B), respectively).

Statistical analysis of atom probe data: detecting the early stages of solute clustering and/or co-segregation.

PubMed

Hyde, J M; Cerezo, A; Williams, T J

2009-04-01

Statistical analysis of atom probe data has improved dramatically in the last decade and it is now possible to determine the size, the number density and the composition of individual clusters or precipitates such as those formed in reactor pressure vessel (RPV) steels during irradiation. However, the characterisation of the onset of clustering or co-segregation is more difficult and has traditionally focused on the use of composition frequency distributions (for detecting clustering) and contingency tables (for detecting co-segregation). In this work, the authors investigate the possibility of directly examining the neighbourhood of each individual solute atom as a means of identifying the onset of solute clustering and/or co-segregation. The methodology involves comparing the mean observed composition around a particular type of solute with that expected from the overall composition of the material. The methodology has been applied to atom probe data obtained from several irradiated RPV steels. The results show that the new approach is more sensitive to fine scale clustering and co-segregation than that achievable using composition frequency distribution and contingency table analyses.

Effects of single atom doping on the ultrafast electron dynamics of M1Au24(SR)18 (M = Pd, Pt) nanoclusters

NASA Astrophysics Data System (ADS)

Zhou, Meng; Qian, Huifeng; Sfeir, Matthew Y.; Nobusada, Katsuyuki; Jin, Rongchao

2016-03-01

Atomically precise, doped metal clusters are receiving wide research interest due to their synergistic properties dependent on the metal composition. To understand the electronic properties of doped clusters, it is highly desirable to probe the excited state behavior. Here, we report the ultrafast relaxation dynamics of doped M1@Au24(SR)18 (M = Pd, Pt; R = CH2CH2Ph) clusters using femtosecond visible and near infrared transient absorption spectroscopy. Three relaxation components are identified for both mono-doped clusters: (1) sub-picosecond relaxation within the M1Au12 core states; (2) core to shell relaxation in a few picoseconds; and (3) relaxation back to the ground state in more than one nanosecond. Despite similar relaxation pathways for the two doped nanoclusters, the coupling between the metal core and surface ligands is accelerated by over 30% in the case of the Pt dopant compared with the Pd dopant. Compared to Pd doping, the case of Pt doping leads to much more drastic changes in the steady state and transient absorption of the clusters, which indicates that the 5d orbitals of the Pt atom are more strongly mixed with Au 5d and 6s orbitals than the 4d orbitals of the Pd dopant. These results demonstrate that a single foreign atom can lead to entirely different excited state spectral features of the whole cluster compared to the parent Au25(SR)18 cluster. The detailed excited state dynamics of atomically precise Pd/Pt doped gold clusters help further understand their properties and benefit the development of energy-related applications.Atomically precise, doped metal clusters are receiving wide research interest due to their synergistic properties dependent on the metal composition. To understand the electronic properties of doped clusters, it is highly desirable to probe the excited state behavior. Here, we report the ultrafast relaxation dynamics of doped M1@Au24(SR)18 (M = Pd, Pt; R = CH2CH2Ph) clusters using femtosecond visible and near infrared transient absorption spectroscopy. Three relaxation components are identified for both mono-doped clusters: (1) sub-picosecond relaxation within the M1Au12 core states; (2) core to shell relaxation in a few picoseconds; and (3) relaxation back to the ground state in more than one nanosecond. Despite similar relaxation pathways for the two doped nanoclusters, the coupling between the metal core and surface ligands is accelerated by over 30% in the case of the Pt dopant compared with the Pd dopant. Compared to Pd doping, the case of Pt doping leads to much more drastic changes in the steady state and transient absorption of the clusters, which indicates that the 5d orbitals of the Pt atom are more strongly mixed with Au 5d and 6s orbitals than the 4d orbitals of the Pd dopant. These results demonstrate that a single foreign atom can lead to entirely different excited state spectral features of the whole cluster compared to the parent Au25(SR)18 cluster. The detailed excited state dynamics of atomically precise Pd/Pt doped gold clusters help further understand their properties and benefit the development of energy-related applications. Electronic supplementary information (ESI) available: The pump dependent transient absorption spectra and the corresponding global analysis results. See DOI: 10.1039/c6nr01008c

Experimental and theoretical study of the microsolvation of sodium atoms in methanol clusters: differences and similarities to sodium-water and sodium-ammonia.

PubMed

Dauster, Ingo; Suhm, Martin A; Buck, Udo; Zeuch, Thomas

2008-01-07

Methanol clusters are generated in a continuous He-seeded supersonic expansion and doped with sodium atoms in a pick-up cell. By this method, clusters of the type Na(CH(3)OH)(n) are formed and subsequently photoionized by applying a tunable dye-laser system. The microsolvation process of the Na 3s electron is studied by determining the ionization potentials (IPs) of these clusters size-selectively for n = 2-40. A decrease is found from n = 2 to 6 and a constant value of 3.19 +/- 0.07 eV for n = 6-40. The experimentally-determined ionization potentials are compared with ionization potentials derived from quantum-chemical calculations, assuming limiting vertical and adiabatic processes. In the first case, energy differences are calculated between the neutral and the ionized cationic clusters of the same geometry. In the second case, the ionized clusters are used in their optimized relaxed geometry. These energy differences and relative stabilities of isomeric clusters vary significantly with the applied quantum-chemical method (B3LYP or MP2). The comparison with the experiment for n = 2-7 reveals strong variations of the ionization potential with the cluster structure indicating that structural diversity and non-vertical pathways give significant signal contributions at the threshold. Based on these findings, a possible explanation for the remarkable difference in IP evolutions of methanol or water and ammonia is presented: for methanol and water a rather localized surface or semi-internal Na 3s electron is excited to either high Rydberg or more localized states below the vertical ionization threshold. This excitation is followed by a local structural relaxation that couples to an autoionization process. For small clusters with n < 6 for methanol and n < 4 for water the addition of solvent molecules leads to larger solvent-metal-ion interaction energies, which consequently lead to lower ionization thresholds. For n = 6 (methanol) and n = 4 (water) this effect comes to a halt, which may be connected with the completion of the first cationic solvation shell limiting the release of local relaxation energy. For Na(NH(3))(n), a largely delocalized and internal electron is excited to autoionizing electronic states, a process that is no longer local and consequently may depend on cluster size up to very large n.

Structural and electronic properties for atomic clusters

NASA Astrophysics Data System (ADS)

Sun, Yan

We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

Helium segregation on surfaces of plasma-exposed tungsten

NASA Astrophysics Data System (ADS)

Maroudas, Dimitrios; Blondel, Sophie; Hu, Lin; Hammond, Karl D.; Wirth, Brian D.

2016-02-01

We report a hierarchical multi-scale modeling study of implanted helium segregation on surfaces of tungsten, considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations based on a reliable interatomic interaction potential, including molecular-statics simulations to understand the origin of helium surface segregation, targeted molecular-dynamics (MD) simulations of near-surface cluster reactions, and large-scale MD simulations of implanted helium evolution in plasma-exposed tungsten. We find that small, mobile He n (1  ⩽  n  ⩽  7) clusters in the near-surface region are attracted to the surface due to an elastic interaction force that provides the thermodynamic driving force for surface segregation. This elastic interaction force induces drift fluxes of these mobile He n clusters, which increase substantially as the migrating clusters approach the surface, facilitating helium segregation on the surface. Moreover, the clusters’ drift toward the surface enables cluster reactions, most importantly trap mutation, in the near-surface region at rates much higher than in the bulk material. These near-surface cluster dynamics have significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure. We integrate the findings of such atomic-scale simulations into a properly parameterized and validated spatially dependent, continuum-scale reaction-diffusion cluster dynamics model, capable of predicting implanted helium evolution, surface segregation, and its near-surface effects in tungsten. This cluster-dynamics model sets the stage for development of fully atomistically informed coarse-grained models for computationally efficient simulation predictions of helium surface segregation, as well as helium retention and surface morphological evolution, toward optimal design of plasma facing components.

Classical plasma dynamics of Mie-oscillations in atomic clusters

NASA Astrophysics Data System (ADS)

Kull, H.-J.; El-Khawaldeh, A.

2018-04-01

Mie plasmons are of basic importance for the absorption of laser light by atomic clusters. In this work we first review the classical Rayleigh-theory of a dielectric sphere in an external electric field and Thomson’s plum-pudding model applied to atomic clusters. Both approaches allow for elementary discussions of Mie oscillations, however, they also indicate deficiencies in describing the damping mechanisms by electrons crossing the cluster surface. Nonlinear oscillator models have been widely studied to gain an understanding of damping and absorption by outer ionization of the cluster. In the present work, we attempt to address the issue of plasmon relaxation in atomic clusters in more detail based on classical particle simulations. In particular, we wish to study the role of thermal motion on plasmon relaxation, thereby extending nonlinear models of collective single-electron motion. Our simulations are particularly adopted to the regime of classical kinetics in weakly coupled plasmas and to cluster sizes extending the Debye-screening length. It will be illustrated how surface scattering leads to the relaxation of Mie oscillations in the presence of thermal motion and of electron spill-out at the cluster surface. This work is intended to give, from a classical perspective, further insight into recent work on plasmon relaxation in quantum plasmas [1].

Molecular dynamics investigation of dynamical heterogeneity and local structure in the supercooled liquid and glass states of Al

NASA Astrophysics Data System (ADS)

Li, Maozhi; Wang, Cai-Zhuang; Mendelev, Mikhail I.; Ho, Kai-Ming

2008-05-01

Molecular dynamics simulations are performed to study the structure and dynamical heterogeneity in the liquid and glass states of Al using a frequently employed embedded atom potential. While the pair correlation function of the glass and liquid states displays only minor differences, the icosahedral short-range order (ISRO) and the dynamics of the two states are very different. The ISRO is much stronger in the glass than in the liquid. It is also found that both the most mobile and the most immobile atoms in the glass state tend to form clusters, and the clusters formed by the immobile atoms are more compact. In order to investigate the local environment of each atom in the liquid and glass states, a local density is defined to characterize the local atomic packing. There is a strong correlation between the local packing density and the mobility of the atoms. These results indicate that dynamical heterogeneity in glasses is directly correlated to the local structure. We also analyze the diffusion mechanisms of atoms in the liquid and glass states. It is found that for the mobile atoms in the glass state, initially they are confined in the cages formed by their nearest neighbors and vibrating. On the time scale of β relaxation, the mobile atoms try to break up the cage confinement and hop into new cages. In the supercooled liquid states, however, atoms continuously diffuse. Furthermore, it is found that on the time scale of β relaxation, some of the mobile atoms in the glass state cooperatively hop, which is facilitated by the stringlike cluster structures. On the longer time scale, it is found that a certain fraction of atoms can simultaneously hop, although they are not nearest neighbors. Further analysis shows that these hopping atoms form big and more compact clusters than the characterized most mobile atoms. The cooperative rearrangement of these big compact clusters might facilitate the simultaneous hopping of atoms in the glass states on the long time scale.

Conductive tracks of 30-MeV C60 clusters in doped and undoped tetrahedral amorphous carbon

NASA Astrophysics Data System (ADS)

Krauser, J.; Gehrke, H.-G.; Hofsäss, H.; Trautmann, C.; Weidinger, A.

2013-07-01

In insulating tetrahedral amorphous carbon (ta-C), the irradiation with 30-MeV C60 cluster ions leads to the formation of well conducting tracks. While electrical currents through individual tracks produced with monoatomic projectiles (e.g. Au or U) often exhibit rather large track to track fluctuations, C60 clusters are shown to generate highly conducting tracks with very narrow current distributions. Additionally, all recorded current-voltage curves show linear characteristics. These findings are attributed to the large specific energy loss dE/dx of the 30-MeV C60 clusters. We also investigated C60 tracks in ta-C films which were slightly doped with B, N or Fe during film growth. Doping apparently increases the ion track conductivity. However, at the same time the insulating characteristics of the pristine ta-C film can be reduced. The present C60 results are compared with data from earlier experiments with monoatomic heavy ion beams. The investigations were performed by means of atomic force microscopy including temperature dependent conductivity measurements of single ion tracks.

Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy

2018-05-01

This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters. Copyright © 2018 Elsevier Inc. All rights reserved.

The adsorption of Run (n = 1-4) on γ-Al2O3 Surface: A DFT study

NASA Astrophysics Data System (ADS)

Liu, Zhe; Guo, Yafei; Chen, Yu; Shen, Rong

2018-05-01

The density functional theory (DFT) was adopted to study the adsorption and growth of Run (n = 1-4) clusters on γ-Al2O3 surface, which is of great significances for the design of many important catalysts, especially for carbon dioxide methanation. It is found that both the Rusbnd Ru bond length and adsorption energy Eads of Ru clusters with the surface increase with the Run clusters increasing. The growth ability of the supported Run cluster is weaker than the gas phase Run clusters through comparing their respective growth process, which ascribes to the stabilization of γ-Al2O3 support. An interesting discovery is that the basin structure was supposed to be the most favorable adsorption geometry for Run clusters. Additionally, the distances between Ru atoms in the adsorbed clusters are longer than that in their isolated counterparts. Bader charge analysis was conducted for the most stable configurations of Run (n = 1-4) clusters on γ-Al2O3 surface as well. And the results suggest that Run (n = 1-4) clusters serve as the electron donators. The result of projected density of states (PDOS) shows that strong adsorption of Ru atom on the γ-Al2O3 surface correlates with strong interaction between d orbital of Ru atom and p orbital of Al or O atom of the Al2O3 support.

Study of methods to increase cluster/dislocation loop densities in electrodes

NASA Astrophysics Data System (ADS)

Yang, Xiaoling; Miley, George H.

2009-03-01

Recent research has developed a technique for imbedding ultra-high density deuterium ``clusters'' (50 to 100 atoms per cluster) in various metals such as Palladium (Pd), Beryllium (Be) and Lithium (Li). It was found the thermally dehydrogenated PdHx retained the clusters and exhibited up to 12 percent lower resistance compared to the virginal Pd samplesootnotetextA. G. Lipson, et al. Phys. Solid State. 39 (1997) 1891. SQUID measurements showed that in Pd these condensed matter clusters approach metallic conditions, exhibiting superconducting propertiesootnotetextA. Lipson, et al. Phys. Rev. B 72, 212507 (2005ootnotetextA. G. Lipson, et al. Phys. Lett. A 339, (2005) 414-423. If the fabrication methods under study are successful, a large packing fraction of nuclear reactive clusters can be developed in the electrodes by electrolyte or high pressure gas loading. This will provide a much higher low-energy-nuclear- reaction (LENR) rate than achieved with earlier electrodeootnotetextCastano, C.H., et al. Proc. ICCF-9, Beijing, China 19-24 May, 2002..

Clustering on Magnesium Surfaces - Formation and Diffusion Energies.

PubMed

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and [Formula: see text]. In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a [Formula: see text], clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface [Formula: see text] is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich-Schwoebel barriers converge as the step height is three atomic layers or thicker. Adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.

Structure assignment, electronic properties, and magnetism quenching of endohedrally doped neutral silicon clusters, Si(n)Co (n = 10-12).

PubMed

Li, Yejun; Tam, Nguyen Minh; Claes, Pieterjan; Woodham, Alex P; Lyon, Jonathan T; Ngan, Vu Thi; Nguyen, Minh Tho; Lievens, Peter; Fielicke, André; Janssens, Ewald

2014-09-18

The structures of neutral cobalt-doped silicon clusters have been assigned by a combined experimental and theoretical study. Size-selective infrared spectra of neutral Si(n)Co (n = 10-12) clusters are measured using a tunable IR-UV two-color ionization scheme. The experimental infrared spectra are compared with calculated spectra of low-energy structures predicted at the B3P86 level of theory. It is shown that the Si(n)Co (n = 10-12) clusters have endohedral caged structures, where the silicon frameworks prefer double-layered structures encapsulating the Co atom. Electronic structure analysis indicates that the clusters are stabilized by an ionic interaction between the Co dopant atom and the silicon cage due to the charge transfer from the silicon valence sp orbitals to the cobalt 3d orbitals. Strong hybridization between the Co dopant atom and the silicon host quenches the local magnetic moment on the encapsulated Co atom.

Clustering methods for the optimization of atomic cluster structure

NASA Astrophysics Data System (ADS)

Bagattini, Francesco; Schoen, Fabio; Tigli, Luca

2018-04-01

In this paper, we propose a revised global optimization method and apply it to large scale cluster conformation problems. In the 1990s, the so-called clustering methods were considered among the most efficient general purpose global optimization techniques; however, their usage has quickly declined in recent years, mainly due to the inherent difficulties of clustering approaches in large dimensional spaces. Inspired from the machine learning literature, we redesigned clustering methods in order to deal with molecular structures in a reduced feature space. Our aim is to show that by suitably choosing a good set of geometrical features coupled with a very efficient descent method, an effective optimization tool is obtained which is capable of finding, with a very high success rate, all known putative optima for medium size clusters without any prior information, both for Lennard-Jones and Morse potentials. The main result is that, beyond being a reliable approach, the proposed method, based on the idea of starting a computationally expensive deep local search only when it seems worth doing so, is capable of saving a huge amount of searches with respect to an analogous algorithm which does not employ a clustering phase. In this paper, we are not claiming the superiority of the proposed method compared to specific, refined, state-of-the-art procedures, but rather indicating a quite straightforward way to save local searches by means of a clustering scheme working in a reduced variable space, which might prove useful when included in many modern methods.

First stages of oxide growth on Al(1 1 0) and core-level shifts from density functional theory calculations

NASA Astrophysics Data System (ADS)

Lousada, Cláudio M.; Korzhavyi, Pavel A.

2018-05-01

The formation of islands of O-atoms is the dominant mode of growth of the oxide in the first stages of oxidation of Al(1 1 1). It is however unknown if a similar mechanism exists for other low index surfaces of Al. We performed a density functional theory (DFT) and ab initio molecular dynamics investigation of the first stages of the oxidation of Al(1 1 0) using two distinct models: a homogeneous surface disposition of O-atoms; and a model where the O-atoms are close-spaced forming clusters or islands. We investigated the surface reactions with oxygen up to a coverage of 2 ML and found that for both models the adsorption energy per dissociating O2(g) becomes more negative with increasing coverage. Our results show that for coverages up to 1.25 ML the oxide forms clusters or islands while for coverages higher than 1.5 ML the oxide covers the surface homogeneously. This is because the O-atoms bind preferably to neighboring sites even at the minimum coverage. With increasing coverage, the clusters of O start to form stripes along the [1 1 bar 0] direction. The work function (ϕ) of the surface decreases when going from bare Al(1 1 0) to up to 1 ML coverage of O-atoms, but for coverages of 1.25 ML and higher, ϕ increases. The Al 2p surface core level shifts (SCLS) shift towards higher binding energies with increasing surface coverage of O-atoms and start to approach the values of Al 2p in Al2O3 already at a coverage of 2ML. A relation between the SCLS and the coordination number of Al to O-atoms was made. The Al 2p SCLS increases with increasing coordination to O-atoms, for single, twofold and three-fourfold coordinated cations. For the O-atoms that terminate the surface at the short-bridge sites, the SCLS of O 1s, is largely affected by the proximity to other O-atoms. These results demonstrate that the cooperative effects between surface bound O-atoms have important roles in the mechanism of growth of the oxide at Al(1 1 0), and similarly to what happens for Al(1 1 1), the initial oxidation of Al(1 1 0) proceeds via the formation of islands of O-atoms.

Atomically precise arrays of fluorescent silver clusters: a modular approach for metal cluster photonics on DNA nanostructures.

PubMed

Copp, Stacy M; Schultz, Danielle E; Swasey, Steven; Gwinn, Elisabeth G

2015-03-24

The remarkable precision that DNA scaffolds provide for arraying nanoscale optical elements enables optical phenomena that arise from interactions of metal nanoparticles, dye molecules, and quantum dots placed at nanoscale separations. However, control of ensemble optical properties has been limited by the difficulty of achieving uniform particle sizes and shapes. Ligand-stabilized metal clusters offer a route to atomically precise arrays that combine desirable attributes of both metals and molecules. Exploiting the unique advantages of the cluster regime requires techniques to realize controlled nanoscale placement of select cluster structures. Here we show that atomically monodisperse arrays of fluorescent, DNA-stabilized silver clusters can be realized on a prototypical scaffold, a DNA nanotube, with attachment sites separated by <10 nm. Cluster attachment is mediated by designed DNA linkers that enable isolation of specific clusters prior to assembly on nanotubes and preserve cluster structure and spectral purity after assembly. The modularity of this approach generalizes to silver clusters of diverse sizes and DNA scaffolds of many types. Thus, these silver cluster nano-optical elements, which themselves have colors selected by their particular DNA templating oligomer, bring unique dimensions of control and flexibility to the rapidly expanding field of nano-optics.

Tailoring Ion Charge State Distribution in Tetramethyltin Clusters under Influence of Moderate Intensity Picosecond Laser Pulse: Role of Laser Wavelength and Rate of Energy Deposition

NASA Astrophysics Data System (ADS)

Sharma, Pramod; Das, Soumitra; Vatsa, Rajesh K.

2017-07-01

Systematic manipulation of ionic-outcome in laser-cluster interaction process has been realized for studies carried out on tetramethyltin (TMT) clusters under picosecond laser conditions, determined by choice of laser wavelength and intensity. As a function of laser intensity, TMT clusters exhibit gradual enhancement in overall ionization of its cluster constituents, up to a saturation level of ionization, which was distinct for different wavelengths (266, 355, and 532 nm). Simultaneously, systematic appearance of higher multiply charged atomic ions and shift in relative abundance of multiply charged atomic ions towards higher charge state was observed, using time-of-flight mass spectrometer. At saturation level, multiply charged atomic ions up to (C2+, Sn2+) at 266 nm, (C4+, Sn4+) at 355 nm, and (C4+, Sn6+) at 532 nm were detected. In addition, at 355 nm intra-cluster ion chemistry within the ionized cluster leads to generation of molecular hydrogen ion (H2 +) and triatomic molecular hydrogen ion (H3 +). Generation of multiply charged atomic ions is ascribed to efficient coupling of laser pulse with the cluster media, facilitated by inner-ionized electrons produced within the cluster, at the leading edge of laser pulse. Role of inner-ionized electrons is authenticated by measuring kinetic energy distribution of electrons liberated upon disintegration of excessively ionized cluster, under the influence of picosecond laser pulse.

Formation of fivefold axes in the FCC-metal nanoclusters

NASA Astrophysics Data System (ADS)

Myasnichenko, Vladimir S.; Starostenkov, Mikhail D.

2012-11-01

Formation of atomistic structures of metallic Cu, Au, Ag clusters and bimetallic Cu-Au clusters was studied with the help of molecular dynamics using the many-body tight-binding interatomic potential. The simulation of the crystallization process of clusters with the number of atoms ranging from 300 to 1092 was carried out. The most stable configurations of atoms in the system, corresponding to the minimum of potential energy, was found during super-fast cooling from 1000 K. Atoms corresponding to fcc, hcp, and Ih phases were identified by the method of common neighbor analysis. Incomplete icosahedral core can be discovered at the intersection of one of the Ih axes with the surface of monometallic cluster. The decahedron-shaped structure of bimetallic Cu-Au cluster with seven completed icosahedral cores was obtained. The principles of the construction of small bimetallic clusters with icosahedral symmetry and increased fractal dimensionality were offered.

Equilibrium geometries, electronic and magnetic properties of small AunNi- (n = 1-9) clusters

NASA Astrophysics Data System (ADS)

Tang, Cui-Ming; Chen, Xiao-Xu; Yang, Xiang-Dong

2014-05-01

Geometrical, electronic and magnetic properties of small AunNi- (n = 1-9) clusters have been investigated based on density functional theory (DFT) at PW91P86 level. An extensive structural search shows that the relative stable structures of AunNi- (n = 1-9) clusters adopt 2D structure for n = 1-5, 7 and 3D structure for n = 6, 8-9. And the substitution of a Ni atom for an Au atom in the Au-n+1 cluster obviously changes the structure of the host cluster. Moreover, an odd-even alternation phenomenon has been found for HOMO-LUMO energy gaps, indicating that the relative stable structures of the AunNi- clusters with odd-numbered gold atoms have a higher relative stability. Finally, the natural population analysis (NPA) and the vertical detachment energies (VDE) are studied, respectively. The theoretical values of VDE are reported for the first time to our best knowledge.

Catalysis by clusters with precise numbers of atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tyo, Eric C.; Vajda, Stefan

2015-07-03

Clusters that contain only a small number of atoms can exhibit unique and often unexpected properties. The clusters are of particular interest in catalysis because they can act as individual active sites, and minor changes in size and composition – such as the addition or removal of a single atom – can have a substantial influence on the activity and selectivity of a reaction. Here we review recent progress in the synthesis, characterization and catalysis of well-defined sub-nanometre clusters. We examine work on size-selected supported clusters in ultra-high vacuum environments and under realistic reaction conditions, and explore the use ofmore » computational methods to provide a mechanistic understanding of their catalytic properties. We also highlight the potential of size-selected clusters to provide insights into important catalytic processes and their use in the development of novel catalytic systems.« less

Thermodynamic properties of small aggregates of rare-gas atoms

NASA Technical Reports Server (NTRS)

Etters, R. D.; Kaelberer, J.

1975-01-01

The present work reports on the equilibrium thermodynamic properties of small clusters of xenon, krypton, and argon atoms, determined from a biased random-walk Monte Carlo procedure. Cluster sizes ranged from 3 to 13 atoms. Each cluster was found to have an abrupt liquid-gas phase transition at a temperature much less than for the bulk material. An abrupt solid-liquid transition is observed for thirteen- and eleven-particle clusters. For cluster sizes smaller than 11, a gradual transition from solid to liquid occurred over a fairly broad range of temperatures. Distribution of number of bond lengths as a function of bond length was calculated for several systems at various temperatures. The effects of box boundary conditions are discussed. Results show the importance of a correct description of boundary conditions. A surprising result is the slow rate at which system properties approach bulk behavior as cluster size is increased.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Numakura, H.

The structure and the formation mechanism of oxides during internal oxidation have attracted much attention, and extensive studies have been carried out on this subject. Recently, Jang et al. reported the results of atom-probe microanalysis of oxide particles, or solute-oxygen clusters, in an internally oxidized Cu-0.16 at.% Mg alloy. They found that the composition varies from particle to particle even in the same specimen, and reported that some clusters consist only of magnesium atoms. On the basis of the results, they suggested that the oxidation proceeds in this alloy as follows: (1) the solute atoms form clusters, (2) the clustersmore » absorb oxygen atoms to form both hypo- and hyperstoichiometric oxide particles, (3) the particles grow to form the stoichiometric oxide, MgO. They show the presence of Mg atom clusters with no oxygen association. By assuming that the analyzed area is in the unoxidized region, i.e., ahead of the oxidation front, they interpret this observation as evidence for clustering of the solute atoms prior to oxide formation. However, according to the phase diagram, such clustering is not expected in the absence of oxygen, since the solute concentration, 0.16 at.%, is far below the solubility limit at the oxidation temperature of 900[degree]C, about 3.5 at.%. In atom probe experiments, it sometimes happens that detection efficiencies for different ion species are considerably different because some experimental parameters are not chosen properly. It seems possible that the data resulted from an unusually low detection efficiency for O ions. Since their conclusion raises an important issue on the mechanism of internal oxidation, it is desirable to examine experimental conditions carefully, and to check the reproducibility of data.« less

Tuning optical properties of magic number cluster (SiO2)4O2H4 by substitutional bonding with gold atoms.

PubMed

Cai, Xiulong; Zhang, Peng; Ma, Liuxue; Zhang, Wenxian; Ning, Xijing; Zhao, Li; Zhuang, Jun

2009-04-30

By bonding gold atoms to the magic number cluster (SiO(2))(4)O(2)H(4), two groups of Au-adsorbed shell-like clusters Au(n)(SiO(2))(4)O(2)H(4-n) (n = 1-4) and Au(n)(SiO(2))(4)O(2) (n = 5-8) were obtained, and their spectral properties were studied. The ground-state structures of these clusters were optimized by density functional theory, and the results show that in despite of the different numbers and types of the adsorbed Au atoms, the cluster core (SiO(2))(4)O(2) of T(d) point-group symmetry keeps almost unchanged. The absorption spectra were obtained by time-dependent density functional theory. From one group to the other, an extension of absorption wavelength from the UV-visible to the NIR region was observed, and in each group the absorption strengths vary linearly with the number of Au atoms. These features indicate their advantages for exploring novel materials with easily controlled tunable optical properties. Furthermore, due to the weak electronic charge transfer between the Au atoms, the clusters containing Au(2) dimers, especially Au(8)(SiO(2))(4)O(2), absorb strongly NIR light at 900 approximately 1200 nm. Such strong absorption suggests potential applications of these shell-like clusters in tumor cells thermal therapy, like the gold-coated silica nanoshells with larger sizes.

Calculating hyperfine couplings in large ionic crystals containing hundreds of QM atoms: subsystem DFT is the key.

PubMed

Kevorkyants, Ruslan; Wang, Xiqiao; Close, David M; Pavanello, Michele

2013-11-14

We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.

Structures and stability of metal-doped Ge nM (n = 9, 10) clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua

The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge 9 and Ge 10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge n clusters. However, the neutral and cationic FeGe 9,10,MnGe 9,10 and Ge 10Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge n clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge 9,10Fe and Ge 9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Structures and stability of metal-doped Ge nM (n = 9, 10) clusters

DOE PAGES

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; ...

2015-06-26

The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge 9 and Ge 10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge n clusters. However, the neutral and cationic FeGe 9,10,MnGe 9,10 and Ge 10Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge n clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge 9,10Fe and Ge 9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Structures and stability of metal-doped GenM (n = 9, 10) clusters

NASA Astrophysics Data System (ADS)

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

2015-06-01

The lowest-energy structures of neutral and cationic GenM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Such cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.

Size and Site Dependence of the Catalytic Activity of Iridium Clusters toward Ethane Dehydrogenation.

PubMed

Ge, Yingbin; Jiang, Hao; Kato, Russell; Gummagatta, Prasuna

2016-12-01

This research focuses on optimizing transition metal nanocatalyst immobilization and activity to enhance ethane dehydrogenation. Ethane dehydrogenation, catalyzed by thermally stable Ir n (n = 8, 12, 18) atomic clusters that exhibit a cuboid structure, was studied using the B3LYP method with triple-ζ basis sets. Relativistic effects and dispersion corrections were included in the calculations. In the dehydrogenation reaction Ir n + C 2 H 6 → H-Ir n -C 2 H 5 → (H) 2 -Ir n -C 2 H 4 , the first H-elimination is the rate-limiting step, primarily because the reaction releases sufficient heat to facilitate the second H-elimination. The catalytic activity of the Ir clusters strongly depends on the Ir cluster size and the specific catalytic site. Cubic Ir 8 is the least reactive toward H-elimination in ethane: Ir 8 + C 2 H 6 → H-Ir 8 -C 2 H 5 has a large (65 kJ/mol) energy barrier, whereas Ir 12 (3 × 2 × 2 cuboid) and Ir 18 (3 × 3 × 2 cuboid) lower this energy barrier to 22 and 3 kJ/mol, respectively. The site dependence is as prominent as the size effect. For example, the energy barrier for the Ir 18 + C 2 H 6 → H-Ir 18 -C 2 H 5 reaction is 3, 48, and 71 kJ/mol at the corner, edge, or face-center sites of the Ir 18 cuboid, respectively. Energy release due to Ir cluster insertion into an ethane C-H bond facilitates hydrogen migration on the Ir cluster surface, and the second H-elimination of ethane. In an oxygen-rich environment, oxygen molecules may be absorbed on the Ir cluster surface. The oxygen atoms bonded to the Ir cluster surface may slightly increase the energy barrier for H-elimination in ethane. However, the adsorption of oxygen and its reaction with H atoms on the Ir cluster releases sufficient heat to yield an overall thermodynamically favored reaction: Ir n + C 2 H 6 + 1 / 2 O 2 → Ir n + C 2 H 4 + H 2 O. These results will be useful toward reducing the energy cost of ethane dehydrogenation in industry.

Theoretical investigation of M@Pb122- and M@Sn122- Zintl clusters (M = Lrn+, Lun+, La3+, Ac3+ and n = 0, 1, 2, 3).

PubMed

Joshi, Meenakshi; Chandrasekar, Aditi; Ghanty, Tapan K

2018-06-06

The positions of lawrencium (Lr), lutetium (Lu), actinium (Ac) and lanthanum (La) in the periodic table have been a controversial topic for quite some time. According to studies carried out by different groups with their justifications, these elements may potentially be placed in the d-block, p-block or all four in a 15 element f-block. The present work looks into this issue from a new perspective, which involves encapsulation of these four elements into Zintl ion clusters, Pb122- and Sn122-, followed by the determination of the structural, thermodynamic and electronic properties of these endohedral M@Pb122- and M@Sn122- clusters (M = Lrn+, Lun+ with n = 0, 1, 2, 3) using first principles based density functional theory (DFT). These parameters are compared with similar clusters encapsulated La3+ and Ac3+ ions in order to seek out similarities and differences to draw conclusions about their placement in the periodic table. For the first time the structural, energetic, and electronic properties of these metal atom/ion encapsulated Pb122- and Sn122- clusters have been investigated thoroughly. Structural parameters such as bond distances, geometry and symmetry, electronic properties viz. the density of states, the molecular orbital ordering, the electron localization function, bond critical point properties and charge distributions have been analyzed. Additionally, the thermodynamic property of the binding energy during the encapsulation process has also been calculated. All M@Pb12+ and M@Sn12+ (M = Lr and Lu) clusters form stable 18 bonding electron magic number systems with shell closing. They show negative values of binding energy and relatively large HOMO-LUMO energy gaps indicating the stability of such clusters. All the calculated parameters for Lr encapsulated clusters closely match with the corresponding calculated parameters of Lu encapsulated clusters, confirming the similarity between Lr and Lu metal atoms in various oxidation states, though their atomic ground state valence electronic configurations are different. The effect of spin orbit coupling has also been investigated using the ZORA approach. It is interesting to discover that La and Ac showed striking similarities to Lr and Lu with respect to all the properties investigated and have formed a stable 18-electron system.

Structural, electronic and vibrational properties of small GaxNy (x+y = 2 5) nanoclusters: a B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Yadav, P. S.; Yadav, R. K.; Agrawal, B. K.

2007-02-01

An ab initio study of the stability, structural and electronic properties has been made for 49 gallium nitride nanoclusters, GaxNy (x+y = 2-5). Among the various configurations corresponding to a fixed x+y = n value, the configuration possessing the maximum value of binding energy (BE) is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize the geometries of the nanoclusters fully. The binding energies (BEs), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps and the bond lengths have been obtained for all the clusters. We have considered the zero-point energy (ZPE) corrections ignored by the earlier workers. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have been investigated for the most stable structures. The configurations containing the N atoms in majority are seen to be the most stable structures. The strong N-N bond has an important role in stabilizing the clusters. For clusters containing one Ga atom and all the others as N atoms, the BE increases monotonically with the number of the N atoms. The HOMO-LUMO gap and IP fluctuate with the cluster size n, having larger values for the clusters containing odd number of N atoms. On the other hand, the EA decreases with the cluster size up to n = 3, and shows slow fluctuations thereafter for the larger clusters. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA) because of the lower energies of the most stable ground state of the cationic (anionic) clusters. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in experiments.

Comparing selected morphological models of hydrated Nafion using large scale molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Knox, Craig K.

Experimental elucidation of the nanoscale structure of hydrated Nafion, the most popular polymer electrolyte or proton exchange membrane (PEM) to date, and its influence on macroscopic proton conductance is particularly challenging. While it is generally agreed that hydrated Nafion is organized into distinct hydrophilic domains or clusters within a hydrophobic matrix, the geometry and length scale of these domains continues to be debated. For example, at least half a dozen different domain shapes, ranging from spheres to cylinders, have been proposed based on experimental SAXS and SANS studies. Since the characteristic length scale of these domains is believed to be ˜2 to 5 nm, very large molecular dynamics (MD) simulations are needed to accurately probe the structure and morphology of these domains, especially their connectivity and percolation phenomena at varying water content. Using classical, all-atom MD with explicit hydronium ions, simulations have been performed to study the first-ever hydrated Nafion systems that are large enough (~2 million atoms in a ˜30 nm cell) to directly observe several hydrophilic domains at the molecular level. These systems consisted of six of the most significant and relevant morphological models of Nafion to-date: (1) the cluster-channel model of Gierke, (2) the parallel cylinder model of Schmidt-Rohr, (3) the local-order model of Dreyfus, (4) the lamellar model of Litt, (5) the rod network model of Kreuer, and (6) a 'random' model, commonly used in previous simulations, that does not directly assume any particular geometry, distribution, or morphology. These simulations revealed fast intercluster bridge formation and network percolation in all of the models. Sulfonates were found inside these bridges and played a significant role in percolation. Sulfonates also strongly aggregated around and inside clusters. Cluster surfaces were analyzed to study the hydrophilic-hydrophobic interface. Interfacial area and cluster volume significantly increased during the simulations, suggesting the need for morphological model refinement and improvement. Radial distribution functions and structure factors were calculated. All nonrandom models exhibited the characteristic experimental scattering peak, underscoring the insensitivity of this measurement to hydrophilic domain structure and highlighting the need for future work to clearly distinguish morphological models of Nafion.

Thermal O-H Bond Activation of Water as Mediated by Heteronuclear [Al2Mg2O5]•+: Evidence for Oxygen-Atom Scrambling.

PubMed

Geng, Caiyun; Li, Jilai; Weiske, Thomas; Schwarz, Helmut

2018-06-25

Mechanistic insight into the thermal O-H bond activation of water by the cubane-like, prototypical heteronuclear oxide cluster [Al 2 Mg 2 O 5 ] •+ has been derived from a combined experimental/computational study. Experiments in the highly diluted gas phase using Fourier transform ion-cyclotron resonance mass spectrometry show that hydrogen-atom abstraction from water by the cluster cation [Al 2 Mg 2 O 5 ] •+ occurs at ambient conditions accompanied by the liberation of an OH • radical. Due to a complete randomization of all oxygen atoms prior to fragmentation about 83% of the oxygen atoms of the hydroxyl radical released originate from the oxide cluster itself. The experimental findings are supported by detailed high-level quantum chemical calculations. The theoretical analysis reveals that the transfer of a formal hydrogen atom from water to the metal-oxide cation can proceed mechanistically via proton- or hydrogen-atom transfer exploiting different active sites of the cluster oxide. In addition to the unprecedented oxygen-atom scrambling, one of the more general and quite unexpected findings concerns the role of spin density at the hydrogen-acceptor oxide atom. While this feature is so crucial for [M-O] + /CH 4 couples, it is much less important in the O-H bond activation of water.

New Scenario of Dynamical Heterogeneity in Supercooled Liquid and Glassy States of 2D Monatomic System.

PubMed

Van Hoang, Vo; Teboul, Victor; Odagaki, Takashi

2015-12-24

Via analysis of spatiotemporal arrangements of atoms based on their dynamics in supercooled liquid and glassy states of a 2D monatomic system with a double-well Lennard-Jones-Gauss (LJG) interaction potential, we find a new scenario of dynamical heterogeneity. Atoms with the same or very close mobility have a tendency to aggregate into clusters. The number of atoms with high mobility (and size of their clusters) increases with decreasing temperature passing over a maximum before decreasing down to zero. Position of the peak moves toward a lower temperature if mobility of atoms in clusters is lower together with an enhancement of height of the peak. In contrast, the number of atoms with very low mobility or solidlike atoms (and size of their clusters) has a tendency to increase with decreasing temperature and then it suddenly increases in the vicinity of the glass transition temperature leading to the formation of a glassy state. A sudden increase in the number of strongly correlated solidlike atoms in the vicinity of a glass transition temperature (Tg) may be an origin of a drastical increase in viscosity of the glass-forming systems approaching the glass transition. In fact, we find that the diffusion coefficient decays exponentially with a fraction of solidlike atoms exhibiting a sudden decrease in the vicinity of the glass transition region.

Rigid-Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies

PubMed Central

Kim, Moon K.; Jernigan, Robert L.; Chirikjian, Gregory S.

2005-01-01

We present a rigid-body-based technique (called rigid-cluster elastic network interpolation) to generate feasible transition pathways between two distinct conformations of a macromolecular assembly. Many biological molecules and assemblies consist of domains which act more or less as rigid bodies during large conformational changes. These collective motions are thought to be strongly related with the functions of a system. This fact encourages us to simply model a macromolecule or assembly as a set of rigid bodies which are interconnected with distance constraints. In previous articles, we developed coarse-grained elastic network interpolation (ENI) in which, for example, only Cα atoms are selected as representatives in each residue of a protein. We interpolate distance differences of two conformations in ENI by using a simple quadratic cost function, and the feasible conformations are generated without steric conflicts. Rigid-cluster interpolation is an extension of the ENI method with rigid-clusters replacing point masses. Now the intermediate conformations in an anharmonic pathway can be determined by the translational and rotational displacements of large clusters in such a way that distance constraints are observed. We present the derivation of the rigid-cluster model and apply it to a variety of macromolecular assemblies. Rigid-cluster ENI is then modified for a hybrid model represented by a mixture of rigid clusters and point masses. Simulation results show that both rigid-cluster and hybrid ENI methods generate sterically feasible pathways of large systems in a very short time. For example, the HK97 virus capsid is an icosahedral symmetric assembly composed of 60 identical asymmetric units. Its original Hessian matrix size for a Cα coarse-grained model is >(300,000)2. However, it reduces to (84)2 when we apply the rigid-cluster model with icosahedral symmetry constraints. The computational cost of the interpolation no longer scales heavily with the size of structures; instead, it depends strongly on the minimal number of rigid clusters into which the system can be decomposed. PMID:15833998

Influence of Cr doping on the stability and structure of small cobalt oxide clusters.

PubMed

Tung, Nguyen Thanh; Tam, Nguyen Minh; Nguyen, Minh Tho; Lievens, Peter; Janssens, Ewald

2014-07-28

The stability of mass-selected pure cobalt oxide and chromium doped cobalt oxide cluster cations, ConO+m and Con-1CrO+m (n = 2, 3; m = 2-6 and n = 4; m = 3-8), has been investigated using photodissociation mass spectrometry. Oxygen-rich ConO+m clusters (m ≥ n + 1 for n = 2, 4 and m ≥ n + 2 for n = 3) prefer to photodissociate via the loss of an oxygen molecule, whereas oxygen poorer clusters favor the evaporation of oxygen atoms. Substituting a single Co atom by a single Cr atom alters the dissociation behavior. All investigated Con-1 CrO+m clusters, except CoCrO+2 and CoCrO+3, prefer to decay by eliminating a neutral oxygen molecule. Co2O+2, Co4O+3, Co4O+4, and CoCrO+2 are found to be relatively difficult to dissociate and appear as fragmentation product of several larger clusters, suggesting that they are particularly stable. The geometric structures of pure and Cr doped cobalt oxide species are studied using density functional theory calculations. Dissociation energies for different evaporation channels are calculated and compared with the experimental observations. The influence of the dopant atom on the structure and the stability of the clusters is discussed.

Surface heating of electrons in atomic clusters irradiated by ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Krainov, V. P.; Sofronov, A. V.

2014-04-01

We consider a mechanism for electron heating in atomic clusters at the reflections of free electrons from the cluster surface. Electrons acquire energy from the external laser field during these reflections. A simple analytical expression has been obtained for acquired electron kinetic energy during the laser pulse. We find conditions when this mechanism dominates compared to the electron heating due to the well-known induced inverse bremsstrahlung at the electron-ion collisions inside clusters.

Magic Numbers in Small Iron Clusters: A First-Principles Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Eunja; Mohrland, Andrew B.; Weck, Philippe F.

2014-10-03

We perform ab initio spin-polarized density functional calculations of Fen aggregates with n ≤ 17 atoms to reveal the origin of the observed magic numbers, which indicate particularly high stability of clusters with 7, 13 and 15 atoms. Our results clarify the controversy regarding the ground state geometry of clusters such as Fe5and indicate that magnetism plays an important role in determining the stability and magic numbers in small iron clusters.

Effect of Spin Multiplicity in O2 Adsorption and Dissociation on Small Bimetallic AuAg Clusters.

PubMed

García-Cruz, Raúl; Poulain, Enrique; Hernández-Pérez, Isaías; Reyes-Nava, Juan A; González-Torres, Julio C; Rubio-Ponce, A; Olvera-Neria, Oscar

2017-08-17

To dispose of atomic oxygen, it is necessary the O 2 activation; however, an energy barrier must be overcome to break the O-O bond. This work presents theoretical calculations of the O 2 adsorption and dissociation on small pure Au n and Ag m and bimetallic Au n Ag m (n + m ≤ 6) clusters using the density functional theory (DFT) and the zeroth-order regular approximation (ZORA) to explicitly include scalar relativistic effects. The most stable Au n Ag m clusters contain a higher concentration of Au with Ag atoms located in the center of the cluster. The O 2 adsorption energy on pure and bimetallic clusters and the ensuing geometries depend on the spin multiplicity of the system. For a doublet multiplicity, O 2 is adsorbed in a bridge configuration, whereas for a triplet only one O-metal bond is formed. The charge transfer from metal toward O 2 occupies the σ* O-O antibonding natural bond orbital, which weakens the oxygen bond. The Au 3 ( 2 A) cluster presents the lowest activation energy to dissociate O 2 , whereas the opposite applies to the AuAg ( 3 A) system. In the O 2 activation, bimetallic clusters are not as active as pure Au n clusters due to the charge donated by Ag atoms being shared between O 2 and Au atoms.

Finding Semirigid Domains in Biomolecules by Clustering Pair-Distance Variations

PubMed Central

Schreiner, Wolfgang

2014-01-01

Dynamic variations in the distances between pairs of atoms are used for clustering subdomains of biomolecules. We draw on a well-known target function for clustering and first show mathematically that the assignment of atoms to clusters has to be crisp, not fuzzy, as hitherto assumed. This reduces the computational load of clustering drastically, and we demonstrate results for several biomolecules relevant in immunoinformatics. Results are evaluated regarding the number of clusters, cluster size, cluster stability, and the evolution of clusters over time. Crisp clustering lends itself as an efficient tool to locate semirigid domains in the simulation of biomolecules. Such domains seem crucial for an optimum performance of subsequent statistical analyses, aiming at detecting minute motional patterns related to antigen recognition and signal transduction. PMID:24959586

Comparative investigation of pure and mixed rare gas atoms on coronene molecules.

PubMed

Rodríguez-Cantano, Rocío; Bartolomei, Massimiliano; Hernández, Marta I; Campos-Martínez, José; González-Lezana, Tomás; Villarreal, Pablo; Pérez de Tudela, Ricardo; Pirani, Fernando; Hernández-Rojas, Javier; Bretón, José

2017-01-21

Clusters formed by the combination of rare gas (RG) atoms of He, Ne, Ar, and Kr on coronene have been investigated by means of a basin-hopping algorithm and path integral Monte Carlo calculations at T = 2 K. Energies and geometries have been obtained and the role played by the specific RG-RG and RG-coronene interactions on the final results is analysed in detail. Signatures of diffuse behavior of the He atoms on the surface of the coronene are in contrast with the localization of the heavier species, Ar and Kr. The observed coexistence of various geometries for Ne suggests the motion of the RG atoms on the multi-well potential energy surface landscape offered by the coronene. Therefore, the investigation of different clusters enables a comparative analysis of localized versus non-localized features. Mixed Ar-He-coronene clusters have also been considered and the competition of the RG atoms to occupy the docking sites on the molecule is discussed. All the obtained information is crucial to assess the behavior of coronene, a prototypical polycyclic aromatic hydrocarbon clustering with RG atoms at a temperature close to that of interstellar medium, which arises from the critical balance of the interactions involved.

Probing structure, thermochemistry, electron affinity, and magnetic moment of thulium-doped silicon clusters TmSi n (n = 3-10) and their anions with density functional theory.

PubMed

Huang, Xintao; Yang, Jucai

2017-12-26

The most stable structures and electronic properties of TmSi n (n = 3-10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi n and their anions can be regarded as substituting a Si atom of the ground state structure of Si n + 1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi n (n = 3-10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster. The NPA analyses indicated that the 4f electron of Tm atom in TmSi n (n = 3-10) and their anions do not participate in bonding. The total magnetic moments of TmSi n are mainly provided by the 4f electrons of Tm atom. The dissociation energy of Tm atom from the most stable structure of TmSi n and their anions has been calculated to examine relative stability.

High reactivity of nanosized niobium oxide cluster cations in methane activation: A comparison with vanadium oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Xun-Lei, E-mail: dingxl@ncepu.edu.cn, E-mail: chemzyx@iccas.ac.cn; Wang, Dan; Wu, Xiao-Nan

2015-09-28

The reactions between methane and niobium oxide cluster cations were studied and compared to those employing vanadium oxides. Hydrogen atom abstraction (HAA) reactions were identified over stoichiometric (Nb{sub 2}O{sub 5}){sub N}{sup +} clusters for N as large as 14 with a time-of-flight mass spectrometer. The reactivity of (Nb{sub 2}O{sub 5}){sub N}{sup +} clusters decreases as the N increases, and it is higher than that of (V {sub 2}O{sub 5}){sub N}{sup +} for N ≥ 4. Theoretical studies were conducted on (Nb{sub 2}O{sub 5}){sub N}{sup +} (N = 2–6) by density functional calculations. HAA reactions on these clusters are all favorablemore » thermodynamically and kinetically. The difference of the reactivity with respect to the cluster size and metal type (Nb vs V) was attributed to thermodynamics, kinetics, the electron capture ability, and the distribution of the unpaired spin density. Nanosized Nb oxide clusters show higher HAA reactivity than V oxides, indicating that niobia may serve as promising catalysts for practical methane conversion.« less

Probabilistic distributions of pinhole defects in atomic layer deposited films on polymeric substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yersak, Alexander S., E-mail: alexander.yersak@colorado.edu; Lee, Yung-Cheng

Pinhole defects in atomic layer deposition (ALD) coatings were measured in an area of 30 cm{sup 2} in an ALD reactor, and these defects were represented by a probabilistic cluster model instead of a single defect density value with number of defects over area. With the probabilistic cluster model, the pinhole defects were simulated over a manufacturing scale surface area of ∼1 m{sup 2}. Large-area pinhole defect simulations were used to develop an improved and enhanced design method for ALD-based devices. A flexible thermal ground plane (FTGP) device requiring ALD hermetic coatings was used as an example. Using a single defectmore » density value, it was determined that for an application with operation temperatures higher than 60 °C, the FTGP device would not be possible. The new probabilistic cluster model shows that up to 40.3% of the FTGP would be acceptable. With this new approach the manufacturing yield of ALD-enabled or other thin film based devices with different design configurations can be determined. It is important to guide process optimization and control and design for manufacturability.« less

The Electronic Structure of Transition Metal Coated Fullerenes

NASA Astrophysics Data System (ADS)

Patton, David C.; Pederson, Mark R.; Kaxiras, Efthimios

1998-03-01

Clusters composed of fullerene molecules with an outer shell of transition metal atoms in the composition C_60M_62 (M being a transition metal) have been produced with laser vaporisation techniques(F. Tast, N. Malinowski, S. Frank, M. Heinebrodt, I.M.L. Billas, and T. P. Martin, Z. Phys D 40), 351 (1997).. We have studied several of these very large systems with a parallel version of the all-electron NRLMOL cluster code. Optimized geometries of the metal encased fullerenes C_60Ti_62 and C_60V_62 are presented along with their HOMO-LUMO gaps, electron affinities, ionization energies, and cohesive energies. We compare the stability of these clusters to relaxed met-car structures (e.g. Ti_8C_12) and to relaxed rocksalt metal-carbide fragments (TiC)n with n=8 and 32. In addition to metal-coated fullerenes we consider the possibility of a trilayered structure consisting of a small shell of metal atoms enclosed by a metal coated fullerene. The nature of bonding in these systems is analyzed by studying the electronic charge distributions.

Nanosized (mu12-Pt)Pd164-xPtx(CO)72(PPh3)20 (x approximately 7) containing Pt-centered four-shell 165-atom Pd-Pt core with unprecedented intershell bridging carbonyl ligands: comparative analysis of icosahedral shell-growth patterns with geometrically related Pd145(CO)x(PEt3)30 (x approximately 60) containing capped three-shell Pd145 core.

PubMed

Mednikov, Evgueni G; Jewell, Matthew C; Dahl, Lawrence F

2007-09-19

Presented herein are the preparation and crystallographic/microanalytical/magnetic/spectroscopic characterization of the Pt-centered four-shell 165-atom Pd-Pt cluster, (mu(12)-Pt)Pd(164-x)Pt(x)(CO)(72)(PPh(3))(20) (x approximately 7), 1, that replaces the geometrically related capped three-shell icosahedral Pd(145) cluster, Pd(145)(CO)(x)(PEt(3))(30) (x approximately 60), 2, as the largest crystallographically determined discrete transition metal cluster with direct metal-metal bonding. A detailed comparison of their shell-growth patterns gives rise to important stereochemical implications concerning completely unexpected structural dissimilarities as well as similarities and provides new insight concerning possible synthetic approaches for generation of multi-shell metal clusters. 1 was reproducibly prepared in small yields (<10%) from the reaction of Pd(10)(CO)(12)(PPh(3))(6) with Pt(CO)(2)(PPh(3))(2). Its 165-atom metal-core geometry and 20 PPh(3) and 72 CO ligands were established from a low-temperature (100 K) CCD X-ray diffraction study. The well-determined crystal structure is attributed largely to 1 possessing cubic T(h) (2/m3) site symmetry, which is the highest crystallographic subgroup of the noncrystallographic pseudo-icosahedral I(h) (2/m35) symmetry. The "full" four-shell Pd-Pt anatomy of 1 consists of: (a) shell 1 with the centered (mu(12)-Pt) atom encapsulated by the 12-atom icosahedral Pt(x)Pd(12-x) cage, x = 1.2(3); (b) shell 2 with the 42-atom nu(2) icosahedral Pt(x)Pd(42-x) cage, x = 3.5(5); (c) shell 3 with the anti-Mackay 60-atom semi-regular rhombicosidodecahedral Pt(x)Pd(60-x) cage, x = 2.2(6); (d) shell 4 with the 50-atom nu(2) pentagonal dodecahedral Pd(50) cage. The total number of crystallographically estimated Pt atoms, 8 +/- 3, which was obtained from least-squares (Pt(x)/Pd(1-x))-occupancy analysis of the X-ray data that conclusively revealed the central atom to be pure Pt (occupancy factor, x = 1.00(3)), is fortuitously in agreement with that of 7.6(7) found from an X-ray Pt/Pd microanalysis (WDS spectrometer) on three crystals of 1. Our utilization of this site-occupancy (Pt(x)Pd(1-x))-analysis for shells 1-3 originated from the microanalytical results; otherwise, the presumed metal-core composition would have been (mu(12)-Pt)Pd(164). [Alternatively, the (mu(12)-Pt)M(164) core-geometry of 1 may be viewed as a pseudo-Ih Pt-centered six-shell successive nu(1) polyhedral system, each with radially equivalent vertex atoms: Pt@M(12)(icosahedron)@M(30)(icosidodecahedron)@M(12)(icosahedron)@M(60)(rhombicosidodecahedron)@M(30)(icosidodecahedron)@M(20)(pentagonal dodecahedron)]. Completely surprising structural dissimilarities between 1 and 2 are: (1) to date 1 is only reproducibly isolated as a heterometallic Pd-Pt cluster with a central Pt instead of Pd atom; (2) the 50 atoms comprising the outer fourth nu(2) pentagonal dodecahedral shell in 1 are less than the 60 atoms of the inner third shell in 1, in contradistinction to shell-by-shell growth processes in all other known shell-based structures; (3) the 10 fewer PR3 ligands in 1 necessitate larger bulky PPh(3) ligands to protect the Pd-Pt core-geometry; (4) the 72 CO ligands consist of six bridging COs within each of the 12 pentagons in shell 4 that are coordinated to intershell metal atoms. SQUID magnetometry measurements showed a single-crystal sample of 1 to be diamagnetic over the entire temperature range of 10-300 K.

Characterization of physio-chemical properties of polymeric and electrochemical materials for aerospace flight

NASA Technical Reports Server (NTRS)

Rock, M.; Kunigahalli, V.; Khan, S.; Mcnair, A.

1984-01-01

Sealed nickel cadmium cells having undergone a large number of cycles were discharged using the Hg/HgO reference electrode. The negative electrode exhibited the second plateau. SEM of negative plates of such cells show clusters of large crystals of cadmium hydroxide. These large crystals on the negative plates disappear after continuous overcharging in flooded cells. Atomic Absorption Spectroscopy and standard wet chemical methods are being used to determine the cell materials viz: nickel, cadmium, cobalt, potassum and carbonate. The anodes and cathodes are analyzed after careful examination and the condition of the separator material is evaluated.

Electronic effects on melting: Comparison of aluminum cluster anions and cations

NASA Astrophysics Data System (ADS)

Starace, Anne K.; Neal, Colleen M.; Cao, Baopeng; Jarrold, Martin F.; Aguado, Andrés; López, José M.

2009-07-01

Heat capacities have been measured as a function of temperature for aluminum cluster anions with 35-70 atoms. Melting temperatures and latent heats are determined from peaks in the heat capacities; cohesive energies are obtained for solid clusters from the latent heats and dissociation energies determined for liquid clusters. The melting temperatures, latent heats, and cohesive energies for the aluminum cluster anions are compared to previous measurements for the corresponding cations. Density functional theory calculations have been performed to identify the global minimum energy geometries for the cluster anions. The lowest energy geometries fall into four main families: distorted decahedral fragments, fcc fragments, fcc fragments with stacking faults, and "disordered" roughly spherical structures. The comparison of the cohesive energies for the lowest energy geometries with the measured values allows us to interpret the size variation in the latent heats. Both geometric and electronic shell closings contribute to the variations in the cohesive energies (and latent heats), but structural changes appear to be mainly responsible for the large variations in the melting temperatures with cluster size. The significant charge dependence of the latent heats found for some cluster sizes indicates that the electronic structure can change substantially when the cluster melts.

Kinematics of the Doped Quantum Vortices in Superfluid Helium Droplets

NASA Astrophysics Data System (ADS)

Bernando, Charles; Vilesov, Andrey F.

2018-05-01

Recent observation of quantum vortices in superfluid 4He droplets measuring a few hundreds of nanometers in diameter involved decoration of vortex cores by clusters containing large numbers of Xe atoms, which served as X-ray contrast agents. Here, we report on the study of the kinematics of the combined vortex-cluster system in a cylinder and in a sphere. Equilibrium states, characterized by total angular momentum, L, were found by minimizing the total energy, E, which sums from the kinetic energy of the liquid due to the vortex and due to orbiting Xe clusters, as well as solvation energy of the cluster in the droplet. Calculations show that, at small mass of the cluster, the equilibrium displacement of the system from the rotation axis is close to that for the bare vortex. However, upon decrease in L beyond certain critical value, which is larger for heavier clusters, the displacement bifurcates toward the surface region, where the motion of the system is governed by the clusters. In addition, at even smaller L, bare orbiting clusters become energetically favorable, opening the possibility for the vortex to detach from the cluster and to annihilate at the droplet's surface.

Size resolved infrared spectroscopy of Na(CH3OH)n (n = 4-7) clusters in the OH stretching region: unravelling the interaction of methanol clusters with a sodium atom and the emergence of the solvated electron.

PubMed

Forck, Richard M; Pradzynski, Christoph C; Wolff, Sabine; Ončák, Milan; Slavíček, Petr; Zeuch, Thomas

2012-03-07

Size resolved IR action spectra of neutral sodium doped methanol clusters have been measured using IR excitation modulated photoionisation mass spectroscopy. The Na(CH(3)OH)(n) clusters were generated in a supersonic He seeded expansion of methanol by subsequent Na doping in a pick-up cell. A combined analysis of IR action spectra, IP evolutions and harmonic predictions of IR spectra (using density functional theory) of the most stable structures revealed that for n = 4, 5 structures with an exterior Na atom showing high ionisation potentials (IPs) of ~4 eV dominate, while for n = 6, 7 clusters with lower IPs (~3.2 eV) featuring fully solvated Na atoms and solvated electrons emerge and dominate the IR action spectra. For n = 4 simulations of photoionisation spectra using an ab initio MD approach confirm the dominance of exterior structures and explain the previously reported appearance IP of 3.48 eV by small fractions of clusters with partly solvated Na atoms. Only for this cluster size a shift in the isomer composition with cluster temperature has been observed, which may be related to kinetic stabilisation of less Na solvated clusters at low temperatures. Features of slow fragmentation dynamics of cationic Na(+)(CH(3)OH)(6) clusters have been observed for the photoionisation near the adiabatic limit. This finding points to the relevance of previously proposed non-vertical photoionisation dynamics of this system.

Effects of single atom doping on the ultrafast electron dynamics of M1Au24(SR)18 (M = Pd, Pt) nanoclusters.

PubMed

Zhou, Meng; Qian, Huifeng; Sfeir, Matthew Y; Nobusada, Katsuyuki; Jin, Rongchao

2016-04-07

Atomically precise, doped metal clusters are receiving wide research interest due to their synergistic properties dependent on the metal composition. To understand the electronic properties of doped clusters, it is highly desirable to probe the excited state behavior. Here, we report the ultrafast relaxation dynamics of doped M1@Au24(SR)18 (M = Pd, Pt; R = CH2CH2Ph) clusters using femtosecond visible and near infrared transient absorption spectroscopy. Three relaxation components are identified for both mono-doped clusters: (1) sub-picosecond relaxation within the M1Au12 core states; (2) core to shell relaxation in a few picoseconds; and (3) relaxation back to the ground state in more than one nanosecond. Despite similar relaxation pathways for the two doped nanoclusters, the coupling between the metal core and surface ligands is accelerated by over 30% in the case of the Pt dopant compared with the Pd dopant. Compared to Pd doping, the case of Pt doping leads to much more drastic changes in the steady state and transient absorption of the clusters, which indicates that the 5d orbitals of the Pt atom are more strongly mixed with Au 5d and 6s orbitals than the 4d orbitals of the Pd dopant. These results demonstrate that a single foreign atom can lead to entirely different excited state spectral features of the whole cluster compared to the parent Au25(SR)18 cluster. The detailed excited state dynamics of atomically precise Pd/Pt doped gold clusters help further understand their properties and benefit the development of energy-related applications.

Effects of single atom doping on the ultrafast electron dynamics of M 1Au 24(SR) 18 (M = Pd, Pt) nanoclusters

DOE PAGES

Zhou, Meng; Qian, Huifeng; Sfeir, Matthew Y.; ...

2016-02-29

Atomically precise, doped metal clusters are receiving wide research interest due to their synergistic properties dependent on the metal composition. To understand the electronic properties of doped clusters, it is highly desirable to probe the excited state behavior. Here, we report the ultrafast relaxation dynamics of doped M 1@Au 24(SR) 18 (M = Pd, Pt; R = CH 2CH 2Ph) clusters using femtosecond visible and near infrared transient absorption spectroscopy. Three relaxation components are identified for both mono-doped clusters: (1) sub-picosecond relaxation within the M 1Au 12 core states; (2) core to shell relaxation in a few picoseconds; and (3)more » relaxation back to the ground state in more than one nanosecond. Despite similar relaxation pathways for the two doped nanoclusters, the coupling between the metal core and surface ligands is accelerated by over 30% in the case of the Pt dopant compared with the Pd dopant. Compared to Pd doping, the case of Pt doping leads to much more drastic changes in the steady state and transient absorption of the clusters, which indicates that the 5d orbitals of the Pt atom are more strongly mixed with Au 5d and 6s orbitals than the 4d orbitals of the Pd dopant. These results demonstrate that a single foreign atom can lead to entirely different excited state spectral features of the whole cluster compared to the parent Au 25(SR) 18 cluster. As a result, the detailed excited state dynamics of atomically precise Pd/Pt doped gold clusters help further understand their properties and benefit the development of energy-related applications.« less

Chandra Catches Early Phase of Cosmic Assembly

NASA Astrophysics Data System (ADS)

2004-08-01

A NASA Chandra X-ray Observatory image has revealed a complex of several intergalactic hot gas clouds in the process of merging. The superb Chandra spatial resolution made it possible to distinguish individual galaxies from the massive clouds of hot gas. One of the clouds, which that envelops hundreds of galaxies, has an extraordinarily low concentration of iron atoms, indicating that it is in the very early stages of cluster evolution. "We may be seeing hot intergalactic gas in a relatively pristine state before it has been polluted by gas from galaxies," said Q. Daniel Wang of the University of Massachusetts in Amherst, and lead author on an upcoming Astrophysical Journal article describing the study. "This discovery should provide valuable insight into how the most massive structures in the universe are assembled." 3-Panel Image of Abell 2125, Its Core & Galaxy C153 3-Panel Image of Abell 2125, Its Core & Galaxy C153 The complex, known as Abell 2125,is about 3 billion light years from Earth, and is seen at a time about 11 billion years after the Big Bang, when many galaxy clusters are believed to have formed. The Chandra Abell 2125 image shows several huge elongated clouds of multimillion degree gas coming together from different directions. These hot gas clouds, each of which contains hundreds of galaxies, appear to be in the process of merging to form a single massive galaxy cluster. Chandra, Hubble Space Telescope, and Very Large Array radio telescope data show that several galaxies in the Abell 2125 core cluster are being stripped of their gas as they fall through surrounding high-pressure hot gas. This stripping process has enriched the core cluster's gas in heavy elements such as iron. Abell 2125's Core & Galaxy C153 Abell 2125's Core & Galaxy C153 The gas in the pristine cloud, which is still several million light years away from the core cluster, is conspicuous for its lack of iron atoms. This anemic cloud must be in a very early evolutionary stage. The iron atoms produced by supernovas in the embedded galaxies must still be contained in and around the galaxies, perhaps in grains of dust not well mixed with the observed X-ray-emitting gas. Over time, as the cluster merges with the other clusters and the hot gas pressure increases, the dust grains will be driven from the galaxies, mixed with the hot gas, and destroyed, liberating the iron atoms. Building a massive galaxy cluster is a step-by-step enterprise that takes billions of years. Exactly how long it takes for such a cluster to form depends on many factors, such as the density of subclusters in the vicinity, the rate of the expansion of the universe, and the relative amounts of dark energy and dark matter. Chandra X-ray Image of Abell 2125, Low Energy Chandra X-ray Image of Abell 2125, Low Energy Cluster formation also involves complex interactions between the galaxies and the hot gas that may determine how large the galaxies in the cluster can ultimately become. These interactions determine how the galaxies maintain their gas content, the fuel for star formation. The observations of Abell 2125 provide a rare glimpse into the early steps in this process. NASA's Marshall Space Flight Center, Huntsville, Ala., manages the Chandra program for NASA's Office of Space Science, Washington. Northrop Grumman of Redondo Beach, Calif., formerly TRW, Inc., was the prime development contractor for the observatory. The Smithsonian Astrophysical Observatory controls science and flight operations from the Chandra X-ray Center in Cambridge, Mass. Additional information and images are available at: http://chandra.harvard.edu and http://chandra.nasa.gov

Energy spectra of small bosonic clusters having a large two-body scattering length

NASA Astrophysics Data System (ADS)

Gattobigio, M.; Kievsky, A.; Viviani, M.

2012-10-01

In this work we investigate small clusters of bosons using the hyperspherical harmonic basis. We consider systems with A=2,3,4,5,6 particles interacting through a soft interparticle potential. In order to make contact with a real system, we use an attractive Gaussian potential that reproduces the values of the dimer binding energy and the atom-atom scattering length obtained with one of the most widely used 4He-4He interactions, the LM2M2 potential of Aziz and Slaman. The intensity of the potential is varied in order to explore the clusters’ spectra in different regions with large positive and large negative values of the two-body scattering length. In addition, we include a repulsive three-body force to reproduce the trimer binding energy. With this model, consisting in the sum of a two- and three-body potential, we have calculated the spectrum of the four-, five-, and six-particle systems. In all the regions explored, we have found that these systems present two states, one deep and one shallow close to the A-1 threshold. Some universal relations between the energy levels are extracted; in particular, we have estimated the universal ratios between thresholds of the three-, four-, and five-particle continua using the two-body Gaussian potential. They agree with recent measurements and theoretical predictions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiong, Haifeng; Lin, Sen; Goetze, Joris

CeO2 supports are unique in their ability to trap ionic Pt, providing exceptional stability for isolated single atoms of Pt. Here, we explore the reactivity and stability of single atom Pt species for the industrially important reaction of light alkane dehydrogenation. The single atom Pt/CeO2 catalysts are stable during propane dehydrogenation, but we observe no selectivity towards propene. DFT calculations show strong adsorption of the olefin produced, leading to further unwanted reactions. In contrast, when Sn is added to ceria, the single atom Pt catalyst undergoes an activation phase where it transforms into Pt-Sn clusters under reaction conditions. Formation ofmore » small Pt-Sn clusters allows the catalyst to achieve high selectivity towards propene, due to facile desorption of the product. The CeO2-supported Pt-Sn clusters are very stable, even during extended reaction at 680 °C. By adding water vapor to the feed, coke formation can almost completely be suppressed. Furthermore, the Pt-Sn clusters can be readily transformed back to the atomically dispersed species on ceria via oxidation, making Pt-Sn/CeO2 a fully regenerable catalyst.« less

Equilibrium structure and atomic vibrations of Nin clusters

NASA Astrophysics Data System (ADS)

Borisova, Svetlana D.; Rusina, Galina G.

2017-12-01

The equilibrium bond lengths and binding energy, second differences in energy and vibrational frequencies of free clusters Nin (2 ≤ n ≤ 20) were calculated with the use of the interaction potential obtained in the tight-binding approximation (TBA). The results show that the minimum vibration frequency plays a significant role in the evaluation of the dynamic stability of the clusters. A nonmonotonic dependence of the minimum vibration frequency of clusters on their size and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 are demonstrated. This result agrees with the theoretical and experimental data on stable structures of small metallic clusters.

Density-functional theory study of the geometries, stabilities, and electronic properties of Au n Rb (n = 1-10) clusters: comparison with pure gold clusters

NASA Astrophysics Data System (ADS)

Hu, Yan-Fei; Jiang, Gang; Meng, Da-Qiao

2012-01-01

The density functional method with the relativistic effective core potential has been employed to investigate systematically the geometric structures, relative stabilities, growth-pattern behavior, and electronic properties of small bimetallic Au n Rb (n = 1-10) and pure gold Au n (n ≤ 11) clusters. For the geometric structures of the Au n Rb (n = 1-10) clusters, the dominant growth pattern is for a Rb-substituted Au n +1 cluster or one Au atom capped on a Au n -1Rb cluster, and the turnover point from a two-dimensional to a three-dimensional structure occurs at n = 4. Moreover, the stability of the ground-state structures of these clusters has been examined via an analysis of the average atomic binding energies, fragmentation energies, and the second-order difference of energies as a function of cluster size. The results exhibit a pronounced even-odd alternation phenomenon. The same pronounced even-odd alternations are found for the HOMO-LUMO gap, VIPs, VEAs, and the chemical hardness. In addition, about one electron charge transfers from the Au n host to the Rb atom in each corresponding Au n Rb cluster.

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

DOE PAGES

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chu, Haijian; Huang, Hanchen; Wang, Jian

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

A DFT study of the stability of SIAs and small SIA clusters in the vicinity of solute atoms in Fe

NASA Astrophysics Data System (ADS)

Becquart, C. S.; Ngayam Happy, R.; Olsson, P.; Domain, C.

2018-03-01

The energetics, defect volume and magnetic properties of single SIAs and small SIA clusters up to size 6 have been calculated by DFT for different configurations like the parallel 〈110〉 dumbbell, the non parallel 〈110〉 dumbbell and the C15 structure. The most stable configurations of each type have been further analyzed to determine the influence on their stability of various solute atoms (Ti, V, Cr, Mn, Co, Ni, Cu, Mo, W, Pd, Al, Si, P), relevant for steels used under irradiation. The results show that the presence of solute atoms does not change the relative stability order among SIA clusters. The small SIA clusters investigated can bind to both undersized and oversized solutes. Several descriptors have been considered to derive interesting trends from results. It appears that the local atomic volume available for the solute is the main physical quantity governing the binding energy evolution, whatever the solute type (undersized or oversized) and the cluster configuration (size and type).

Classification of ligand molecules in PDB with graph match-based structural superposition.

PubMed

Shionyu-Mitsuyama, Clara; Hijikata, Atsushi; Tsuji, Toshiyuki; Shirai, Tsuyoshi

2016-12-01

The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom-atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set. The characteristic feature in the current classification system is the increased number of singleton clusters, which contained only one ligand molecule in a cluster. Inspections of the singletons in the current classification system but not in the previous one implied that the major factors for the isolation were differences in chirality, cyclic conformations, separation of substructures, and bond length. Comparisons between current and previous classification systems revealed that the superposition-based classification was effective in clustering functionally related ligands, such as drugs targeted to specific biological processes, owing to the strictness of the atom-atom matching.

Catalyst Architecture for Stable Single Atom Dispersion Enables Site-Specific Spectroscopic and Reactivity Measurements of CO Adsorbed to Pt Atoms, Oxidized Pt Clusters, and Metallic Pt Clusters on TiO2.

PubMed

DeRita, Leo; Dai, Sheng; Lopez-Zepeda, Kimberly; Pham, Nicholas; Graham, George W; Pan, Xiaoqing; Christopher, Phillip

2017-10-11

Oxide-supported precious metal nanoparticles are widely used industrial catalysts. Due to expense and rarity, developing synthetic protocols that reduce precious metal nanoparticle size and stabilize dispersed species is essential. Supported atomically dispersed, single precious metal atoms represent the most efficient metal utilization geometry, although debate regarding the catalytic activity of supported single precious atom species has arisen from difficulty in synthesizing homogeneous and stable single atom dispersions, and a lack of site-specific characterization approaches. We propose a catalyst architecture and characterization approach to overcome these limitations, by depositing ∼1 precious metal atom per support particle and characterizing structures by correlating scanning transmission electron microscopy imaging and CO probe molecule infrared spectroscopy. This is demonstrated for Pt supported on anatase TiO 2 . In these structures, isolated Pt atoms, Pt iso , remain stable through various conditions, and spectroscopic evidence suggests Pt iso species exist in homogeneous local environments. Comparing Pt iso to ∼1 nm preoxidized (Pt ox ) and prereduced (Pt metal ) Pt clusters on TiO 2 , we identify unique spectroscopic signatures of CO bound to each site and find CO adsorption energy is ordered: Pt iso ≪ Pt metal < Pt ox . Pt iso species exhibited a 2-fold greater turnover frequency for CO oxidation than 1 nm Pt metal clusters but share an identical reaction mechanism. We propose the active catalytic sites are cationic interfacial Pt atoms bonded to TiO 2 and that Pt iso exhibits optimal reactivity because every atom is exposed for catalysis and forms an interfacial site with TiO 2 . This approach should be generally useful for studying the behavior of supported precious metal atoms.

Diffusion of two-dimensional epitaxial clusters on metal (100) surfaces: Facile versus nucleation-mediated behavior and their merging for larger sizes

NASA Astrophysics Data System (ADS)

Lai, King C.; Liu, Da-Jiang; Evans, James W.

2017-12-01

For diffusion of two-dimensional homoepitaxial clusters of N atoms on metal (100) surfaces mediated by edge atom hopping, macroscale continuum theory suggests that the diffusion coefficient scales like DN˜ N-β with β =3 /2 . However, we find quite different and diverse behavior in multiple size regimes. These include: (i) facile diffusion for small sizes N <9 ; (ii) slow nucleation-mediated diffusion with small β <1 for "perfect" sizes N = Np= L2 or L (L +1 ) , for L =3 ,4 , ... having unique ground-state shapes, for moderate sizes 9 ≤N ≤O (102) ; the same also applies for N =Np+3 , Np+ 4 , ... (iii) facile diffusion but with large β >2 for N =Np+1 and Np+2 also for moderate sizes 9 ≤N ≤O (102) ; (iv) merging of the above distinct branches and subsequent anomalous scaling with 1 ≲β <3 /2 , reflecting the quasifacetted structure of clusters, for larger N =O (102) to N =O (103) ; (v) classic scaling with β =3 /2 for very large N =O (103) and above. The specified size ranges apply for typical model parameters. We focus on the moderate size regime where we show that diffusivity cycles quasiperiodically from the slowest branch for Np+3 (not Np) to the fastest branch for Np+1 . Behavior is quantified by kinetic Monte Carlo simulation of an appropriate stochastic lattice-gas model. However, precise analysis must account for a strong enhancement of diffusivity for short time increments due to back correlation in the cluster motion. Further understanding of this enhancement, of anomalous size scaling behavior, and of the merging of various branches, is facilitated by combinatorial analysis of the number of the ground-state and low-lying excited state cluster configurations, and also of kink populations.

Diffusion of two-dimensional epitaxial clusters on metal (100) surfaces: Facile versus nucleation-mediated behavior and their merging for larger sizes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lai, King C.; Liu, Da -Jiang; Evans, James W.

For diffusion of two-dimensional homoepitaxial clusters of N atoms on metal(100) surfaces mediated by edge atom hopping, macroscale continuum theory suggests that the diffusion coefficient scales like DN ~ N -β with β = 3/2. However, we find quite different and diverse behavior in multiple size regimes. These include: (i) facile diffusion for small sizes N < 9; (ii) slow nucleation-mediated diffusion with small β < 1 for “perfect” sizes N = N p = L 2 or L(L+1), for L = 3, 4,… having unique ground state shapes, for moderate sizes 9 ≤ N ≤ O(10 2); the samemore » also applies for N = N p +3, N p + 4,… (iii) facile diffusion but with large β > 2 for N = Np + 1 and N p + 2 also for moderate sizes 9 ≤ N ≤ O(10 2); (iv) merging of the above distinct branches and subsequent anomalous scaling with 1 ≲ β < 3/2, reflecting the quasi-facetted structure of clusters, for larger N = O(10 2) to N = O(10 3); and (v) classic scaling with β = 3/2 for very large N = O(103) and above. The specified size ranges apply for typical model parameters. We focus on the moderate size regime where show that diffusivity cycles quasi-periodically from the slowest branch for N p + 3 (not Np) to the fastest branch for Np + 1. Behavior is quantified by Kinetic Monte Carlo simulation of an appropriate stochastic lattice-gas model. However, precise analysis must account for a strong enhancement of diffusivity for short time increments due to back-correlation in the cluster motion. Further understanding of this enhancement, of anomalous size scaling behavior, and of the merging of various branches, is facilitated by combinatorial analysis of the number of the ground state and low-lying excited state cluster configurations, and also of kink populations.« less

Diffusion of two-dimensional epitaxial clusters on metal (100) surfaces: Facile versus nucleation-mediated behavior and their merging for larger sizes

DOE PAGES

Lai, King C.; Liu, Da -Jiang; Evans, James W.

2017-12-05

For diffusion of two-dimensional homoepitaxial clusters of N atoms on metal(100) surfaces mediated by edge atom hopping, macroscale continuum theory suggests that the diffusion coefficient scales like DN ~ N -β with β = 3/2. However, we find quite different and diverse behavior in multiple size regimes. These include: (i) facile diffusion for small sizes N < 9; (ii) slow nucleation-mediated diffusion with small β < 1 for “perfect” sizes N = N p = L 2 or L(L+1), for L = 3, 4,… having unique ground state shapes, for moderate sizes 9 ≤ N ≤ O(10 2); the samemore » also applies for N = N p +3, N p + 4,… (iii) facile diffusion but with large β > 2 for N = Np + 1 and N p + 2 also for moderate sizes 9 ≤ N ≤ O(10 2); (iv) merging of the above distinct branches and subsequent anomalous scaling with 1 ≲ β < 3/2, reflecting the quasi-facetted structure of clusters, for larger N = O(10 2) to N = O(10 3); and (v) classic scaling with β = 3/2 for very large N = O(103) and above. The specified size ranges apply for typical model parameters. We focus on the moderate size regime where show that diffusivity cycles quasi-periodically from the slowest branch for N p + 3 (not Np) to the fastest branch for Np + 1. Behavior is quantified by Kinetic Monte Carlo simulation of an appropriate stochastic lattice-gas model. However, precise analysis must account for a strong enhancement of diffusivity for short time increments due to back-correlation in the cluster motion. Further understanding of this enhancement, of anomalous size scaling behavior, and of the merging of various branches, is facilitated by combinatorial analysis of the number of the ground state and low-lying excited state cluster configurations, and also of kink populations.« less

Synthesis, structures, and solution dynamics of tetrasubstituted nine-atom germanium deltahedral clusters.

PubMed

Li, Feng; Sevov, Slavi C

2014-08-27

Reported are the rational synthesis, structures, and solution dynamics of three tetrasubstituted and neutral Ge9-based deltahedral clusters [Ge9R3R'](0), where R = Si(SiMe3)3 and R' = Et (1), Sn(n)Bu3 (2), or Tl (3). The first step of the synthesis is a reaction of an acetonitrile suspension of the intermetallic precursor compound K4Ge9 with {Si(SiMe3)3}Cl which produces the trisubstituted monoanions [Ge9{Si(SiMe3)3}](-). A benzene suspension of the latter is then reacted with Sn(n)Bu3Cl or TlCp to produce 2 and 3, respectively, while the same acetonitrile solution is reacted with EtBr in order to produce 1. All three structures can be viewed as tricapped trigonal prisms of Ge9 with the three "hypersilyl" substituents, Si(SiMe3)3, exo-bonded to the capping atoms. The fourth substituent in 1, the ethyl group, is exo-bonded to one of the six available Ge atoms with the Ge-C bond positioned radially to the Ge9 core. In the case of 2, on the other hand, the tin fragment is found above one of the triangular bases of the prism interacting with one or more Ge atoms in three crystallographically different molecules in the structure. Lastly, the Tl atom in the structure of 3 is found capping a pseudosquare face between two hypersilyl substituents. NMR spectroscopy indicates that all three compounds are dynamic at room temperature. Variable-temperature studies suggest that the process in 1 and 2 is intramolecular while the process in 3 involves dissociation of the Tl(+) ion from the molecule followed by association at the same or another equivalent pseudosquare face of the molecule. Thus, the latter compound may be considered to a large extent to be ionic as it is made of a thallium cation and a trisubstituted cluster anion.

Titanium embedded cage structure formation in Al{sub n}Ti{sup +} clusters and their interaction with Ar

DOE Office of Scientific and Technical Information (OSTI.GOV)

Torres, M. B., E-mail: begonia@ubu.es; Vega, A.; Balbás, L. C.

2014-05-07

Recently, Ar physisorption was used as a structural probe for the location of the Ti dopant atom in aluminium cluster cations, Al{sub n}Ti{sup +} [Lang et al., J. Am. Soc. Mass Spectrom. 22, 1508 (2011)]. As an experiment result, the lack of Ar complexes for n > n{sub c} determines the cluster size for which the Ti atom is located inside of an Al cage. To elucidate the decisive factors for the formation of endohedrally Al{sub n}Ti{sup +}, experimentalists proposed detailed computational studies as indispensable. In this work, we investigated, using the density functional theory, the structural and electronic propertiesmore » of singly titanium doped cationic clusters, Al{sub n}Ti{sup +} (n = 16–21) as well as the adsorption of an Ar atom on them. The first endohedral doped cluster, with Ti encapsulated in a fcc-like cage skeleton, appears at n{sub c} = 21, which is the critical number consistent with the exohedral-endohedral transition experimentally observed. At this critical size the non-crystalline icosahedral growth pattern, related to the pure aluminium clusters, with the Ti atom in the surface, changes into a endohedral fcc-like pattern. The map of structural isomers, relative energy differences, second energy differences, and structural parameters were determined and analyzed. Moreover, we show the critical size depends on the net charge of the cluster, being different for the cationic clusters (n{sub c} = 21) and their neutral counterparts (n{sub c} = 20). For the Al {sub n} Ti {sup +} · Ar complexes, and for n < 21, the preferred Ar adsorption site is on top of the exohedral Ti atom, with adsorption energy in very good agreement with the experimental value. Instead, for n = 21, the Ar adsorption occurs on the top an Al atom with very low absorption energy. For all sizes the geometry of the Al{sub n}Ti{sup +} clusters keeps unaltered in the Ar-cluster complexes. This fact indicates that Ar adsorption does not influence the cluster structure, providing support to the experimental technique used. For n{sub c} = 21, the smallest size of endohedral Ti doped cationic clusters, the Ar binding energy decreases drastically, whereas the Ar-cluster distance increases substantially, point to Ar physisorption, as assumed by the experimentalists. Calculated Ar adsorption energies agree well with available experimental binding energies.« less

Sigma-phase packing of icosahedral clusters in 780-atom tetragonal crystals of Cr5Ni3Si2 and V15Ni10Si that by twinning achieve 8-fold rotational point-group symmetry

PubMed Central

Pauling, Linus

1988-01-01

A 780-atom primitive tetragonal unit with edges 27.3, 27.3, and 12.6 Å is assigned to rapidly solidified Cu5Ni3Si2 and V15Ni10Si by analysis of electron diffraction photographs with the assumption that the crystals contain icosahedral clusters. There are thirty 26-atom clusters at the sigma-phase positions. Apparent 8-fold symmetry results from 45° twinning on the basal plane. PMID:16593915

Sigma-phase packing of icosahedral clusters in 780-atom tetragonal crystals of Cr(5)Ni(3)Si(2) and V(15)Ni(10)Si that by twinning achieve 8-fold rotational point-group symmetry.

PubMed

Pauling, L

1988-04-01

A 780-atom primitive tetragonal unit with edges 27.3, 27.3, and 12.6 A is assigned to rapidly solidified Cu(5)Ni(3)Si(2) and V(15)Ni(10)Si by analysis of electron diffraction photographs with the assumption that the crystals contain icosahedral clusters. There are thirty 26-atom clusters at the sigma-phase positions. Apparent 8-fold symmetry results from 45 degrees twinning on the basal plane.

Direct evidence for radiative charge transfer after inner-shell excitation and ionization of large clusters

NASA Astrophysics Data System (ADS)

Hans, Andreas; Stumpf, Vasili; Holzapfel, Xaver; Wiegandt, Florian; Schmidt, Philipp; Ozga, Christian; Reiß, Philipp; Ben Ltaief, Ltaief; Küstner-Wetekam, Catmarna; Jahnke, Till; Ehresmann, Arno; Demekhin, Philipp V.; Gokhberg, Kirill; Knie, André

2018-01-01

We directly observe radiative charge transfer (RCT) in Ne clusters by dispersed vacuum-ultraviolet photon detection. The doubly ionized Ne2+-{{{N}}{{e}}}n-1 initial states of RCT are populated after resonant 1s-3p photoexcitation or 1s photoionization of Ne n clusters with < n> ≈ 2800. These states relax further producing Ne+-Ne+-{{{N}}{{e}}}n-2 final states, and the RCT photon is emitted. Ab initio calculations assign the observed RCT signal to the{}{{{N}}{{e}}}2+(2{{{p}}}-2{[}1{{D}}]){--}{{{N}}{{e}}}n-1 initial state, while transitions from other possible initial states are proposed to be quenched by competing relaxation processes. The present results are in agreement with the commonly discussed scenario, where the doubly ionized atom in a noble gas cluster forms a dimer which dissipates its vibrational energy on a picosecond timescale. Our study complements the picture of the RCT process in weakly bound clusters, providing information which is inaccessible by charged particle detection techniques.

Dual beam organic depth profiling using large argon cluster ion beams

PubMed Central

Holzweber, M; Shard, AG; Jungnickel, H; Luch, A; Unger, WES

2014-01-01

Argon cluster sputtering of an organic multilayer reference material consisting of two organic components, 4,4′-bis[N-(1-naphthyl-1-)-N-phenyl- amino]-biphenyl (NPB) and aluminium tris-(8-hydroxyquinolate) (Alq3), materials commonly used in organic light-emitting diodes industry, was carried out using time-of-flight SIMS in dual beam mode. The sample used in this study consists of a ∽400-nm-thick NPB matrix with 3-nm marker layers of Alq3 at depth of ∽50, 100, 200 and 300 nm. Argon cluster sputtering provides a constant sputter yield throughout the depth profiles, and the sputter yield volumes and depth resolution are presented for Ar-cluster sizes of 630, 820, 1000, 1250 and 1660 atoms at a kinetic energy of 2.5 keV. The effect of cluster size in this material and over this range is shown to be negligible. © 2014 The Authors. Surface and Interface Analysis published by John Wiley & Sons Ltd. PMID:25892830

Going beyond Clustering in MD Trajectory Analysis: An Application to Villin Headpiece Folding

PubMed Central

Rajan, Aruna; Freddolino, Peter L.; Schulten, Klaus

2010-01-01

Recent advances in computing technology have enabled microsecond long all-atom molecular dynamics (MD) simulations of biological systems. Methods that can distill the salient features of such large trajectories are now urgently needed. Conventional clustering methods used to analyze MD trajectories suffer from various setbacks, namely (i) they are not data driven, (ii) they are unstable to noise and changes in cut-off parameters such as cluster radius and cluster number, and (iii) they do not reduce the dimensionality of the trajectories, and hence are unsuitable for finding collective coordinates. We advocate the application of principal component analysis (PCA) and a non-metric multidimensional scaling (nMDS) method to reduce MD trajectories and overcome the drawbacks of clustering. To illustrate the superiority of nMDS over other methods in reducing data and reproducing salient features, we analyze three complete villin headpiece folding trajectories. Our analysis suggests that the folding process of the villin headpiece is structurally heterogeneous. PMID:20419160

Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding.

PubMed

Rajan, Aruna; Freddolino, Peter L; Schulten, Klaus

2010-04-15

Recent advances in computing technology have enabled microsecond long all-atom molecular dynamics (MD) simulations of biological systems. Methods that can distill the salient features of such large trajectories are now urgently needed. Conventional clustering methods used to analyze MD trajectories suffer from various setbacks, namely (i) they are not data driven, (ii) they are unstable to noise and changes in cut-off parameters such as cluster radius and cluster number, and (iii) they do not reduce the dimensionality of the trajectories, and hence are unsuitable for finding collective coordinates. We advocate the application of principal component analysis (PCA) and a non-metric multidimensional scaling (nMDS) method to reduce MD trajectories and overcome the drawbacks of clustering. To illustrate the superiority of nMDS over other methods in reducing data and reproducing salient features, we analyze three complete villin headpiece folding trajectories. Our analysis suggests that the folding process of the villin headpiece is structurally heterogeneous.

Cluster Beam Studies.

DTIC Science & Technology

1988-04-01

Continue on reverse if necessary and identify by block number) Cluster beams offer a means of depositing high-quality thin films at low...either directly inclustered vapors of nonvolatile materials or Indirectly by bombarding the film duringdeposition with clusters of inert gases. When a...electron volt energy per atom. The suprathermal energy of thej depositing atoms is thought to produce unique thin films (either in quality, or in the ability

Thermodynamic properties of arsenic compounds and the heat of formation of the As atom from high level electronic structure calculations.

PubMed

Feller, David; Vasiliu, Monica; Grant, Daniel J; Dixon, David A

2011-12-29

Structures, vibrational frequencies, atomization energies at 0 K, and heats of formation at 0 and 298 K are predicted for the compounds As(2), AsH, AsH(2), AsH(3), AsF, AsF(2), and AsF(3) from frozen core coupled cluster theory calculations performed with large correlation consistent basis sets, up through augmented sextuple zeta quality. The coupled cluster calculations involved up through quadruple excitations. For As(2) and the hydrides, it was also possible to examine the impact of full configuration interaction on some of the properties. In addition, adjustments were incorporated to account for extrapolation to the frozen core complete basis set limit, core/valence correlation, scalar relativistic effects, the diagonal Born-Oppenheimer correction, and atomic spin orbit corrections. Based on our best theoretical D(0)(As(2)) and the experimental heat of formation of As(2), we propose a revised 0 K arsenic atomic heat of formation of 68.86 ± 0.8 kcal/mol. While generally good agreement was found between theory and experiment, the heat of formation of AsF(3) was an exception. Our best estimate is more than 7 kcal/mol more negative than the single available experimental value, which argues for a re-examination of that measurement. © 2011 American Chemical Society

Enhanced Atom Mobility on the Surface of a Metastable Film

NASA Astrophysics Data System (ADS)

Picone, A.; Riva, M.; Fratesi, G.; Brambilla, A.; Bussetti, G.; Finazzi, M.; Duò, L.; Ciccacci, F.

2014-07-01

A remarkable enhancement of atomic diffusion is highlighted by scanning tunneling microscopy performed on ultrathin metastable body-centered tetragonal Co films grown on Fe(001). The films follow a nearly perfect layer-by-layer growth mode with a saturation island density strongly dependent on the layer on which the nucleation occurs, indicating a lowering of the diffusion barrier. Density functional theory calculations reveal that this phenomenon is driven by the increasing capability of the film to accommodate large deformations as the thickness approaches the limit at which a structural transition occurs. These results disclose the possibility of tuning surface diffusion dynamics and controlling cluster nucleation and self-organization.

Enhanced atom mobility on the surface of a metastable film.

PubMed

Picone, A; Riva, M; Fratesi, G; Brambilla, A; Bussetti, G; Finazzi, M; Duò, L; Ciccacci, F

2014-07-25

A remarkable enhancement of atomic diffusion is highlighted by scanning tunneling microscopy performed on ultrathin metastable body-centered tetragonal Co films grown on Fe(001). The films follow a nearly perfect layer-by-layer growth mode with a saturation island density strongly dependent on the layer on which the nucleation occurs, indicating a lowering of the diffusion barrier. Density functional theory calculations reveal that this phenomenon is driven by the increasing capability of the film to accommodate large deformations as the thickness approaches the limit at which a structural transition occurs. These results disclose the possibility of tuning surface diffusion dynamics and controlling cluster nucleation and self-organization.

Cluster size selectivity in the product distribution of ethene dehydrogenation on niobium clusters.

PubMed

Parnis, J Mark; Escobar-Cabrera, Eric; Thompson, Matthew G K; Jacula, J Paul; Lafleur, Rick D; Guevara-García, Alfredo; Martínez, Ana; Rayner, David M

2005-08-18

Ethene reactions with niobium atoms and clusters containing up to 25 constituent atoms have been studied in a fast-flow metal cluster reactor. The clusters react with ethene at about the gas-kinetic collision rate, indicating a barrierless association process as the cluster removal step. Exceptions are Nb8 and Nb10, for which a significantly diminished rate is observed, reflecting some cluster size selectivity. Analysis of the experimental primary product masses indicates dehydrogenation of ethene for all clusters save Nb10, yielding either Nb(n)C2H2 or Nb(n)C2. Over the range Nb-Nb6, the extent of dehydrogenation increases with cluster size, then decreases for larger clusters. For many clusters, secondary and tertiary product masses are also observed, showing varying degrees of dehydrogenation corresponding to net addition of C2H4, C2H2, or C2. With Nb atoms and several small clusters, formal addition of at least six ethene molecules is observed, suggesting a polymerization process may be active. Kinetic analysis of the Nb atom and several Nb(n) cluster reactions with ethene shows that the process is consistent with sequential addition of ethene units at rates corresponding approximately to the gas-kinetic collision frequency for several consecutive reacting ethene molecules. Some variation in the rate of ethene pick up is found, which likely reflects small energy barriers or steric constraints associated with individual mechanistic steps. Density functional calculations of structures of Nb clusters up to Nb(6), and the reaction products Nb(n)C2H2 and Nb(n)C2 (n = 1...6) are presented. Investigation of the thermochemistry for the dehydrogenation of ethene to form molecular hydrogen, for the Nb atom and clusters up to Nb6, demonstrates that the exergonicity of the formation of Nb(n)C2 species increases with cluster size over this range, which supports the proposal that the extent of dehydrogenation is determined primarily by thermodynamic constraints. Analysis of the structural variations present in the cluster species studied shows an increase in C-H bond lengths with cluster size that closely correlates with the increased thermodynamic drive to full dehydrogenation. This correlation strongly suggests that all steps in the reaction are barrierless, and that weakening of the C-H bonds is directly reflected in the thermodynamics of the overall dehydrogenation process. It is also demonstrated that reaction exergonicity in the initial partial dehydrogenation step must be carried through as excess internal energy into the second dehydrogenation step.

Two-component relativistic coupled-cluster methods using mean-field spin-orbit integrals

NASA Astrophysics Data System (ADS)

Liu, Junzi; Shen, Yue; Asthana, Ayush; Cheng, Lan

2018-01-01

A novel implementation of the two-component spin-orbit (SO) coupled-cluster singles and doubles (CCSD) method and the CCSD augmented with the perturbative inclusion of triple excitations [CCSD(T)] method using mean-field SO integrals is reported. The new formulation of SO-CCSD(T) features an atomic-orbital-based algorithm for the particle-particle ladder term in the CCSD equation, which not only removes the computational bottleneck associated with the large molecular-orbital integral file but also accelerates the evaluation of the particle-particle ladder term by around a factor of 4 by taking advantage of the spin-free nature of the instantaneous electron-electron Coulomb interaction. Benchmark calculations of the SO splittings for the thallium atom and a set of diatomic 2Π radicals as well as of the bond lengths and harmonic frequencies for a set of closed-shell diatomic molecules are presented. The basis-set and core-correlation effects in the calculations of these properties have been carefully analyzed.

Nickel-aluminum alloy clusters -- structural and dynamical properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jellinek, J.; Krissinel, E.B.

1997-08-01

Structural and dynamical properties of mixed Ni{sub n}Al{sub m} alloy clusters mimicked by a many-body potential are studied computationally for all the possible compositions n and m such that n + m = 13. It is shown that the manifold of the usually very large number of the different possible structural forms can be systematized by introducing classes of structures corresponding to the same concentration of the components, geometry and type of the central atom. General definitions of mixing energy and mixing coefficient are introduced, and it is shown that the energy ordering of the structural forms within each classmore » is governed by the mixing coefficient. The peculiarities of the solid-to-liquid-like transition are described as a function of the concentration of the two types of atoms. These peculiarities are correlated with and explained in terms of the energy spectra of the structural forms. Class-dependent features of the dynamics are described and analyzed.« less

A universal matter-wave interferometer with optical ionization gratings in the time-domain

PubMed Central

Haslinger, Philipp; Dörre, Nadine; Geyer, Philipp; Rodewald, Jonas; Nimmrichter, Stefan; Arndt, Markus

2015-01-01

Matter-wave interferometry with atoms1 and molecules2 has attracted a rapidly growing interest throughout the last two decades both in demonstrations of fundamental quantum phenomena and in quantum-enhanced precision measurements. Such experiments exploit the non-classical superposition of two or more position and momentum states which are coherently split and rejoined to interfere3-11. Here, we present the experimental realization of a universal near-field interferometer built from three short-pulse single-photon ionization gratings12,13. We observe quantum interference of fast molecular clusters, with a composite de Broglie wavelength as small as 275 fm. Optical ionization gratings are largely independent of the specific internal level structure and are therefore universally applicable to different kinds of nanoparticles, ranging from atoms to clusters, molecules and nanospheres. The interferometer is sensitive to fringe shifts as small as a few nanometers and yet robust against velocity-dependent phase shifts, since the gratings exist only for nanoseconds and form an interferometer in the time-domain. PMID:25983851

Ion mobility studies of PdC{sub n}{sup +} clusters: Where are the fullerenes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shelimov, K.B.; Jarrold, M.F.

1995-12-14

Gas-phase ion mobility measurements have been used to study the structures and isomerization of PdC{sub n}{sup +} (n = 10-60) clusters. Non-fullerene isomers of PdC{sub n}{sup +} clusters are similar to those of C{sub n}{sup +} and MC{sub n}{sup +} (M = La and Nb) clusters, and include metal-containing mono- and bicyclic rings and graphite sheets. Neither endohedral nor nonendohedral PdC{sub n} {sup +} fullerene isomers are detected. When collisionally heated, PdC{sub n}{sup +} clusters efficiently convert into fullerenes, but the exothermicity of this process results in the loss of the Pd atom and the formation of a pure carbonmore » cluster cation. PdC{sub n}{sup +} bicyclic rings with an odd number of carbon atoms efficiently isomerize into monocyclic rings, while no evidence is found for this isomerization process for bicyclic rings with an even number of carbon atoms. 18 refs., 4 figs.« less

Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.

PubMed

Sammond, Deanne W; Kastelowitz, Noah; Himmel, Michael E; Yin, Hang; Crowley, Michael F; Bomble, Yannick J

2016-01-01

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.

Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms

PubMed Central

Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.; Yin, Hang; Crowley, Michael F.; Bomble, Yannick J.

2016-01-01

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions. PMID:26741367

A screened independent atom model for the description of ion collisions from atomic and molecular clusters

NASA Astrophysics Data System (ADS)

Lüdde, Hans Jürgen; Horbatsch, Marko; Kirchner, Tom

2018-05-01

We apply a recently introduced model for an independent-atom-like calculation of ion-impact electron transfer and ionization cross sections to proton collisions from water, neon, and carbon clusters. The model is based on a geometrical interpretation of the cluster cross section as an effective area composed of overlapping circular disks that are representative of the atomic contributions. The latter are calculated using a time-dependent density-functional-theory-based single-particle description with accurate exchange-only ground-state potentials. We find that the net capture and ionization cross sections in p-X n collisions are proportional to n α with 2/3 ≤ α ≤ 1. For capture from water clusters at 100 keV impact energy α is close to one, which is substantially different from the value α = 2/3 predicted by a previous theoretical work based on the simplest-level electron nuclear dynamics method. For ionization at 100 keV and for capture at lower energies we find smaller α values than for capture at 100 keV. This can be understood by considering the magnitude of the atomic cross sections and the resulting overlaps of the circular disks that make up the cluster cross section in our model. Results for neon and carbon clusters confirm these trends. Simple parametrizations are found which fit the cross sections remarkably well and suggest that they depend on the relevant bond lengths.

Structures and stability of metal-doped Ge{sub n}M (n = 9, 10) clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin, Wei, E-mail: qinw@qdu.edu.cn; Xia, Lin-Hua; Zhao, Li-Zhen

The lowest-energy structures of neutral and cationic Ge{sub n}M (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge{sub 9} and Ge{sub 10} clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge{sub n} clusters. However, the neutral and cationic FeGe{sub 9,10},MnGe{sub 9,10} and Ge{sub 10}Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge{sub n} clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge{sub 9,10}Fe and Ge{sub 9}Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Related Structure Characters and Stability of Structural Defects in a Metallic Glass

PubMed Central

Niu, Xiaofeng; Feng, Shidong; Pan, Shaopeng

2018-01-01

Structural defects were investigated by a recently proposed structural parameter, quasi-nearest atom (QNA), in a modeled Zr50Cu50 metallic glass through molecular dynamics simulations. More QNAs around an atom usually means that more defects are located near the atom. Structural analysis reveals that the spatial distribution of the numbers of QNAs displays to be clearly heterogeneous. Furthermore, QNA is closely correlated with cluster connections, especially four-atom cluster connections. Atoms with larger coordination numbers usually have less QNAs. When two atoms have the same coordination number, the atom with larger five-fold symmetry has less QNAs. The number of QNAs around an atom changes rather frequently and the change of QNAs might be correlated with the fast relaxation metallic glasses. PMID:29565298

Delivery of Iron-Sulfur Clusters to the Hydrogen-Oxidizing [NiFe]-Hydrogenases in Escherichia coli Requires the A-Type Carrier Proteins ErpA and IscA

PubMed Central

Pinske, Constanze; Sawers, R. Gary

2012-01-01

During anaerobic growth Escherichia coli synthesizes two membrane-associated hydrogen-oxidizing [NiFe]-hydrogenases, termed hydrogenase 1 and hydrogenase 2. Each enzyme comprises a catalytic subunit containing the [NiFe] cofactor, an electron-transferring small subunit with a particular complement of [Fe-S] (iron-sulfur) clusters and a membrane-anchor subunit. How the [Fe-S] clusters are delivered to the small subunit of these enzymes is unclear. A-type carrier (ATC) proteins of the Isc (iron-sulfur-cluster) and Suf (sulfur mobilization) [Fe-S] cluster biogenesis pathways are proposed to traffic pre-formed [Fe-S] clusters to apoprotein targets. Mutants that could not synthesize SufA had active hydrogenase 1 and hydrogenase 2 enzymes, thus demonstrating that the Suf machinery is not required for hydrogenase maturation. In contrast, mutants devoid of the IscA, ErpA or IscU proteins of the Isc machinery had no detectable hydrogenase 1 or 2 activities. Lack of activity of both enzymes correlated with the absence of the respective [Fe-S]-cluster-containing small subunit, which was apparently rapidly degraded. During biosynthesis the hydrogenase large subunits receive their [NiFe] cofactor from the Hyp maturation machinery. Subsequent to cofactor insertion a specific C-terminal processing step occurs before association of the large subunit with the small subunit. This processing step is independent of small subunit maturation. Using western blotting experiments it could be shown that although the amount of each hydrogenase large subunit was strongly reduced in the iscA and erpA mutants, some maturation of the large subunit still occurred. Moreover, in contrast to the situation in Isc-proficient strains, these processed large subunits were not membrane-associated. Taken together, our findings demonstrate that both IscA and ErpA are required for [Fe-S] cluster delivery to the small subunits of the hydrogen-oxidizing hydrogenases; however, delivery of the Fe atom to the active site might have different requirements. PMID:22363723

ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution

PubMed Central

Kurkcuoglu, Zeynep; Bahar, Ivet; Doruker, Pemra

2016-01-01

Accurate sampling of conformational space and, in particular, the transitions between functional substates has been a challenge in molecular dynamic (MD) simulations of large biomolecular systems. We developed an Elastic Network Model (ENM)-based computational method, ClustENM, for sampling large conformational changes of biomolecules with various sizes and oligomerization states. ClustENM is an iterative method that combines ENM with energy minimization and clustering steps. It is an unbiased technique, which requires only an initial structure as input, and no information about the target conformation. To test the performance of ClustENM, we applied it to six biomolecular systems: adenylate kinase (AK), calmodulin, p38 MAP kinase, HIV-1 reverse transcriptase (RT), triosephosphate isomerase (TIM), and the 70S ribosomal complex. The generated ensembles of conformers determined at atomic resolution show good agreement with experimental data (979 structures resolved by X-ray and/or NMR) and encompass the subspaces covered in independent MD simulations for TIM, p38, and RT. ClustENM emerges as a computationally efficient tool for characterizing the conformational space of large systems at atomic detail, in addition to generating a representative ensemble of conformers that can be advantageously used in simulating substrate/ligand-binding events. PMID:27494296

Thermodynamics of the clusterization process of cis isomers of unsaturated fatty acids at the air/water interface.

PubMed

Vysotsky, Yu B; Belyaeva, E A; Fainerman, V B; Vollhardt, D; Aksenenko, E V; Miller, R

2009-04-02

In the framework of the semiempirical PM3 method, the thermodynamic parameters of cis isomers of unsaturated carboxylic acids at the air/water interface are studied. The model systems used are unsaturated cis fatty acid of the composition Delta = 12-15 and omega = 6-11, where Delta and omega refer to the number of carbon atoms between the functional group and double bond, and that between the double bond and methyl group, respectively. For dimers, trimers, and tetramers of the four acid series, the thermodynamic parameters of clusterization are calculated. It is shown that the position of the double bond does not significantly affect the values of thermodynamic parameters of formation and clusterization of carboxylic acids for equal chain lengths (n = Delta + omega). The calculated results show that for cis unsaturated fatty acid with odd Delta values the spontaneous clusterization threshold corresponds to n = 17-18 carbon atoms in the alkyl chain, while for monounsaturated acids with even Delta values this threshold corresponds to n = 18-19 carbon atoms in the alkyl chain. These differences in the clusterization threshold between the acids with even and odd Delta values are attributed to the formation of additional intermolecular hydrogen bonds between the ketonic oxygen atom of one monomer and the hydrogen atom linked to the alpha-carbon atom of the second monomer for the acids with odd Delta values or between the hydroxyl oxygen atom of one monomer and hydrogen atom linked to the alpha-carbon atom of the second monomer for the acids with even Delta values. The results obtained in the study agree satisfactorily with our experimental data for cis unsaturated nervonic (Delta15, omega9) and erucic acids (Delta13, omega9), and published data for some fatty acids, namely cis-16-heptadecenoic (Delta16, omega1), cis-9-hexadecenoic (Delta7, omega9), cis-11-eicosenoic (Delta11, omega9) and cis-9-octadecenoic acid (Delta9, omega9).

On Ion Clusters in the Interstellar Gas

NASA Technical Reports Server (NTRS)

Donn, Bertram

1960-01-01

In a recent paper V.I. Krassovsky (1958) predicts the occurrence of clusters of large numbers of atoms and molecules around ions in the interstellar gas. He then proposes a number of physicochemical processes that would be considerably enhanced by the high particle density in such clusters. In particular, he suggests that absorption by negative ions formed in the clusters would account for the interstellar extinction without any necessity for the presence of grains. Because of the important consequences that ion clusters could have, it is necessary to examine their occurrence more fully. This note re-examines the formation of ion clusters in space and shows that even ion-molecule pairs are essentially non-existent. Ion clusters have been considered by Bloom and Margenau (1952) from the same point of view as that used by Krassovsky, whose basic reference (Joffe and Semenov 1933) unfortunately is not available. A different approach has been used by Eyring, Hirschfelder, and Taylor (1936) following the methods of chemical equilibrium. Both the references cited here enable one to conclude that clustering is negligible. Therefore, the treatment of Eyring et al. is more appropriate than the method of Bloom and Margenau, which depends on the statistical equilibrium of an atmosphere in a force field.

The Design, Synthesis, and Characterization of Open Sites on Metal Clusters

NASA Astrophysics Data System (ADS)

Nigra, Michael Mark

Coordinatively unsaturated corner and edge atoms have been hypothesized to have the highest activity of sites responsible for many catalytic reactions on a metal surface. Recent studies have validated this hypothesis in varied reaction systems. However, quantification of different types of coordinatively unsaturated sites, and elucidation of their individual catalytic rates has remained a largely unresolved challenge when understanding catalysis on metal surfaces. Yet such structure-function knowledge would be invaluable to the design of more active and selective metal-surface catalysts in the future. I investigated the catalytic contributions of undercoordinated sites such as corner and edge atoms are investigated in a model reaction system using organic ligands bound to the gold nanoparticle surface. The catalyst consisted of 4 nm gold nanoparticles on a metal oxide support, using resazurin to resorufin as a model reaction system. My results demonstrate that in this system, corner atom sites are the most undercoordinated sites, and are over an order of magnitude more active when compared to undercoordinated edge atom sites, while terrace sites remain catalytically inactive for the reduction reaction of resazurin to resorufin. Catalytic activity has been also demonstrated for calixarene-bound gold nanoparticles using the reduction of 4-nitrophenol. With the 4-nitrophenol reduction reaction, a comparative study was undertaken to compare calixarene phosphine and calixarene thiol bound 4 nm gold particles. The results of the study suggested that a leached site was responsible for catalysis and not sites on the original gold nanoparticles. Future experiments with calixarene bound gold clusters could investigate ligand effects in reactions where the active site is not a leached or aggregated gold species, possibly in oxidation reactions, where electron-rich gold is hypothesized to be a good catalyst. The results that emphasize the enhanced catalytic activity of undercoordinated sites led me to synthesize small gold clusters consisting of a high fraction of coordinatively unsaturated open sites. This was enabled through an approach that utilized bulky calix[4]arene ligands that are bound to a gold core. Since the size of the calix[4]arene ligand is commensurate with the size of the gold cluster core, the calix[4]arene ligand does not pack closely together on the gold cluster surface. This in turn results in areas of accessible gold atom sites between ligands. Additionally, these calix[4]arene ligands prevent cluster aggregation and electronically tune the gold core in a manner conceptually similar to enzymes affecting reactivity through organic side-chains acting as ligands. I quantified the number of open sites that result from this packing problem on the gold cluster surface, using fluorescence probe chemisorption experiments. The results of these chemisorption measurements support the mechanical model of accessibility whereby accessibility is not dependent on the identity of the functional group, whether it be calixarene phosphines or N-heterocyclic carbenes, bound to the gold surface, but rather to the relative radii of curvature of bound ligands and the gold cluster core. Additional materials characterization was completed with transmission electron microscopy in both bright-field imaging of zeolites, in MCM-22 and delaminated ITQ-2 and UCB-1 materials, and in dark field imaging of glucan coatings on oxide particles. These materials could prove to be interesting materials as to use as supports for the calixarene-bound metal clusters described above or for other metal clusters.

Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the 199Hg Atom

NASA Astrophysics Data System (ADS)

Sahoo, B. K.; Das, B. P.

2018-05-01

Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P ,T -odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P ,T -odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to 199Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the ^{199}Hg Atom.

PubMed

Sahoo, B K; Das, B P

2018-05-18

Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P,T-odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P,T-odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to ^{199}Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

Fragmentation of ionized doped helium nanodroplets: theoretical evidence for a dopant ejection mechanism.

PubMed

Bonhommeau, D; Lewerenz, M; Halberstadt, N

2008-02-07

We report a theoretical study of the effect induced by a helium nanodroplet environment on the fragmentation dynamics of a dopant. The dopant is an ionized neon cluster Ne(n) (+) (n=4-6) surrounded by a helium nanodroplet composed of 100 atoms. A newly designed mixed quantum/classical approach is used to take into account both the large helium cluster zero-point energy due to the light mass of the helium atoms and all the nonadiabatic couplings between the Ne(n) (+) potential-energy surfaces. The results reveal that the intermediate ionic dopant can be ejected from the droplet, possibly with some helium atoms still attached, thereby reducing the cooling power of the droplet. Energy relaxation by helium atom evaporation and dissociation, the other mechanism which has been used in most interpretations of doped helium cluster dynamics, also exhibits new features. The kinetic energy distribution of the neutral monomer fragments can be fitted to the sum of two Boltzmann distributions, one with a low kinetic energy and the other with a higher kinetic energy. This indicates that cooling by helium atom evaporation is more efficient than was believed so far, as suggested by recent experiments. The results also reveal the predominance of Ne(2) (+) and He(q)Ne(2) (+) fragments and the absence of bare Ne(+) fragments, in agreement with available experimental data (obtained for larger helium nanodroplets). Moreover, the abundance in fragments with a trimeric neon core is found to increase with the increase in dopant size. Most of the fragmentation is achieved within 10 ps and the only subsequent dynamical process is the relaxation of hot intermediate He(q)Ne(2) (+) species to Ne(2) (+) by helium atom evaporation. The dependence of the ionic fragment distribution on the parent ion electronic state reached by ionization is also investigated. It reveals that He(q)Ne(+) fragments are produced only from the highest electronic state, whereas He(q)Ne(2) (+) fragments originate from all the electronic states. Surprisingly, the highest electronic states also lead to fragments that still contain the original ionic dopant species. A mechanism is conjectured to explain this fragmentation inhibition.

1997 Technical Digest Series. Volume 7: Applications of High Field and Short Wavelength Sources VII

DTIC Science & Technology

1997-03-01

clusters irradiated with ultrashort , high intensity laser pulses can exhibit "ionization ig- nition" which leads...8, 9]. 25-atom Ne clusters and 25-atom Ar clusters are modelled as irradiated by a 800 nm, 15 fs (fwhm) laser pulse with peak intensities ranging...Measurements of the spatial and spectral properties of ultrashort , intense laser pulses propagating in underdense plasmas demonstrate

Intramolecular energy transfer and the driving mechanisms for large-amplitude collective motions of clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2009-04-01

This paper uncovers novel and specific dynamical mechanisms that initiate large-amplitude collective motions in polyatomic molecules. These mechanisms are understood in terms of intramolecular energy transfer between modes and driving forces. Structural transition dynamics of a six-atom cluster between a symmetric and an elongated isomer is highlighted as an illustrative example of what is a general message. First, we introduce a general method of hyperspherical mode analysis to analyze the energy transfer among internal modes of polyatomic molecules. In this method, the (3n-6) internal modes of an n-atom molecule are classified generally into three coarse level gyration-radius modes, three fine level twisting modes, and (3n-12) fine level shearing modes. We show that a large amount of kinetic energy flows into the gyration-radius modes when the cluster undergoes structural transitions by changing its mass distribution. Based on this fact, we construct a reactive mode as a linear combination of the three gyration-radius modes. It is shown that before the reactive mode acquires a large amount of kinetic energy, activation or inactivation of the twisting modes, depending on the geometry of the isomer, plays crucial roles for the onset of a structural transition. Specifically, in a symmetric isomer with a spherical mass distribution, activation of specific twisting modes drives the structural transition into an elongated isomer by inducing a strong internal centrifugal force, which has the effect of elongating the mass distribution of the system. On the other hand, in an elongated isomer, inactivation of specific twisting modes initiates the structural transition into a symmetric isomer with lower potential energy by suppressing the elongation effect of the internal centrifugal force and making the effects of the potential force dominant. This driving mechanism for reactions as well as the present method of hyperspherical mode analysis should be widely applicable to molecular reactions in which a system changes its overall mass distribution in a significant way.

Spectra of helium clusters with up to six atoms using soft-core potentials

NASA Astrophysics Data System (ADS)

Gattobigio, M.; Kievsky, A.; Viviani, M.

2011-11-01

In this paper, we investigate small clusters of helium atoms using the hyperspherical harmonic basis. We consider systems with A=2,3,4,5,6 atoms with an interparticle potential which does not present a strong repulsion at short distances. We use an attractive Gaussian potential that reproduces the values of the dimer binding energy, the atom-atom scattering length, and the effective range obtained with one of the widely used He-He interactions, the Aziz and Slaman potential, called LM2M2. In systems with more than two atoms, we consider a repulsive three-body force that, by construction, reproduces the trimer binding energy of the LM2M2 potential. With this model, consisting of the sum of a two- and three-body potential, we have calculated the spectrum of clusters formed by four, five, and six helium atoms. We have found that these systems present two bound states, one deep and one shallow, close to the threshold fixed by the energy of the (A-1)-atom system. Universal relations between the energies of the excited state of the A-atom system and the ground-state energy of the (A-1)-atom system are extracted, as well as the ratio between the ground state of the A-atom system and the ground-state energy of the trimer.

Perspective: Size selected clusters for catalysis and electrochemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro

We report that size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this Perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition,more » cluster-support interactions and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modelling based on density functional theory sampling of local minima and energy barriers or ab initio Molecular Dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Lastly, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.« less

Perspective: Size selected clusters for catalysis and electrochemistry

DOE PAGES

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro; ...

2018-03-15

We report that size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this Perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition,more » cluster-support interactions and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modelling based on density functional theory sampling of local minima and energy barriers or ab initio Molecular Dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Lastly, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.« less

Perspective: Size selected clusters for catalysis and electrochemistry

NASA Astrophysics Data System (ADS)

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro; Vajda, Stefan

2018-03-01

Size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization, and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition, cluster-support interactions, and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modeling based on density functional theory sampling of local minima and energy barriers or ab initio molecular dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Finally, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.

Effect of solute atom concentration on vacancy cluster formation in neutron-irradiated Ni alloys

NASA Astrophysics Data System (ADS)

Sato, Koichi; Itoh, Daiki; Yoshiie, Toshimasa; Xu, Qiu; Taniguchi, Akihiro; Toyama, Takeshi

2011-10-01

The dependence of microstructural evolution on solute atom concentration in Ni alloys was investigated by positron annihilation lifetime measurements. The positron annihilation lifetimes in pure Ni, Ni-0.05 at.%Si, Ni-0.05 at.%Sn, Ni-Cu, and Ni-Ge alloys were about 400 ps even at a low irradiation dose of 3 × 10 -4 dpa, indicating the presence of microvoids in these alloys. The size of vacancy clusters in Ni-Si and Ni-Sn alloys decreased with an increase in the solute atom concentration at irradiation doses less than 0.1 dpa; vacancy clusters started to grow at an irradiation dose of about 0.1 dpa. In Ni-2 at.%Si, irradiation-induced segregation was detected by positron annihilation coincidence Doppler broadening measurements. This segregation suppressed one-dimensional (1-D) motion of the interstitial clusters and promoted mutual annihilation of point defects. The frequency and mean free path of the 1-D motion depended on the solute atom concentration and the amount of segregation.

Molecular dynamics study of the melting of a supported 887-atom Pd decahedron.

PubMed

Schebarchov, D; Hendy, S C; Polak, W

2009-04-08

We employ classical molecular dynamics simulations to investigate the melting behaviour of a decahedral Pd(887) cluster on a single layer of graphite (graphene). The interaction between Pd atoms is modelled with an embedded-atom potential, while the adhesion of Pd atoms to the substrate is approximated with a Lennard-Jones potential. We find that the decahedral structure persists at temperatures close to the melting point, but that just below the melting transition, the cluster accommodates to the substrate by means of complete melting and then recrystallization into an fcc structure. These structural changes are in qualitative agreement with recently proposed models, and they verify the existence of an energy barrier preventing softly deposited clusters from 'wetting' the substrate at temperatures below the melting point.

Melting of isolated tin nanoparticles

PubMed

Bachels; Guntherodt; Schafer

2000-08-07

The melting of isolated neutral tin cluster distributions with mean sizes of about 500 atoms has been investigated in a molecular beam experiment by calorimetrically measuring the clusters' formation energies as a function of their internal temperature. For this purpose the possibility to adjust the temperature of the clusters' internal degrees of freedom by means of the temperature of the cluster source's nozzle was exploited. The melting point of the investigated tin clusters was found to be lowered by 125 K and the latent heat of fusion per atom is reduced by 35% compared to bulk tin. The melting behavior of the isolated tin clusters is discussed with respect to the occurrence of surface premelting.

Structural and magnetic evolution of bimetallic MnAu clusters driven by asymmetric atomic migration.

PubMed

Wei, Xiaohui; Zhou, Rulong; Lefebvre, Williams; He, Kai; Le Roy, Damien; Skomski, Ralph; Li, Xingzhong; Shield, Jeffrey E; Kramer, Matthew J; Chen, Shuang; Zeng, Xiao Cheng; Sellmyer, David J

2014-03-12

The nanoscale structural, compositional, and magnetic properties are examined for annealed MnAu nanoclusters. The MnAu clusters order into the L1(0) structure, and monotonic size-dependences develop for the composition and lattice parameters, which are well reproduced by our density functional theory calculations. Simultaneously, Mn diffusion forms 5 Å nanoshells on larger clusters inducing significant magnetization in an otherwise antiferromagnetic system. The differing atomic mobilities yield new cluster nanostructures that can be employed generally to create novel physical properties.

Ultra-small rhenium clusters supported on graphene.

PubMed

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J; Mariscal, Marcelo M; Yacaman, Miguel José

2015-03-28

The adsorption of very small rhenium clusters (2-13 atoms) supported on graphene was studied by high-angle annular dark field-scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional theory calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones.

Ultra-small rhenium clusters supported on graphene

PubMed Central

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J.; Mariscal, Marcelo M.; Yacaman, Miguel José

2015-01-01

The adsorption of very small rhenium clusters (2 – 13 atoms) supported on graphene was studied with high annular dark field - scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones. PMID:25721176

Melting of Cu nanoclusters by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Wang, Li; Zhang, Yanning; Bian, Xiufang; Chen, Ying

2003-04-01

We present a detailed molecular dynamics study of the melting of copper nanoclusters with up to 8628 atoms within the framework of the embedded-atom method. The finding indicates that there exists an intermediate nanocrystal regime above 456 atoms. The linear relation between the cluster size and its thermodynamics properties is obeyed in this regime. Melting first occurs at the surface of the clusters, leading to Tm, N= Tm,Bulk- αN-1/3, dropping from Tm,Bulk=1360 K to Tm,456=990 K. In addition, the size, surface energy as well as the root mean square displacement (RMSD) of the clusters in the intermediate regime have been investigated.

Solving the scalability issue in quantum-based refinement: Q|R#1.

PubMed

Zheng, Min; Moriarty, Nigel W; Xu, Yanting; Reimers, Jeffrey R; Afonine, Pavel V; Waller, Mark P

2017-12-01

Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately as n m , where n is the number of atoms and m (≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package called Q|R, this issue is referred to as Q|R#1. A divide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1. Firstly, the atomic model of a crystal structure is analyzed to detect noncovalent interactions between residues, and the results of the analysis are represented as an interaction graph. Secondly, a graph-clustering algorithm is used to partition the interaction graph into a set of clusters in such a way as to minimize disruption to the noncovalent interaction network. Thirdly, the environment surrounding each individual cluster is analyzed and any residue that is interacting with a particular cluster is assigned to the buffer region of that particular cluster. A fragment is defined as a cluster plus its buffer region. The gradients for all atoms from each of the fragments are computed, and only the gradients from each cluster are combined to create the total gradients. A quantum-based refinement is carried out using the total gradients as chemical restraints. In order to validate this interaction graph-based fragmentation approach in Q|R, the entire atomic model of an amyloid cross-β spine crystal structure (PDB entry 2oNA) was refined.

Self-Learning Off-Lattice Kinetic Monte Carlo method as applied to growth on metal surfaces

NASA Astrophysics Data System (ADS)

Trushin, Oleg; Kara, Abdelkader; Rahman, Talat

2007-03-01

We propose a new development in the Self-Learning Kinetic Monte Carlo (SLKMC) method with the goal of improving the accuracy with which atomic mechanisms controlling diffusive processes on metal surfaces may be identified. This is important for diffusion of small clusters (2 - 20 atoms) in which atoms may occupy Off-Lattice positions. Such a procedure is also necessary for consideration of heteroepitaxial growth. The new technique combines an earlier version of SLKMC [1] with the inclusion of off-lattice occupancy. This allows us to include arbitrary positions of adatoms in the modeling and makes the simulations more realistic and reliable. We have tested this new approach for the case of the diffusion of small 2D Cu clusters diffusion on Cu(111) and found good performance and satisfactory agreement with results obtained from previous version of SLKMC. The new method also helped reveal a novel atomic mechanism contributing to cluster migration. We have also applied this method to study the diffusion of Cu clusters on Ag(111), and find that Cu atoms generally prefer to occupy off-lattice sites. [1] O. Trushin, A. Kara, A. Karim, T.S. Rahman Phys. Rev B 2005

Atomically manufactured nickel-silicon quantum dots displaying robust resonant tunneling and negative differential resistance

NASA Astrophysics Data System (ADS)

Cheng, Jian-Yih; Fisher, Brandon L.; Guisinger, Nathan P.; Lilley, Carmen M.

2017-12-01

Providing a spin-free host material in the development of quantum information technology has made silicon a very interesting and desirable material for qubit design. Much of the work and experimental progress has focused on isolated phosphorous atoms. In this article, we report on the exploration of Ni-Si clusters that are atomically manufactured via self-assembly from the bottom-up and behave as isolated quantum dots. These small quantum dot structures are probed at the atomic-scale with scanning tunneling microscopy and spectroscopy, revealing robust resonance through discrete quantized energy levels within the Ni-Si clusters. The resonance energy is reproducible and the peak spacing of the quantum dot structures increases as the number of atoms in the cluster decrease. Probing these quantum dot structures on degenerately doped silicon results in the observation of negative differential resistance in both I-V and dI/dV spectra. At higher surface coverage of nickel, a well-known √19 surface modification is observed and is essentially a tightly packed array of the clusters. Spatial conductance maps reveal variations in the local density of states that suggest the clusters are influencing the electronic properties of their neighbors. All of these results are extremely encouraging towards the utilization of metal modified silicon surfaces to advance or complement existing quantum information technology.

Atomically manufactured nickel–silicon quantum dots displaying robust resonant tunneling and negative differential resistance

DOE PAGES

Cheng, Jian -Yih; Fisher, Brandon L.; Guisinger, Nathan P.; ...

2017-05-22

Providing a spin-free host material in the development of quantum information technology has made silicon a very interesting and desirable material for qubit design. Much of the work and experimental progress has focused on isolated phosphorous atoms. In this article, we report on the exploration of Ni–Si clusters that are atomically manufactured via self-assembly from the bottom-up and behave as isolated quantum dots. These small quantum dot structures are probed at the atomic-scale with scanning tunneling microscopy and spectroscopy, revealing robust resonance through discrete quantized energy levels within the Ni–Si clusters. The resonance energy is reproducible and the peak spacingmore » of the quantum dot structures increases as the number of atoms in the cluster decrease. Probing these quantum dot structures on degenerately doped silicon results in the observation of negative differential resistance in both I–V and dI/dV spectra. At higher surface coverage of nickel, a well-known √19 surface modification is observed and is essentially a tightly packed array of the clusters. Spatial conductance maps reveal variations in the local density of states that suggest the clusters are influencing the electronic properties of their neighbors. Furthermore, all of these results are extremely encouraging towards the utilization of metal modified silicon surfaces to advance or complement existing quantum information technology.« less

Atomically manufactured nickel–silicon quantum dots displaying robust resonant tunneling and negative differential resistance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Jian -Yih; Fisher, Brandon L.; Guisinger, Nathan P.

Providing a spin-free host material in the development of quantum information technology has made silicon a very interesting and desirable material for qubit design. Much of the work and experimental progress has focused on isolated phosphorous atoms. In this article, we report on the exploration of Ni–Si clusters that are atomically manufactured via self-assembly from the bottom-up and behave as isolated quantum dots. These small quantum dot structures are probed at the atomic-scale with scanning tunneling microscopy and spectroscopy, revealing robust resonance through discrete quantized energy levels within the Ni–Si clusters. The resonance energy is reproducible and the peak spacingmore » of the quantum dot structures increases as the number of atoms in the cluster decrease. Probing these quantum dot structures on degenerately doped silicon results in the observation of negative differential resistance in both I–V and dI/dV spectra. At higher surface coverage of nickel, a well-known √19 surface modification is observed and is essentially a tightly packed array of the clusters. Spatial conductance maps reveal variations in the local density of states that suggest the clusters are influencing the electronic properties of their neighbors. Furthermore, all of these results are extremely encouraging towards the utilization of metal modified silicon surfaces to advance or complement existing quantum information technology.« less

Synthesis, Structure and Electrochemistry of Tetranuclear Oxygen-Centered Copper(II) Clusters with Acetylacetone and Benz-pyrazole Hydrolyzed Derivatives as Ligand.

PubMed

Vafazadeh, Rasoul; Willis, Anthony C

2016-01-01

Two copper(II) clusters Cu(4)OCl(6)(pyrazole)4, 1, and Cu(4)OBr(6)(Br-pyrazole)4, 2, have been synthesized by reacting acetylacetone and benzohydrazide (1:1 ratio) with CuX(2) (X = Cl for 1 and X= Br for 2) in methanol solutions. The structures of both clusters have been established by X-ray crystallography. The clusters contain four Cu, one O, six μ(2)-X atoms, and four pyrazole ligands. The pyrazoles was prepared in situ by the reaction of acetylacetone with benzohydrazide in methanol under reflux. In 2, the methine hydrogens of the pyrazole ligands have been replaced by bromine atoms. The four copper atoms encapsulate the central O atom in a tetrahedral arrangement. All copper atoms are five-coordinate and have similar coordination environments with slightly distorted trigonal bipyramidal geometry. The cyclic voltammogram of the clusters 1 and 2 show a one-electron quasi-reversible reduction wave in the region 0.485 to 0.731 V, and a one-electron quasi-reversible oxidation wave in the region 0.767 to 0.898 V. In 1, one irreversible oxidative response is observed on the positive of side of the voltammogram at 1.512 V and this can be assigned to Cu(II) to Cu(III) oxidation.

Factors driving stable growth of He clusters in W: first-principles study

NASA Astrophysics Data System (ADS)

Feng, Y. J.; Xin, T. Y.; Xu, Q.; Wang, Y. X.

2018-07-01

The evolution of helium (He) bubbles is responsible for the surface morphology variation and subsequent degradation of the properties of plasma-facing materials (PFMs) in nuclear fusion reactors. These severe problems unquestionably trace back to the behavior of He in PFMs, which is closely associated with the interaction between He and the matrix. In this paper, we decomposed the binding energy of the He cluster into three parts, those from W–W, W–He, and He–He interactions, using density functional theory. As a result, we clearly identified the main factors that determine a steplike decrease in the binding energy with increasing number of He atoms, which explains the process of self-trapping and athermal vacancy generation during He cluster growth in the PFM tungsten. The three interactions were found to synergetically shape the features of the steplike decrease in the binding energy. Fairly strong He–He repulsive forces at a short distance, which stem from antibonding states between He atoms, need to be released when additional He atoms are continuously bonded to the He cluster. This causes the steplike feature in the binding energy. The bonding states between W and He atoms in principle facilitate the decreasing trend of the binding energy. The decrease in binding energy with increasing number of He atoms implies that He clusters can grow stably.

Lithium-air batteries, method for making lithium-air batteries

DOEpatents

Vajda, Stefan; Curtiss, Larry A.; Lu, Jun; Amine, Khalil; Tyo, Eric C.

2016-11-15

The invention provides a method for generating Li.sub.2O.sub.2 or composites of it, the method uses mixing lithium ions with oxygen ions in the presence of a catalyst. The catalyst comprises a plurality of metal clusters, their alloys and mixtures, each cluster consisting of between 3 and 18 metal atoms. The invention also describes a lithium-air battery which uses a lithium metal anode, and a cathode opposing the anode. The cathode supports metal clusters, each cluster consisting of size selected clusters, taken from a range of between approximately 3 and approximately 18 metal atoms, and an electrolyte positioned between the anode and the cathode.

Templated Atom-Precise Galvanic Synthesis and Structure Elucidation of a [Ag24Au(SR)18](-) Nanocluster.

PubMed

Bootharaju, Megalamane S; Joshi, Chakra P; Parida, Manas R; Mohammed, Omar F; Bakr, Osman M

2016-01-18

Synthesis of atom-precise alloy nanoclusters with uniform composition is challenging when the alloying atoms are similar in size (for example, Ag and Au). A galvanic exchange strategy has been devised to produce a compositionally uniform [Ag24Au(SR)18](-) cluster (SR: thiolate) using a pure [Ag25(SR)18](-) cluster as a template. Conversely, the direct synthesis of Ag24Au cluster leads to a mixture of [Ag(25-x)Au(x)(SR)18](-), x=1-8. Mass spectrometry and crystallography of [Ag24Au(SR)18](-) reveal the presence of the Au heteroatom at the Ag25 center, forming Ag24Au. The successful exchange of the central Ag of Ag25 with Au causes perturbations in the Ag25 crystal structure, which are reflected in the absorption, luminescence, and ambient stability of the particle. These properties are compared with those of Ag25 and Ag24Pd clusters with same ligand and structural framework, providing new insights into the modulation of cluster properties with dopants at the single-atom level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advanced Electrochemistry of Individual Metal Clusters Electrodeposited Atom by Atom to Nanometer by Nanometer.

PubMed

Kim, Jiyeon; Dick, Jeffrey E; Bard, Allen J

2016-11-15

Metal clusters are very important as building blocks for nanoparticles (NPs) for electrocatalysis and electroanalysis in both fundamental and applied electrochemistry. Attention has been given to understanding of traditional nucleation and growth of metal clusters and to their catalytic activities for various electrochemical applications in energy harvesting as well as analytical sensing. Importantly, understanding the properties of these clusters, primarily the relationship between catalysis and morphology, is required to optimize catalytic function. This has been difficult due to the heterogeneities in the size, shape, and surface properties. Thus, methods that address these issues are necessary to begin understanding the reactivity of individual catalytic centers as opposed to ensemble measurements, where the effect of size and morphology on the catalysis is averaged out in the measurement. This Account introduces our advanced electrochemical approaches to focus on each isolated metal cluster, where we electrochemically fabricated clusters or NPs atom by atom to nanometer by nanometer and explored their electrochemistry for their kinetic and catalytic behavior. Such approaches expand the dimensions of analysis, to include the electrochemistry of (1) a discrete atomic cluster, (2) solely a single NP, or (3) individual NPs in the ensemble sample. Specifically, we studied the electrocatalysis of atomic metal clusters as a nascent electrocatalyst via direct electrodeposition on carbon ultramicroelectrode (C UME) in a femtomolar metal ion precursor. In addition, we developed tunneling ultramicroelectrodes (TUMEs) to study electron transfer (ET) kinetics of a redox probe at a single metal NP electrodeposited on this TUME. Owing to the small dimension of a NP as an active area of a TUME, extremely high mass transfer conditions yielded a remarkably high standard ET rate constant, k 0 , of 36 cm/s for outer-sphere ET reaction. Most recently, we advanced nanoscale scanning electrochemical microscopy (SECM) imaging to resolve the electrocatalytic activity of individual electrodeposited NPs within an ensemble sample yielding consistent high k 0 values of ≥2 cm/s for the hydrogen oxidation reaction (HOR) at different NPs. We envision that our advanced electrochemical approaches will enable us to systematically address structure effects on the catalytic activity, thus providing a quantitative guideline for electrocatalysts in energy-related applications.

Estimating carbon cluster binding energies from measured Cn distributions, n <= 10

NASA Astrophysics Data System (ADS)

Pargellis, A. N.

1990-08-01

Experimental data are presented for the cluster distribution of sputtered negative carbon clusters, C-n, with n≤10. Additionally, clusters have been observed with masses indicating they are CsC-2n, with n≤4. The C-n data are compared with the data obtained by other groups, for neutral and charged clusters, using a variety of sources such as evaporation, sputtering, and laser ablation. The data are used to estimate the cluster binding energies En, using the universal relation, En=(n-1)ΔHn+RTe [ln(Jn/J1)+0.5 ln(n)-α-(ΔSn-ΔS1)/R], derived from basic kinetic and thermodynamic relations. The estimated values agree astonishingly well with values from the literature, varying from published values by at most a few percent. In this equation, Jn is the observed current of n-atom clusters, ΔHn is the heat of vaporization, ΔH1=7.41 eV, and Te ≊0.25 eV (2900 K) is the effective source temperature. The relative change in cluster entropy during sublimation from the solid to vapor phase is approximated to first order by the relation (ΔSn-ΔS1)/R =3.1+0.9(n-2), and is fit to published data for n between 2 and 5 and temperatures between 2000 and 4000 K. The parameter α is empirical, obtained by fitting the data to known binding energies for Cn≤5 clusters. For evaporation sources, α must be zero, but α˜7 when sputtering with Cs+ ions, indicating the sputtered clusters appear to be in thermodynamic equilibrium, but not the atoms. Several possible mechanisms for the formation of clusters during sputtering are examined. One plausible mechanism is that atoms diffuse on the graphite surface to form clusters which are then desorbed by energetic, recoil atoms created in subsequent sputtering events.

Interaction of intense ultrashort pulse lasers with clusters.

NASA Astrophysics Data System (ADS)

Petrov, George

2007-11-01

The last ten years have witnessed an explosion of activity involving the interaction of clusters with intense ultrashort pulse lasers. Atomic or molecular clusters are targets with unique properties, as they are halfway between solid and gases. The intense laser radiation creates hot dense plasma, which can provide a compact source of x-rays and energetic particles. The focus of this investigation is to understand the salient features of energy absorption and Coulomb explosion by clusters. The evolution of clusters is modeled with a relativistic time-dependent 3D Molecular Dynamics (MD) model [1]. The Coulomb interaction between particles is handled by a fast tree algorithm, which allows large number of particles to be used in simulations [2]. The time histories of all particles in a cluster are followed in time and space. The model accounts for ionization-ignition effects (enhancement of the laser field in the vicinity of ions) and a variety of elementary processes for free electrons and charged ions, such as optical field and collisional ionization, outer ionization and electron recapture. The MD model was applied to study small clusters (1-20 nm) irradiated by a high-intensity (10^16-10^20 W/cm^2) sub-picosecond laser pulse. We studied fundamental cluster features such as energy absorption, x-ray emission, particle distribution, average charge per atom, and cluster explosion as a function of initial cluster radius, laser peak intensity and wavelength. Simulations of novel applications, such as table-top nuclear fusion from exploding deuterium clusters [3] and high power synchrotron radiation for biological applications and imaging [4] have been performed. The application for nuclear fusion was motivated by the efficient absorption of laser energy (˜100%) and its high conversion efficiency into ion kinetic energy (˜50%), resulting in neutron yield of 10^6 neutrons/Joule laser energy. Contributors: J. Davis and A. L. Velikovich. [1] G. M. Petrov, et al Phys. Plasmas 12 063103 (2005); 13 033106 (2006) [2] G. M. Petrov, J. Davis, European Phys. J. D 41 629 (2007) [3] G. M. Petrov, J. Davis, A. L. Velikovich, Plasma Phys. Contr. Fusion 48 1721 (2006) [4] G. M. Petrov, J. Davis, A. L. Velikovich, J. Phys. B 39 4617 (2006)

Cluster generator

DOEpatents

Donchev, Todor I [Urbana, IL; Petrov, Ivan G [Champaign, IL

2011-05-31

Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

Field-Dependent Measurement of GaAs Composition by Atom Probe Tomography.

PubMed

Di Russo, Enrico; Blum, Ivan; Houard, Jonathan; Da Costa, Gérald; Blavette, Didier; Rigutti, Lorenzo

2017-12-01

The composition of GaAs measured by laser-assisted atom probe tomography may be inaccurate depending on the experimental conditions. In this work, we assess the role of the DC field and the impinging laser energy on such compositional bias. The DC field is found to have a major influence, while the laser energy has a weaker one within the range of parameters explored. The atomic fraction of Ga may vary from 0.55 at low-field conditions to 0.35 at high field. These results have been interpreted in terms of preferential evaporation of Ga at high field. The deficit of As is most likely explained by the formation of neutral As complexes either by direct ejection from the tip surface or upon the dissociation of large clusters. The study of multiple detection events supports this interpretation.

Nanoscale decomposition of Nb-Ru-O

NASA Astrophysics Data System (ADS)

Music, Denis; Geyer, Richard W.; Chen, Yen-Ting

2016-11-01

A correlative theoretical and experimental methodology has been employed to explore the decomposition of amorphous Nb-Ru-O at elevated temperatures. Density functional theory based molecular dynamics simulations reveal that amorphous Nb-Ru-O is structurally modified within 10 ps at 800 K giving rise to an increase in the planar metal - oxygen and metal - metal population and hence formation of large clusters, which signifies atomic segregation. The driving force for this atomic segregation process is 0.5 eV/atom. This is validated by diffraction experiments and transmission electron microscopy of sputter-synthesized Nb-Ru-O thin films. Room temperature samples are amorphous, while at 800 K nanoscale rutile RuO2 grains, self-organized in an amorphous Nb-O matrix, are observed, which is consistent with our theoretical predictions. This amorphous/crystalline interplay may be of importance for next generation of thermoelectric devices.

Planar CoB18- Cluster: a New Motif for - and Metallo-Borophenes

NASA Astrophysics Data System (ADS)

Chen, Teng-Teng; Jian, Tian; Lopez, Gary; Li, Wan-Lu; Chen, Xin; Li, Jun; Wang, Lai-Sheng

2016-06-01

Combined Photoelectron Spectroscopy (PES) and theoretical calculations have found that anion boron clusters (Bn-) are planar and quasi-planar up to B25-. Recent works show that anion pure boron clusters continued to be planar at B27-,B30-,B35- and B36-. B35- and B36- provide the first experimental evidence for the viability of the two-dimensional (2D) boron sheets (Borophene). The 2D to three-dimensional (3D) transitions are shown to happen at B40-,B39- and B28-, which possess cage-like structures. These fullerene-like boron cage clusters are named as Borospherene. Recently, borophenes or similar structures are claimed to be synthesized by several groups. Following an electronic design principle, a series of transition-metal-doped boron clusters (M©Bn-, n=8-10) are found to possess the monocyclic wheel structures. Meanwhile, CoB12- and RhB12- are revealed to adopt half-sandwich-type structures with the quasi-planar B12 moiety similar to the B12- cluster. Very lately, we show that the CoB16- cluster possesses a highly symmetric Cobalt-centered drum-like structure, with a new record of coordination number at 16. Here we report the CoB18- cluster to possess a unique planar structure, in which the Co atom is doped into the network of a planar boron cluster. PES reveals that the CoB18- cluster is a highly stable electronic system with the first adiabatic detachment energy (ADE) at 4.0 eV. Global minimum searches along with high-level quantum calculations show the global minimum for CoB18- is perfectly planar and closed shell (1A1) with C2v symmetry. The Co atom is bonded with 7 boron atoms in the closest coordination shell and the other 11 boron atoms in the outer coordination shell. The calculated vertical detachment energy (VDE) values match quite well with our experimental results. Chemical bonding analysis by the Adaptive Natural Density Partitioning (AdNDP) method shows the CoB18- cluster is π-aromatic with four 4-centered-2-electron (4c-2e) π bonds and one 19-centered-2-electron (19c-2e) π bond, 10 π electrons in total. This perfectly planar structure reveals the viability of creating a new class of hetero-borophenes and metallo-borophenes by doping metal atoms into the plane of monolayer boron atoms. This gives a new approach to design perspective hetero-borophenes and metallo-borophenes materials with tunable chemical, magnetic and optical properties.

Electronic structures and thermochemical properties of the small silicon-doped boron clusters B(n)Si (n=1-7) and their anions.

PubMed

Tai, Truong Ba; Kadłubański, Paweł; Roszak, Szczepan; Majumdar, Devashis; Leszczynski, Jerzy; Nguyen, Minh Tho

2011-11-18

We perform a systematic investigation on small silicon-doped boron clusters B(n)Si (n=1-7) in both neutral and anionic states using density functional (DFT) and coupled-cluster (CCSD(T)) theories. The global minima of these B(n)Si(0/-) clusters are characterized together with their growth mechanisms. The planar structures are dominant for small B(n)Si clusters with n≤5. The B(6)Si molecule represents a geometrical transition with a quasi-planar geometry, and the first 3D global minimum is found for the B(7)Si cluster. The small neutral B(n)Si clusters can be formed by substituting the single boron atom of B(n+1) by silicon. The Si atom prefers the external position of the skeleton and tends to form bonds with its two neighboring B atoms. The larger B(7)Si cluster is constructed by doping Si-atoms on the symmetry axis of the B(n) host, which leads to the bonding of the silicon to the ring boron atoms through a number of hyper-coordination. Calculations of the thermochemical properties of B(n)Si(0/-) clusters, such as binding energies (BE), heats of formation at 0 K (ΔH(f)(0)) and 298 K (ΔH(f)([298])), adiabatic (ADE) and vertical (VDE) detachment energies, and dissociation energies (D(e)), are performed using the high accuracy G4 and complete basis-set extrapolation (CCSD(T)/CBS) approaches. The differences of heats of formation (at 0 K) between the G4 and CBS approaches for the B(n)Si clusters vary in the range of 0.0-4.6 kcal mol(-1). The largest difference between two approaches for ADE values is 0.15 eV. Our theoretical predictions also indicate that the species B(2)Si, B(4)Si, B(3)Si(-) and B(7)Si(-) are systems with enhanced stability, exhibiting each a double (σ and π) aromaticity. B(5)Si(-) and B(6)Si are doubly antiaromatic (σ and π) with lower stability. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A 3D-analysis of cluster formation and dynamics of the X(-)-benzene (X = F, Cl, Br, I) ionic dimer solvated by Ar atoms.

PubMed

Albertí, Margarita; Huarte-Larrañaga, Fermín; Aguilar, Antonio; Lucas, José M; Pirani, Fernando

2011-05-14

The specific influence of X(-) ions (X = F,Cl, Br, I) in the solvation process of halide-benzene (X(-)-Bz) ionic heterodimers by Ar atoms is investigated by means of molecular dynamic (MD) simulations. The gradual evolution from cluster rearrangement to solvation dynamics is discussed by considering ensembles of n (n = 1-15 and n = 30) Ar atoms around the X(-)-Bz stable ionic dimers. The potential energy surfaces employed are based on an atom/ion-atom and atom/ion-bond decomposition, which has been developed previously by some of the authors. The outcome of the dynamics is analyzed by employing radial distribution functions (RDF) and tridimensional (3D) probability densities.

Insights into geometries, stabilities, electronic structures, reactivity descriptors, and magnetic properties of bimetallic Nim Cun-m (m = 1, 2; n = 3-13) clusters: Comparison with pure copper clusters.

PubMed

Singh, Raman K; Iwasa, Takeshi; Taketsugu, Tetsuya

2018-05-25

A long-range corrected density functional theory (LC-DFT) was applied to study the geometric structures, relative stabilities, electronic structures, reactivity descriptors and magnetic properties of the bimetallic NiCu n -1 and Ni 2 Cu n -2 (n = 3-13) clusters, obtained by doping one or two Ni atoms to the lowest energy structures of Cu n , followed by geometry optimizations. The optimized geometries revealed that the lowest energy structures of the NiCu n -1 and Ni 2 Cu n -2 clusters favor the Ni atom(s) situated at the most highly coordinated position of the host copper clusters. The averaged binding energy, the fragmentation energies and the second-order energy differences signified that the Ni doped clusters can continue to gain an energy during the growth process. The electronic structures revealed that the highest occupied molecular orbital and the lowest unoccupied molecular orbital energies of the LC-DFT are reliable and can be used to predict the vertical ionization potential and the vertical electron affinity of the systems. The reactivity descriptors such as the chemical potential, chemical hardness and electrophilic power, and the reactivity principle such as the minimum polarizability principle are operative for characterizing and rationalizing the electronic structures of these clusters. Moreover, doping of Ni atoms into the copper clusters carry most of the total spin magnetic moment. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Displacement cascades and defect annealing in tungsten, Part III: The sensitivity of cascade annealing in tungsten to the values of kinetic parameters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

2015-07-01

Object kinetic Monte Carlo (OKMC) simulations have been performed to investigate various aspects of cascade aging in bulk tungsten and to determine the sensitivity of the results to the kinetic parameters. The primary focus is on how the kinetic parameters affect the initial recombination of defects in the first few ns of a simulation. The simulations were carried out using the object kinetic Monte Carlo (OKMC) code KSOME (kinetic simulations of microstructure evolution), using a database of cascades obtained from results of molecular dynamics (MD) simulations at various primary knock-on atom (PKA) energies and directions at temperatures of 300, 1025more » and 2050 K. The OKMC model was parameterized using defect migration barriers and binding energies from ab initio calculations. Results indicate that, due to the disparate mobilities of SIA and vacancy clusters in tungsten, annealing is dominated by SIA migration even at temperatures as high as 2050 K. For 100 keV cascades initiated at 300 K recombination is dominated by annihilation of large defect clusters. But for all other PKA energies and temperatures most of the recombination is due to the migration and rotation of small SIA clusters, while all the large SIA clusters escape the cubic simulation cell. The inverse U-shape behavior exhibited by the annealing efficiency as a function of temperature curve, especially for cascades of large PKA energies, is due to asymmetry in SIA and vacancy clustering assisted by the large difference in mobilities of SIAs and vacancies. This annealing behavior is unaffected by the dimensionality of SIA migration persists over a broad range of relative mobilities of SIAs and vacancies.« less

Theoretical predictions of a bucky-diamond SiC cluster.

PubMed

Yu, Ming; Jayanthi, C S; Wu, S Y

2012-06-15

A study of structural relaxations of Si(n)C(m) clusters corresponding to different compositions, different relative arrangements of Si/C atoms, and different types of initial structure, reveals that the Si(n)C(m) bucky-diamond structure can be obtained for an initial network structure constructed from a truncated bulk 3C-SiC for a magic composition corresponding to n = 68 and m = 79. This study was performed using a semi-empirical Hamiltonian (SCED-LCAO) since it allowed an extensive search of different types of initial structures. However, the bucky-diamond structure predicted by this method was also confirmed by a more accurate density functional theory (DFT) based method. The bucky-diamond structure exhibited by a SiC-based system represents an interesting paradigm where a Si atom can form three-coordinated as well as four-coordinated networks with carbon atoms and vice versa and with both types of network co-existing in the same structure. Specifically, the bucky-diamond structure of the Si(68)C(79) cluster consists of a 35-atom diamond-like inner core (four-atom coordinations) suspended inside a 112-atom fullerene-like shell (three-atom coordinations).

Structure and properties of B20Si-/0/+ clusters

NASA Astrophysics Data System (ADS)

Lu, Qi Liang; Luo, Qi Quan; Li, Yi De; Huang, Shou Guo

2018-06-01

A global search for the lowest energy structure of B20Si-, B20Si0 and B20Si+ clusters is conducted. Structural transitions at different charge states are observed. B20Si- is a 2D planar configuration with no polygonal holes, and Si atom occupies a peripheral position. B20Si+ adopts a 3D tubular shape, and each Si is bonded with four B atoms. But for B20Si0, competition among quasi-planar, tubular and cage like structures is found. These structures differ greatly from that of pure B21 - cluster. The structural transition may result from changes in the framework of bonding, sp 2 hybridization, and structural mechanics. Some of the clusters' properties including frontier molecular orbital, on-site charge on Si atom, electron density, and magnetism are also discussed.

Study of Pair and many-body interactions in rare-gas halide atom clusters using negative ion zero electron kinetic energy (ZEKE) and threshold photodetachment spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yourshaw, Ivan

1998-07-09

The diatomic halogen atom-rare gas diatomic complexes KrBr -, XeBr -, and KrCl - are studied in this work by zero electron kinetic energy (ZEKE) spectroscopy in order to characterize the weak intermolecular diatomic potentials of these species. Also, the ZEKE and threshold photodetachment spectra of the polyatomic clusters Ar nBr - (n = 2-9) and Ar nI - (n = 2-19) are studied to obtain information about the non-additive effects on the interactions among the atoms. This work is part of an ongoing effort to characterize the pair and many-body potentials of the complete series of rare gas halidemore » clusters. In these studies we obtain information about both the anionic and neutral clusters.« less

Protein-protected luminescent noble metal quantum clusters: an emerging trend in atomic cluster nanoscience

PubMed Central

Xavier, Paulrajpillai Lourdu; Chaudhari, Kamalesh; Baksi, Ananya; Pradeep, Thalappil

2012-01-01

Noble metal quantum clusters (NMQCs) are the missing link between isolated noble metal atoms and nanoparticles. NMQCs are sub-nanometer core sized clusters composed of a group of atoms, most often luminescent in the visible region, and possess intriguing photo-physical and chemical properties. A trend is observed in the use of ligands, ranging from phosphines to functional proteins, for the synthesis of NMQCs in the liquid phase. In this review, we briefly overview recent advancements in the synthesis of protein protected NMQCs with special emphasis on their structural and photo-physical properties. In view of the protein protection, coupled with direct synthesis and easy functionalization, this hybrid QC-protein system is expected to have numerous optical and bioimaging applications in the future, pointers in this direction are visible in the literature. PMID:22312454

Study of crystallization mechanisms of Fe nanoparticle

NASA Astrophysics Data System (ADS)

Kien, P. H.; Trang, G. T. T.; Hung, P. K.

2017-06-01

In this paper, the nanoparticle (NP) Fe was investigated by means of molecular dynamics simulation. The crystallization mechanism was studied through the time evolution of crystal cluster and potential energies of different atom types. The simulation shows that the NP was crystallized into bcc crystal structure when it was annealed at 900 K for long times. At early stage of the annealing, small nuclei form in different places of NP and dissolve for short times. After long times some nuclei form and gather nearby which create the stable clusters in the core of NP. After that the crystal clusters grow in the direction to cover the core and then to spread into the surface of NP. Analyzing the energies of different type atoms, we found that the crystal growth is originated from specific atomic arrangement in the boundary region of crystal clusters.

Formation of Core-Shell Ethane-Silver Clusters in He Droplets.

PubMed

Loginov, Evgeny; Gomez, Luis F; Sartakov, Boris G; Vilesov, Andrey F

2017-08-17

Ethane core-silver shell clusters consisting of several thousand particles have been assembled in helium droplets upon capture of ethane molecules followed by Ag atoms. The composite clusters were studied via infrared laser spectroscopy in the range of the C-H stretching vibrations of ethane. The spectra reveal a splitting of the vibrational bands, which is ascribed to interaction with Ag. A rigorous analysis of band intensities for a varying number of trapped ethane molecules and Ag atoms indicates that the composite clusters consist of a core of ethane that is covered by relatively small Ag clusters. This metastable structure is stabilized due to fast dissipation in superfluid helium droplets of the cohesion energy of the clusters.

Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research.more » Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. As a result, the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.« less

Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms

DOE PAGES

Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.; ...

2016-01-07

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research.more » Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. As a result, the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.« less

First principles study of vibrational dynamics of ceria-titania hybrid clusters

NASA Astrophysics Data System (ADS)

Majid, Abdul; Bibi, Maryam

2017-04-01

Density functional theory based calculations were performed to study vibrational properties of ceria, titania, and ceria-titania hybrid clusters. The findings revealed the dominance of vibrations related to oxygen when compared to those of metallic atoms in the clusters. In case of hybrid cluster, the softening of normal modes related to exterior oxygen atoms in ceria and softening/hardening of high/low frequency modes related to titania dimmers are observed. The results calculated for monomers conform to symmetry predictions according to which three IR and three Raman active modes were detected for TiO2, whereas two IR active and one Raman active modes were observed for CeO2. The comparative analysis indicates that the hybrid cluster CeTiO4 contains simultaneous vibrational fingerprints of the component dimmers. The symmetry, nature of vibrations, IR and Raman activity, intensities, and atomic involvement in different modes of the clusters are described in detail. The study points to engineering of CeTiO4 to tailor its properties for technological visible region applications in photocatalytic and electrochemical devices.

Static force fields simulations of reduced CeO2 (110) surface: Structure and adsorption of H2O molecule

NASA Astrophysics Data System (ADS)

Vives, Serge; Meunier, Cathy

2018-02-01

The CeO2(110) surface properties are largely involved in the catalysis, energy and biological phenomenon. The Static Force Fields simulations are able to describe large atomic systems surface even if no information on the electronic structure can be obtained. We employ those simulations to study the formation of the neutral 2 CeCe‧ VO•• cluster. We focus on seven different cluster configurations and find that the defect formation energy is the lower for the 1N-2N configurations. Two geometries are possible, as it is the case for the ab initio studies, the in plane and the more stable bridging one. We evidence the modifications of the surface energy and the Potential Energy Surface due to the presence of the 2 CeCe‧ VO•• defect. The physical adsorption of a water molecule is calculated and the geometry described for all the cluster configurations. The H2O molecule physisorption stabilizes the Ce(110) surface and the presence of the 2 CeCe‧ VO•• defect increases this effect.

Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations.

PubMed

Yin, Shi; Bernstein, Elliot R

2016-10-21

A new magnetic-bottle time-of-flight photoelectron spectroscopy (PES) apparatus is constructed in our laboratory. The PES spectra of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide [FeS m (SH) n - ; m, n = 0-3, 0 < (m + n) ≤ 3] cluster anions, obtained at 2.331 eV (532 nm) and 3.492 eV (355 nm) photon energies, are reported. The electronic structure and bonding properties of these clusters are additionally investigated at different levels of density functional theory. The most probable structures and ground state spin multiplicity for these cluster anions are tentatively assigned by comparing their theoretical first vertical detachment energies (VDEs) with their respective experiment values. The behavior of S and (SH) as ligands in these iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions is investigated and compared. The experimental first VDEs for Fe(SH) 1-3 - cluster anions are lower than those found for their respective FeS 1-3 - cluster anions. The experimental first VDEs for FeS 1-3 - clusters are observed to increase for the first two S atoms bound to Fe - ; however, due to the formation of an S-S bond for the FeS 3 - cluster, its first VDE is found to be ∼0.41 eV lower than the first VDE for the FeS 2 - cluster. The first VDEs of Fe(SH) 1-3 - cluster anions are observed to increase with the increasing numbers of SH groups. The calculated partial charges of the Fe atom for ground state FeS 1-3 - and Fe(SH) 1-3 - clusters are apparently related to and correlated with their determined first VDEs. The higher first VDE is correlated with a higher, more positive partial charge for the Fe atom of these cluster anions. Iron sulfide/hydrosulfide mixed cluster anions are also explored in this work: the first VDE for FeS(SH) - is lower than that for FeS 2 - , but higher than that for Fe(SH) 2 - ; the first VDEs for FeS 2 (SH) - and FeS(SH) 2 - are close to that for FeS 3 - , but higher than that for Fe(SH) 3 - . The first VDEs of general iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide clusters [FeS m (SH) n - ; m, n = 0-3, 0 < (m + n) ≤ 3] are dependent on three properties of these anions: 1. the partial charge on the Fe atom, 2. disulfide bond formation (S-S) in the cluster, and 3. the number of hydrosulfide ligands in the cluster. The higher the partial charge on the Fe atom of these clusters, the larger the first VDE; however, cluster S-S bonding and more (SH) ligands in the cluster lower the cluster anion first VDE.

Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations

NASA Astrophysics Data System (ADS)

Yin, Shi; Bernstein, Elliot R.

2016-10-01

A new magnetic-bottle time-of-flight photoelectron spectroscopy (PES) apparatus is constructed in our laboratory. The PES spectra of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide [FeSm(SH)n-; m, n = 0-3, 0 < (m + n) ≤ 3] cluster anions, obtained at 2.331 eV (532 nm) and 3.492 eV (355 nm) photon energies, are reported. The electronic structure and bonding properties of these clusters are additionally investigated at different levels of density functional theory. The most probable structures and ground state spin multiplicity for these cluster anions are tentatively assigned by comparing their theoretical first vertical detachment energies (VDEs) with their respective experiment values. The behavior of S and (SH) as ligands in these iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions is investigated and compared. The experimental first VDEs for Fe(SH)1-3- cluster anions are lower than those found for their respective FeS1-3- cluster anions. The experimental first VDEs for FeS1-3- clusters are observed to increase for the first two S atoms bound to Fe-; however, due to the formation of an S-S bond for the FeS3- cluster, its first VDE is found to be ˜0.41 eV lower than the first VDE for the FeS2- cluster. The first VDEs of Fe(SH)1-3- cluster anions are observed to increase with the increasing numbers of SH groups. The calculated partial charges of the Fe atom for ground state FeS1-3- and Fe(SH)1-3- clusters are apparently related to and correlated with their determined first VDEs. The higher first VDE is correlated with a higher, more positive partial charge for the Fe atom of these cluster anions. Iron sulfide/hydrosulfide mixed cluster anions are also explored in this work: the first VDE for FeS(SH)- is lower than that for FeS2-, but higher than that for Fe(SH)2-; the first VDEs for FeS2(SH)- and FeS(SH)2- are close to that for FeS3-, but higher than that for Fe(SH)3-. The first VDEs of general iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide clusters [FeSm(SH)n-; m, n = 0-3, 0 < (m + n) ≤ 3] are dependent on three properties of these anions: 1. the partial charge on the Fe atom, 2. disulfide bond formation (S-S) in the cluster, and 3. the number of hydrosulfide ligands in the cluster. The higher the partial charge on the Fe atom of these clusters, the larger the first VDE; however, cluster S-S bonding and more (SH) ligands in the cluster lower the cluster anion first VDE.

Observation of correlated electronic decay in expanding clusters triggered by near-infrared fields

PubMed Central

Schütte, B.; Arbeiter, M.; Fennel, T.; Jabbari, G.; Kuleff, A.I.; Vrakking, M.J.J.; Rouzée, A.

2015-01-01

When an excited atom is embedded into an environment, novel relaxation pathways can emerge that are absent for isolated atoms. A well-known example is interatomic Coulombic decay, where an excited atom relaxes by transferring its excess energy to another atom in the environment, leading to its ionization. Such processes have been observed in clusters ionized by extreme-ultraviolet and X-ray lasers. Here, we report on a correlated electronic decay process that occurs following nanoplasma formation and Rydberg atom generation in the ionization of clusters by intense, non-resonant infrared laser fields. Relaxation of the Rydberg states and transfer of the available electronic energy to adjacent electrons in Rydberg states or quasifree electrons in the expanding nanoplasma leaves a distinct signature in the electron kinetic energy spectrum. These so far unobserved electron-correlation-driven energy transfer processes may play a significant role in the response of any nano-scale system to intense laser light. PMID:26469997

Mobility of large clusters on a semiconductor surface: Kinetic Monte Carlo simulation results

NASA Astrophysics Data System (ADS)

M, Esen; A, T. Tüzemen; M, Ozdemir

2016-01-01

The mobility of clusters on a semiconductor surface for various values of cluster size is studied as a function of temperature by kinetic Monte Carlo method. The cluster resides on the surface of a square grid. Kinetic processes such as the diffusion of single particles on the surface, their attachment and detachment to/from clusters, diffusion of particles along cluster edges are considered. The clusters considered in this study consist of 150-6000 atoms per cluster on average. A statistical probability of motion to each direction is assigned to each particle where a particle with four nearest neighbors is assumed to be immobile. The mobility of a cluster is found from the root mean square displacement of the center of mass of the cluster as a function of time. It is found that the diffusion coefficient of clusters goes as D = A(T)Nα where N is the average number of particles in the cluster, A(T) is a temperature-dependent constant and α is a parameter with a value of about -0.64 < α < -0.75. The value of α is found to be independent of cluster sizes and temperature values (170-220 K) considered in this study. As the diffusion along the perimeter of the cluster becomes prohibitive, the exponent approaches a value of -0.5. The diffusion coefficient is found to change by one order of magnitude as a function of cluster size.

Control of Wannier orbitals for generating tunable Ising interactions of ultracold atoms in an optical lattice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Inaba, Kensuke; Tamaki, Kiyoshi; Igeta, Kazuhiro

2014-12-04

In this study, we propose a method for generating cluster states of atoms in an optical lattice. By utilizing the quantum properties of Wannier orbitals, we create an tunable Ising interaction between atoms without inducing the spin-exchange interactions. We investigate the cause of errors that occur during entanglement generations, and then we propose an error-management scheme, which allows us to create high-fidelity cluster states in a short time.

A combined photoelectron spectroscopy and ab initio study of the quasi-planar B24(-) cluster.

PubMed

Popov, Ivan A; Piazza, Zachary A; Li, Wei-Li; Wang, Lai-Sheng; Boldyrev, Alexander I

2013-10-14

The structure and chemical bonding of the 24-atom boron cluster are investigated using photoelectron spectroscopy and ab initio calculations. The joint experimental and theoretical investigation shows that B24(-) possesses a quasi-planar structure containing fifteen outer and nine inner atoms with six of the inner atoms forming a filled pentagonal moiety. The central atom of the pentagonal moiety is puckered out of plane by 0.9 Å, reminiscent of the six-atom pentagonal caps of the well-known B12 icosahedral unit. The next closest isomer at the ROCCSD(T) level of theory has a tubular double-ring structure. Comparison of the simulated spectra with the experimental data shows that the global minimum quasi-planar B24(-) isomer is the major contributor to the observed photoelectron spectrum, while the tubular isomer has no contribution to the experiment. Chemical bonding analyses reveal that the periphery of the quasi-planar B24 constitutes 15 classical 2c-2e B-B σ-bonds, whereas delocalized σ- and π-bonds are found in the interior of the cluster with one unique 6c-2e π-bond responsible for bonding in the B-centered pentagon. The current work suggests that the 24-atom boron cluster continues to be quasi-2D, albeit the tendency to form filled pentagonal units, characteristic of 3D cage-like structures of bulk boron, is observed.

Detection and quantification of solute clusters in a nanostructured ferritic alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Michael K.; Larson, David J.; Reinhard, D. A.

2014-12-26

A series of simulated atom probe datasets were examined with a friends-of-friends method to establish the detection efficiency required to resolve solute clusters in the ferrite phase of a 14YWT nanostructured ferritic alloy. The size and number densities of solute clusters in the ferrite of the as-milled mechanically-alloyed condition and the stir zone of a friction stir weld were estimated with a prototype high-detection-efficiency (~80%) local electrode atom probe. High number densities, 1.8 × 10 24 m –3 and 1.2 × 10 24 m –3, respectively of solute clusters containing between 2 and 9 solute atoms of Ti, Y andmore » O and were detected for these two conditions. Furthermore, these results support first principle calculations that predicted that vacancies stabilize these Ti–Y–O– clusters, which retard diffusion and contribute to the excellent high temperature stability of the microstructure and radiation tolerance of nanostructured ferritic alloys.« less

Stable and solubilized active Au atom clusters for selective epoxidation of cis-cyclooctene with molecular oxygen

DOE PAGES

Qian, Linping; Wang, Zhen; Beletskiy, Evgeny V.; ...

2017-03-28

Here, the ability of Au catalysts to effect the challenging task of utilizing molecular oxygen for the selective epoxidation of cyclooctene is fascinating. Although supported nanometre-size Au particles are poorly active, here we show that solubilized atomic Au clusters, present in ng ml –1 concentrations and stabilized by ligands derived from the oxidized hydrocarbon products, are active. They can be formed from various Au sources. They generate initiators and propagators to trigger the onset of the auto-oxidation reaction with an apparent turnover frequency of 440 s –1, and continue to generate additional initiators throughout the auto-oxidation cycle without direct participationmore » in the cycle. Spectroscopic characterization suggests that 7–8 atom clusters are effective catalytically. Extension of work based on these understandings leads to the demonstration that these Au clusters are also effective in selective oxidation of cyclohexene, and that solubilized Pt clusters are also capable of generating initiators for cyclooctene epoxidation.« less

Stable and solubilized active Au atom clusters for selective epoxidation of cis-cyclooctene with molecular oxygen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qian, Linping; Wang, Zhen; Beletskiy, Evgeny V.

Here, the ability of Au catalysts to effect the challenging task of utilizing molecular oxygen for the selective epoxidation of cyclooctene is fascinating. Although supported nanometre-size Au particles are poorly active, here we show that solubilized atomic Au clusters, present in ng ml –1 concentrations and stabilized by ligands derived from the oxidized hydrocarbon products, are active. They can be formed from various Au sources. They generate initiators and propagators to trigger the onset of the auto-oxidation reaction with an apparent turnover frequency of 440 s –1, and continue to generate additional initiators throughout the auto-oxidation cycle without direct participationmore » in the cycle. Spectroscopic characterization suggests that 7–8 atom clusters are effective catalytically. Extension of work based on these understandings leads to the demonstration that these Au clusters are also effective in selective oxidation of cyclohexene, and that solubilized Pt clusters are also capable of generating initiators for cyclooctene epoxidation.« less

Potential of transition metal atoms embedded in buckled monolayer g-C3N4 as single-atom catalysts.

PubMed

Li, Shu-Long; Yin, Hui; Kan, Xiang; Gan, Li-Yong; Schwingenschlögl, Udo; Zhao, Yong

2017-11-15

We use first-principles calculations to systematically explore the potential of transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au) embedded in buckled monolayer g-C 3 N 4 as single-atom catalysts. We show that clustering of Sc and Ti on g-C 3 N 4 is thermodynamically impeded and that V, Cr, Mn, and Cu are much less susceptible to clustering than the other TM atoms under investigation. Strong bonding of the transition metal atoms in the cavities of g-C 3 N 4 and high diffusion barriers together are responsible for single-atom fixation. Analysis of the CO oxidation process indicates that embedding of Cr and Mn in g-C 3 N 4 gives rise to promising single-atom catalysts at low temperature.

Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

PubMed

Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

2016-10-15

Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Adhesion strength and spreading characteristics of EPS on membrane surfaces during lateral and central growth.

PubMed

Tansel, Berrin; Tansel, Derya Z

2013-11-01

Deposition of extracellular polymeric substances (EPS) on membrane surfaces is a precursor step for bacterial attachment. The purpose of this study was to analyze the morphological changes on a clean polysulfone ultrafilration membrane after exposure to effluent from a membrane bioreactor. The effluent was filtered to remove bacteria before exposing the membrane. The morphological characterization was performed by atomic force microscopy (AFM). The lateral (2D) and central growth characteristics (3D) of the EPS deposits were evaluated by section and topographical analyses of the height images. The contact angle of single EPS units was 9.07 ± 0.50° which increased to 24.41 ± 1.00° for large clusters (over 10 units) and decreased to 18.68 ± 1.00° for the multilayered clusters. The surface tension of the single EPS units was 49.34 ± 1.70 mNm(-1). The surface tension of single layered small and large EPS clusters were 51.26 ± 2.05 and 53.48 ± 2.01 mNm(-1), respectively. For the multilayered clusters, the surface tension was 51.43 ± 2.05 mNm(-1). The spreading values were negative for all deposits on the polysulfone membrane indicating that the EPS clusters did not have tendency to spread but preferred to retain their shapes. Copyright © 2013 Elsevier B.V. All rights reserved.

Fast divide-and-conquer algorithm for evaluating polarization in classical force fields

NASA Astrophysics Data System (ADS)

Nocito, Dominique; Beran, Gregory J. O.

2017-03-01

Evaluation of the self-consistent polarization energy forms a major computational bottleneck in polarizable force fields. In large systems, the linear polarization equations are typically solved iteratively with techniques based on Jacobi iterations (JI) or preconditioned conjugate gradients (PCG). Two new variants of JI are proposed here that exploit domain decomposition to accelerate the convergence of the induced dipoles. The first, divide-and-conquer JI (DC-JI), is a block Jacobi algorithm which solves the polarization equations within non-overlapping sub-clusters of atoms directly via Cholesky decomposition, and iterates to capture interactions between sub-clusters. The second, fuzzy DC-JI, achieves further acceleration by employing overlapping blocks. Fuzzy DC-JI is analogous to an additive Schwarz method, but with distance-based weighting when averaging the fuzzy dipoles from different blocks. Key to the success of these algorithms is the use of K-means clustering to identify natural atomic sub-clusters automatically for both algorithms and to determine the appropriate weights in fuzzy DC-JI. The algorithm employs knowledge of the 3-D spatial interactions to group important elements in the 2-D polarization matrix. When coupled with direct inversion in the iterative subspace (DIIS) extrapolation, fuzzy DC-JI/DIIS in particular converges in a comparable number of iterations as PCG, but with lower computational cost per iteration. In the end, the new algorithms demonstrated here accelerate the evaluation of the polarization energy by 2-3 fold compared to existing implementations of PCG or JI/DIIS.

Al6H18: A baby crystal of γ-AlH3

NASA Astrophysics Data System (ADS)

Kiran, B.; Kandalam, Anil K.; Xu, Jing; Ding, Y. H.; Sierka, M.; Bowen, K. H.; Schnöckel, H.

2012-10-01

Using global-minima search methods based on the density functional theory calculations of (AlH3)n (n = 1-8) clusters, we show that the growth pattern of alanes for n ≥ 4 is dominated by structures containing hexa-coordinated Al atoms. This is in contrast to the earlier studies where either linear or ring structures of AlH3 were predicted to be the preferred structures in which the Al atoms can have a maximum of five-fold coordination. Our calculations also reveal that the Al6H18 cluster, with its hexa-coordination of the Al atoms, resembles the unit-cell of γ-AlH3, thus Al6H18 is designated as the "baby crystal." The fragmentation energies of the (AlH3)n (n = 2-8) along with the dimerization energies for even n clusters indicate an enhanced stability of the Al6H18 cluster. Both covalent (hybridization) and ionic (charge) contribution to the bonding are the driving factors in stabilizing the isomers containing hexa-coordinated Al atoms.

Recent development in deciphering the structure of luminescent silver nanodots

NASA Astrophysics Data System (ADS)

Choi, Sungmoon; Yu, Junhua

2017-05-01

Matrix-stabilized silver clusters and stable luminescent few-atom silver clusters, referred to as silver nanodots, show notable difference in their photophysical properties. We present recent research on deciphering the nature of silver clusters and nanodots and understanding the factors that lead to variations in luminescent mechanisms. Due to their relatively simple structure, the matrix-stabilized clusters have been well studied. However, the single-stranded DNA (ssDNA)-stabilized silver nanodots that show the most diverse emission wavelengths and the best photophysical properties remain mysterious species. It is clear that their photophysical properties highly depend on their protection scaffolds. Analyses from combinations of high-performance liquid chromatography, inductively coupled plasma-atomic emission spectroscopy, electrophoresis, and mass spectrometry indicate that about 10 to 20 silver atoms form emissive complexes with ssDNA. However, it is possible that not all of the silver atoms in the complex form effective emission centers. Investigation of the nanodot structure will help us understand why luminescent silver nanodots are stable in aqueous solution and how to further improve their chemical and photophysical properties.

Do Ag{sub n} (up to n = 8) clusters retain their identity on graphite? Insights from first-principles calculations including dispersion interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Akansha; Sen, Prasenjit, E-mail: prasen@hri.res.in; Majumder, Chiranjib

Adsorption of pre-formed Ag{sub n} clusters for n = 1 − 8 on a graphite substrate is studied within the density functional theory employing the vdW-DF2 functional to treat dispersion interactions. Top sites above surface layer carbon atoms turn out to be most favorable for a Ag adatom, in agreement with experimental observations. The same feature is observed for clusters of almost all sizes which have the lowest energies when the Ag atoms are positioned over top sites. Most gas phase isomers retain their structures over the substrate, though a couple of them undergo significant distortions. Energetics of the adsorptionmore » can be understood in terms of a competition between energy cost of disturbing Ag–Ag bonds in the cluster and energy gain from Ag–C interactions at the surface. Ag{sub 3} turns out to be an exceptional candidate in this regard that undergoes significant structural distortion and has only two of the Ag atoms close to surface C atoms in its lowest energy structure.« less

Sixteenth International Conference on the physics of electronic and atomic collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalgarno, A.; Freund, R.S.; Lubell, M.S.

1989-01-01

This report contains abstracts of papers on the following topics: photons, electron-atom collisions; electron-molecule collisions; electron-ion collisions; collisions involving exotic species; ion- atom collisions, ion-molecule or atom-molecule collisions; atom-atom collisions; ion-ion collisions; collisions involving rydberg atoms; field assisted collisions; collisions involving clusters and collisions involving condensed matter.

Electronic structures of Al-Si clusters and the magic number structure Al8Si4

NASA Astrophysics Data System (ADS)

Du, Ning; Su, Mingzhi; Chen, Hongshan

2018-02-01

The low-energy structures of Al8Sim (m = 1-6) have been determined by using the genetic algorithm combined with density functional theory and the Second-order Moller-Plesset perturbation theory (MP2) models. The results show that the close-packed structures are preferable in energy for Al-Si clusters and in most cases there exist a few isomers with close energies. The valence molecular orbitals, the orbital level structures and the electron localisation function (ELF) consistently demonstrate that the electronic structures of Al-Si clusters can be described by the jellium model. Al8Si4 corresponds to a magic number structure with pronounced stability and large energy gap; the 40 valence electrons form closed 1S21P61D102S21F142P6 shells. The ELF attractors also suggest weak covalent Si-Si, Si-Al and Al-Al bonding, and doping Si in aluminium clusters promotes the covalent interaction between Al atoms.

Spatiotemporal multistage consensus clustering in molecular dynamics studies of large proteins.

PubMed

Kenn, Michael; Ribarics, Reiner; Ilieva, Nevena; Cibena, Michael; Karch, Rudolf; Schreiner, Wolfgang

2016-04-26

The aim of this work is to find semi-rigid domains within large proteins as reference structures for fitting molecular dynamics trajectories. We propose an algorithm, multistage consensus clustering, MCC, based on minimum variation of distances between pairs of Cα-atoms as target function. The whole dataset (trajectory) is split into sub-segments. For a given sub-segment, spatial clustering is repeatedly started from different random seeds, and we adopt the specific spatial clustering with minimum target function: the process described so far is stage 1 of MCC. Then, in stage 2, the results of spatial clustering are consolidated, to arrive at domains stable over the whole dataset. We found that MCC is robust regarding the choice of parameters and yields relevant information on functional domains of the major histocompatibility complex (MHC) studied in this paper: the α-helices and β-floor of the protein (MHC) proved to be most flexible and did not contribute to clusters of significant size. Three alleles of the MHC, each in complex with ABCD3 peptide and LC13 T-cell receptor (TCR), yielded different patterns of motion. Those alleles causing immunological allo-reactions showed distinct correlations of motion between parts of the peptide, the binding cleft and the complementary determining regions (CDR)-loops of the TCR. Multistage consensus clustering reflected functional differences between MHC alleles and yields a methodological basis to increase sensitivity of functional analyses of bio-molecules. Due to the generality of approach, MCC is prone to lend itself as a potent tool also for the analysis of other kinds of big data.

Density functional study of the structural, electronic, and magnetic properties of Mo n and Mo n S ( n = 1 - 10) clusters

NASA Astrophysics Data System (ADS)

Ziane, M.; Amitouche, F.; Bouarab, S.; Vega, A.

2017-12-01

Structural and electronic properties of pure molybdenum Mo n and molybdenum-sulfide Mo n S ( n = 1 - 10) clusters were investigated in the framework of the density functional theory within the generalized gradient approximation to exchange and correlation with the aim of addressing how doping with a single S atom affects the geometries, magnetic properties, and reactivity of pure molybdenum clusters. These clusters exhibit a less marked tendency to dimerization than their isoelectronic Cr counterparts despite sharing their half-filled valence shell configuration. Doping with a single S impurity is enough to change the structure of the host molybdenum cluster to a large extent, as well as to modify the bonding pattern, the magnetic state and the magnetic moment distribution in the Mo host. Vertical ionization potentials and electron affinities are calculated to determine global reactivity indicators like the electronegativity and the chemical hardness. The results are discussed in terms of the thermodynamical and relative stabilities, charge transfer effects, and spin-polarized densities of electronic states.

How localized is ``local?'' Efficiency vs. accuracy of O(N) domain decomposition in local orbital based all-electron electronic structure theory

NASA Astrophysics Data System (ADS)

Havu, Vile; Blum, Volker; Scheffler, Matthias

2007-03-01

Numeric atom-centered local orbitals (NAO) are efficient basis sets for all-electron electronic structure theory. The locality of NAO's can be exploited to render (in principle) all operations of the self-consistency cycle O(N). This is straightforward for 3D integrals using domain decomposition into spatially close subsets of integration points, enabling critical computational savings that are effective from ˜tens of atoms (no significant overhead for smaller systems) and make large systems (100s of atoms) computationally feasible. Using a new all-electron NAO-based code,^1 we investigate the quantitative impact of exploiting this locality on two distinct classes of systems: Large light-element molecules [Alanine-based polypeptide chains (Ala)n], and compact transition metal clusters. Strict NAO locality is achieved by imposing a cutoff potential with an onset radius rc, and exploited by appropriately shaped integration domains (subsets of integration points). Conventional tight rc<= 3å have no measurable accuracy impact in (Ala)n, but introduce inaccuracies of 20-30 meV/atom in Cun. The domain shape impacts the computational effort by only 10-20 % for reasonable rc. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

Plasmon excitations in doped square-lattice atomic clusters

NASA Astrophysics Data System (ADS)

Wang, Yaxin; Yu, Ya-Bin

2017-12-01

Employing the tight-binding model, we theoretically study the properties of the plasmon excitations in doped square-lattice atomic clusters. The results show that the dopant atoms would blur the absorption spectra, and give rise to extra plasmon resonant peaks as reported in the literature; however, our calculated external-field induced oscillating charge density shows that no obvious evidences indicate the so-called local mode of plasmon appearing in two-dimensional-doped atomic clusters, but the dopants may change the symmetry of the charge distribution. Furthermore, we show that the disorder of the energy level due to dopant makes the absorption spectrum has a red- or blue-shift, which depends on the position of impurities; disorder of hopping due to dopant makes a blue- or red-shift, a larger (smaller) hopping gives a blue-shift (red-shift); and a larger (smaller) host-dopant and dopant-dopant intersite coulomb repulsion induces a blue-shift (red-shift).

Atomically precise organomimetic cluster nanomolecules assembled via perfluoroaryl-thiol SNAr chemistry

NASA Astrophysics Data System (ADS)

Qian, Elaine A.; Wixtrom, Alex I.; Axtell, Jonathan C.; Saebi, Azin; Jung, Dahee; Rehak, Pavel; Han, Yanxiao; Moully, Elamar Hakim; Mosallaei, Daniel; Chow, Sylvia; Messina, Marco S.; Wang, Jing Yang; Royappa, A. Timothy; Rheingold, Arnold L.; Maynard, Heather D.; Král, Petr; Spokoyny, Alexander M.

2017-04-01

The majority of biomolecules are intrinsically atomically precise, an important characteristic that enables rational engineering of their recognition and binding properties. However, imparting a similar precision to hybrid nanoparticles has been challenging because of the inherent limitations of existing chemical methods and building blocks. Here we report a new approach to form atomically precise and highly tunable hybrid nanomolecules with well-defined three-dimensionality. Perfunctionalization of atomically precise clusters with pentafluoroaryl-terminated linkers produces size-tunable rigid cluster nanomolecules. These species are amenable to facile modification with a variety of thiol-containing molecules and macromolecules. Assembly proceeds at room temperature within hours under mild conditions, and the resulting nanomolecules exhibit high stabilities because of their full covalency. We further demonstrate how these nanomolecules grafted with saccharides can exhibit dramatically improved binding affinity towards a protein. Ultimately, the developed strategy allows the rapid generation of precise molecular assemblies to investigate multivalent interactions.

Surface structure. Subatomic resolution force microscopy reveals internal structure and adsorption sites of small iron clusters.

PubMed

Emmrich, Matthias; Huber, Ferdinand; Pielmeier, Florian; Welker, Joachim; Hofmann, Thomas; Schneiderbauer, Maximilian; Meuer, Daniel; Polesya, Svitlana; Mankovsky, Sergiy; Ködderitzsch, Diemo; Ebert, Hubert; Giessibl, Franz J

2015-04-17

Clusters built from individual iron atoms adsorbed on surfaces (adatoms) were investigated by atomic force microscopy (AFM) with subatomic resolution. Single copper and iron adatoms appeared as toroidal structures and multiatom clusters as connected structures, showing each individual atom as a torus. For single adatoms, the toroidal shape of the AFM image depends on the bonding symmetry of the adatom to the underlying structure [twofold for copper on copper(110) and threefold for iron on copper(111)]. Density functional theory calculations support the experimental data. The findings correct our previous work, in which multiple minima in the AFM signal were interpreted as a reflection of the orientation of a single front atom, and suggest that dual and triple minima in the force signal are caused by dimer and trimer tips, respectively. Copyright © 2015, American Association for the Advancement of Science.

Gold atoms and dimers on amorphous SiO(2): calculation of optical properties and cavity ringdown spectroscopy measurements.

PubMed

Del Vitto, Annalisa; Pacchioni, Gianfranco; Lim, Kok Hwa; Rösch, Notker; Antonietti, Jean-Marie; Michalski, Marcin; Heiz, Ulrich; Jones, Harold

2005-10-27

We report on the optical absorption spectra of gold atoms and dimers deposited on amorphous silica in size-selected fashion. Experimental spectra were obtained by cavity ringdown spectroscopy. Issues on soft-landing, fragmentation, and thermal diffusion are discussed on the basis of the experimental results. In parallel, cluster and periodic supercell density functional theory (DFT) calculations were performed to model atoms and dimers trapped on various defect sites of amorphous silica. Optically allowed electronic transitions were calculated, and comparisons with the experimental spectra show that silicon dangling bonds [[triple bond]Si(.-)], nonbridging oxygen [[triple bond]Si-O(.-)], and the silanolate group [[triple bond]Si-O(-)] act as trapping centers for the gold particles. The results are not only important for understanding the chemical bonding of atoms and clusters on oxide surfaces, but they will also be of fundamental interest for photochemical studies of size-selected clusters on surfaces.

Negative ion productions in high velocity collision between small carbon clusters and Helium atom target

NASA Astrophysics Data System (ADS)

M, Chabot; K, Béroff; T, Pino; G, Féraud; N, Dothi; Padellec A, Le; G, Martinet; S, Bouneau; Y, Carpentier

2012-11-01

We measured absolute double capture cross section of Cn+ ions (n=1,5) colliding, at 2.3 and 2.6 a.u velocities, with an Helium target atom and the branching ratios of fragmentation of the so formed electronically excited anions Cn-*. We also measured absolute cross section for the electronic attachment on neutral Cn clusters colliding at same velocities with He atom. This is to our knowledge the first measurement of neutral-neutral charge exchange in high velocity collision.

Study on the coloration response of a radiochromic film to MeV cluster ion beams

NASA Astrophysics Data System (ADS)

Yuri, Yosuke; Narumi, Kazumasa; Chiba, Atsuya; Hirano, Yoshimi; Saitoh, Yuichi

2017-11-01

A radiochromic film, Gafchromic HD-V2, is applied to a possible method of measuring a two-dimensional (2D) spatial profile of MeV cluster ion beams. The coloration responses of the HD-V2 film to MeV carbon and gold cluster ion beams are experimentally investigated since some cluster effect may appear. The degree of the film coloration is quantified as a change in optical density (OD) by reading the films with an image scanner for high-resolution measurement of the 2D beam profile. The OD response of HD-V2 is characterized as a function of the ion and atom fluence for comparison. The dependences of the OD response on the cluster size, kinetic energy, and ion species are discussed. It is found that the sensitivity of the OD change is reduced when the cluster size is large. The beam profile of MeV cluster ion beams delivered from the tandem accelerator in TIARA is characterized from the measurement result using HD-V2 films. The present results show that the use of the Gafchromic HD-V2 film is suitable for the detail beam profile measurement of MeV cluster ions, especially C60 ions, whose available intensity is rather low in comparison with that of monatomic ion beams.

Tight-binding study of Si2Cn (n = 3 to 42) fullerene-like or nanodiamonds microclusters: are Si atoms isolated or adjacent?

NASA Astrophysics Data System (ADS)

Leleyter, M.; Olivi-Tran, N.

2008-12-01

We studied in tight-binding approximation involving spν hybridization (ν=2,3), some Si2Cn (n=3 to 42) microclusters. We then investigated, on one hand, fragments of fullerene-like structures (sp2), and on the other hand, nanodiamonds (sp3) of adamantane-type or a 44-atom nanodiamond (with 2 inner atoms which are assumed to play the role of bulk atoms). We compared the stabilities, i.e. the electronic energies of these clusters, according to the various positions of the 2 Si atoms. Results are very different in the two kinds of hybridization. Besides, they can be analysed according to two different points of view: either the clusters are considered as small particles with limited sizes, or they are assumed to be used as models in order to simulate the Si-atom behaviour in very larger systems. In sp2 hybridization (fullerene-like geometries), the most stable isomer is always encountered when the 2 Si atoms build a Si2 group, and this result holds for both viewpoints quoted above. Conversely, in sp3 hybridization (nanodiamonds), since Si atoms “prefer” sites having the minimum connectivity, they are never found in adjacent sites. We see that with a simple and fast computational method we can explain an experimental fact which is very interesting such as the relative position of two heteroatoms in the cluster. This enhances the generality and the fecondity in the tight binding approximation due essentially to the link between this model and the graph theory, link based on the topology of the clusters.

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, In Soo; Li, Zhanyong; Zheng, Jian

Installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 degrees C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and Xray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novelmore » catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support.« less

Metallothionein-like multinuclear clusters of mercury(II) and sulfur in peat

USGS Publications Warehouse

Nagy, K.L.; Manceau, A.; Gasper, J.D.; Ryan, J.N.; Aiken, G.R.

2011-01-01

Strong mercury(II)-sulfur (Hg-SR) bonds in natural organic matter, which influence mercury bioavailability, are difficult to characterize. We report evidence for two new Hg-SR structures using X-ray absorption spectroscopy in peats from the Florida Everglades with added Hg. The first, observed at a mole ratio of organic reduced S to Hg (Sred/Hg) between 220 and 1140, is a Hg4Sx type of cluster with each Hg atom bonded to two S atoms at 2.34 ?? and one S at 2.53 ??, and all Hg atoms 4.12 ?? apart. This model structure matches those of metal-thiolate clusters in metallothioneins, but not those of HgS minerals. The second, with one S atom at 2.34 ?? and about six C atoms at 2.97 to 3.28 ??, occurred at S red/Hg between 0.80 and 4.3 and suggests Hg binding to a thiolated aromatic unit. The multinuclear Hg cluster indicates a strong binding environment to cysteinyl sulfur that might impede methylation. Along with a linear Hg(SR)2 unit with Hg - S bond lengths of 2.34 ?? at Sred/Hg of about 10 to 20, the new structures support a continuum in Hg-SR binding strength in natural organic matter. ?? 2011 American Chemical Society.

Interatomic scattering in energy dependent photoelectron spectra of Ar clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patanen, M.; Benkoula, S.; Nicolas, C.

2015-09-28

Soft X-ray photoelectron spectra of Ar 2p levels of atomic argon and argon clusters are recorded over an extended range of photon energies. The Ar 2p intensity ratios between atomic argon and clusters’ surface and bulk components reveal oscillations similar to photoelectron extended X-ray absorption fine structure signal (PEXAFS). We demonstrate here that this technique allows us to analyze separately the PEXAFS signals from surface and bulk sites of free-standing, neutral clusters, revealing a bond contraction at the surface.

Comparative study of local atomic structures in Zr2CuxNi1-x (x = 0, 0.5, 1) metallic glasses

NASA Astrophysics Data System (ADS)

Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

2015-11-01

Extensive analysis has been performed to understand the key structural motifs accounting for the difference in glass forming ability in the Zr-Cu and Zr-Ni binary alloy systems. Here, the reliable atomic structure models of Zr2CuxNi1-x (x = 0, 0.5, 1) are constructed using the combination of X-ray diffraction experiments, ab initio molecular dynamics simulations and a constrained reverse Monte Carlo method. We observe a systematic variation of the interatomic distance of different atomic pairs with respect to the alloy composition. The ideal icosahedral content in all samples is limited, despite the high content of five-fold symmetry motifs. We also demonstrate that the population of Z-clusters in Zr2Cu glass is much higher than that in the Zr2Ni and Zr2Cu0.5Ni0.5 samples. And Z12 ⟨0, 0, 12, 0⟩ Voronoi polyhedra clusters prefer to form around Cu atoms, while Ni-centered clusters are more like Z11 ⟨0, 2, 8, 1⟩ clusters, which is less energetically stable compared to Z12 clusters. These two different structural properties may account for the higher glass forming ability of Zr2Cu alloy than that of Zr2Ni alloy.

Optimization of self-interstitial clusters in 3C-SiC with genetic algorithm

NASA Astrophysics Data System (ADS)

Ko, Hyunseok; Kaczmarowski, Amy; Szlufarska, Izabela; Morgan, Dane

2017-08-01

Under irradiation, SiC develops damage commonly referred to as black spot defects, which are speculated to be self-interstitial atom clusters. To understand the evolution of these defect clusters and their impacts (e.g., through radiation induced swelling) on the performance of SiC in nuclear applications, it is important to identify the cluster composition, structure, and shape. In this work the genetic algorithm code StructOpt was utilized to identify groundstate cluster structures in 3C-SiC. The genetic algorithm was used to explore clusters of up to ∼30 interstitials of C-only, Si-only, and Si-C mixtures embedded in the SiC lattice. We performed the structure search using Hamiltonians from both density functional theory and empirical potentials. The thermodynamic stability of clusters was investigated in terms of their composition (with a focus on Si-only, C-only, and stoichiometric) and shape (spherical vs. planar), as a function of the cluster size (n). Our results suggest that large Si-only clusters are likely unstable, and clusters are predominantly C-only for n ≤ 10 and stoichiometric for n > 10. The results imply that there is an evolution of the shape of the most stable clusters, where small clusters are stable in more spherical geometries while larger clusters are stable in more planar configurations. We also provide an estimated energy vs. size relationship, E(n), for use in future analysis.

Special and general superatoms.

PubMed

Luo, Zhixun; Castleman, A Welford

2014-10-21

Bridging the gap between atoms and macroscopic matter, clusters continue to be a subject of increasing research interest. Among the realm of cluster investigations, an exciting development is the realization that chosen stable clusters can mimic the chemical behavior of an atom or a group of the periodic table of elements. This major finding known as a superatom concept was originated experimentally from the study of aluminum cluster reactivity conducted in 1989 by noting a dramatic size dependence of the reactivity where cluster anions containing a certain number of Al atoms were unreactive toward oxygen while the other species were etched away. This observation was well interpreted by shell closings on the basis of the jellium model, and the related concept (originally termed "unified atom") spawned a wide range of pioneering studies in the 1990s pertaining to the understanding of factors governing the properties of clusters. Under the inspiration of a superatom concept, advances in cluster science in finding stable species not only shed light on magic clusters (i.e., superatomic noble gas) but also enlightened the exploration of stable clusters to mimic the chemical behavior of atoms leading to the discovery of superhalogens, alkaline-earth metals, superalkalis, etc. Among them, certain clusters could enable isovalent isomorphism of precious metals, indicating application potential for inexpensive superatoms for industrial catalysis, while a few superalkalis were found to validate the interesting "harpoon mechanism" involved in the superatomic cluster reactivity; recently also found were the magnetic superatoms of which the cluster-assembled materials could be used in spin electronics. Up to now, extensive studies in cluster science have allowed the stability of superatomic clusters to be understood within a few models, including the jellium model, also aromaticity and Wade-Mingos rules depending on the geometry and metallicity of the cluster. However, the scope of application of the jellium model and modification of the theory to account for nonspherical symmetry and nonmetal-doped metal clusters are still illusive to be further developed. It is still worth mentioning that a superatom concept has also been introduced in ligand-stabilized metal clusters which could also follow the major shell-closing electron count for a spherical, square-well potential. By proposing a new concept named as special and general superatoms, herein we try to summarize all these investigations in series, expecting to provide an overview of this field with a primary focus on the joint undertakings which have given rise to the superatom concept. To be specific, for special superatoms, we limit to clusters under a strict jellium model and simply classify them into groups based on their valence electron counts. While for general superatoms we emphasize on nonmetal-doped metal clusters and ligand-stabilized metal clusters, as well as a few isovalent cluster systems. Hopefully this summary of special and general superatoms benefits the further development of cluster-related theory, and lights up the prospect of using them as building blocks of new materials with tailored properties, such as inexpensive isovalent systems for industrial catalysis, semiconductive superatoms for transistors, and magnetic superatoms for spin electronics.

Comparative study of energy of particles ejected from coulomb explosion of rare gas and metallic clusters irradiated by intense femtosecond laser field

NASA Astrophysics Data System (ADS)

Boucerredj, N.; Beggas, K.

2016-10-01

We present our study of high intensity femtosecond laser field interaction with large cluster of Kr and Na (contained 2.103 to 2.107 atoms). When laser intensity is above a critical value, it blows off all of electrons from the cluster and forms a non neutral ion cloud. The irradiation of these clusters by the intense laser field leads to highly excitation energy which can be the source of energetic electrons, electronic emission, highly charge, energetic ions and fragmentation process. During the Coulomb explosion of the resulting highly ionized, high temperature nanoplasma, ions acquire again their energy. It is shown that ultra fast ions are produced. The goal of our study is to investigate in detail a comparative study of the expansion and explosion then the ion energy of metallic and rare gas clusters irradiated by an intense femtosecond laser field. We have found that ions have a kinetic energy up to 105 eV and the Coulomb pressure is little than the hydrodynamic pressure. The Coulomb explosion of a cluster may provide a new high energy ion source.

Probing potential Li-ion battery electrolyte through first principles simulation of atomic clusters

NASA Astrophysics Data System (ADS)

Kushwaha, Anoop Kumar; Sahoo, Mihir Ranjan; Nayak, Saroj

2018-04-01

Li-ion battery has wide area of application starting from low power consumer electronics to high power electric vehicles. However, their large scale application in electric vehicles requires further improvement due to their low specific power density which is an essential parameter and is closely related to the working potential windows of the battery system. Several studies have found that these parameters can be taken care of by considering different cathode/anode materials and electrolytes. Recently, a unique approach has been reported on the basis of cluster size in which the use of Li3 cluster has been suggested as a potential component of the battery electrode material. The cluster based approach significantly enhances the working electrode potential up to 0.6V in the acetonitrile solvent. In the present work, using ab-initio quantum chemical calculation and the dielectric continuum model, we have investigated various dielectric solvent medium for the suitable electrolyte for the potential component Li3 cluster. This study suggests that high dielectric electrolytic solvent (ethylene carbonate and propylene carbonate) could be better for lithium cluster due to improvement in the total electrode potential in comparison to the other dielectric solvent.

Probing the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters by density functional calculations

NASA Astrophysics Data System (ADS)

Lu, Sheng-Jie

2018-05-01

We present a theoretical investigation on the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters using density functional theoretical calculations. The results showed that both anionic and neutral PtnC2 (n = 1-7) clusters primarily adopt 2D planar chain-shaped or ring-based structures. The two C atoms directly interact with each other to form a Csbnd C bond for n = 1-3, while the two C atoms are separated by the Pt atoms for n = 4-7, except for neutral Pt5C2. Pt4C2- anion and Pt4C2 neutral both show σ plus π double delocalized bonding patterns.

Correlation study of sodium-atom chemisorption on the GaAs(110) surface

NASA Astrophysics Data System (ADS)

Song, K. M.; Khan, D. C.; Ray, A. K.

1994-01-01

Different possible adsorption sites of sodium atoms on a gallium arsenide surface have been investigated using ab initio self-consistent unrestricted Hartree-Fock total-energy cluster calculations with Hay-Wadt effective core potentials. The effects of electron correlation have been included by invoking the concepts of many-body perturbation theory and are found to be highly significant. We find that the Na-atom adsorption at a site modeled with an NaGa5As4H12 cluster is most favored energetically followed by Na adsorption at the site modeled with the NaGa4As5H12 cluster. The effects of charge transfer from Na to the GaAs surface as also possibilities of metallization are also analyzed and discussed.

Development of purely structure-based pharmacophores for the topoisomerase I-DNA-ligand binding pocket

NASA Astrophysics Data System (ADS)

Drwal, Malgorzata N.; Agama, Keli; Pommier, Yves; Griffith, Renate

2013-12-01

Purely structure-based pharmacophores (SBPs) are an alternative method to ligand-based approaches and have the advantage of describing the entire interaction capability of a binding pocket. Here, we present the development of SBPs for topoisomerase I, an anticancer target with an unusual ligand binding pocket consisting of protein and DNA atoms. Different approaches to cluster and select pharmacophore features are investigated, including hierarchical clustering and energy calculations. In addition, the performance of SBPs is evaluated retrospectively and compared to the performance of ligand- and complex-based pharmacophores. SBPs emerge as a valid method in virtual screening and a complementary approach to ligand-focussed methods. The study further reveals that the choice of pharmacophore feature clustering and selection methods has a large impact on the virtual screening hit lists. A prospective application of the SBPs in virtual screening reveals that they can be used successfully to identify novel topoisomerase inhibitors.

Theoretical study of Ag doping-induced vacancies defects in armchair graphene

NASA Astrophysics Data System (ADS)

Benchallal, L.; Haffad, S.; Lamiri, L.; Boubenider, F.; Zitoune, H.; Kahouadji, B.; Samah, M.

2018-06-01

We have performed a density functional theory (DFT) study of the absorption of silver atoms (Ag,Ag2 and Ag3) in graphene using SIESTA code, in the generalized gradient approximation (GGA). The absorption energy, geometry, magnetic moments and charge transfer of Ag clusters-graphene system are calculated. The minimum energy configuration demonstrates that all structures remain planar and silver atoms fit into this plane. The charge transfer between the silver clusters and carbon atoms constituting the graphene surface is an indicative of a strong bond. The structure doped with a single silver atom has a magnetic moment and the two other are nonmagnetic.

Formation mechanism of atomic cluster structures in Al-Mg alloy during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liu, Feng-xiang; Liu, Rang-su; Hou, Zhao-yang; Liu, Hai-Rong; Tian, Ze-an; Zhou, Li-li

2009-02-01

The rapid solidification processes of Al 50Mg 50 liquid alloy consisting of 50,000 atoms have been simulated by using molecular dynamics method based on the effective pair potential derived from the pseudopotential theory. The formation mechanisms of atomic clusters during the rapid solidification processes have been investigated adopting a new cluster description method—cluster-type index method (CTIM). The simulated partial structure factors are in good agreement with the experimental results. And Al-Mg amorphous structure characterized with Al-centered icosahedral topological short-range order (SRO) is found to form during the rapid solidification processes. The icosahedral cluster plays a key role in the microstructure transition. Besides, it is also found that the size distribution of various clusters in the system presents a magic number sequence of 13, 19, 23, 25, 29, 31, 33, 37, …. The magic clusters are more stable and mainly correspond to the incompact arrangements of linked icosahedra in the form of rings, chains or dendrites. And each magic number point stands correspondingly for one certain combining form of icosahedra. This magic number sequence is different from that generated in the solidification structure of liquid Al and those obtained by methods of gaseous deposition and ionic spray, etc.

Role of radial nonuniformities in the interaction of an intense laser with atomic clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holkundkar, Amol R.; Gupta, N. K.

A model for the interaction of an intense laser with atomic clusters is presented. The model takes into account the spatial nonuniformities of the cluster as it evolves in time. The cluster is treated as a stratified sphere having an arbitrary number of layers. Electric and magnetic fields are obtained by solving the vector Helmholtz equation coupled with one-dimensional Lagrangian hydrodynamics. Results are compared with the uniform density nanoplasma model. Enhancement in the amount of energy absorbed is seen over the uniform density model. In some cases the absorbed energy increases by as much as a factor of 40.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-01

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra.

PubMed

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-07

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

A Wsbnd Ne interatomic potential for simulation of neon implantation in tungsten

NASA Astrophysics Data System (ADS)

Backman, Marie; Juslin, Niklas; Huang, Guiyang; Wirth, Brian D.

2016-08-01

An interatomic pair potential for Wsbnd Ne is developed for atomistic molecular dynamics simulations of neon implantation in tungsten. The new potential predicts point defect energies and binding energies of small clusters that are in good agreement with electronic structure calculations. Molecular dynamics simulations of small neon clusters in tungsten show that trap mutation, in which an interstitial neon cluster displaces a tungsten atom from its lattice site, occurs for clusters of three or more neon atoms. However, near a free surface, trap mutation can occur at smaller sizes, including even a single neon interstitial in close proximity to a (100) or (110) surface.

A model for sputtering from solid surfaces bombarded by energetic clusters

NASA Astrophysics Data System (ADS)

Benguerba, Messaoud

2018-04-01

A model is developed to explain and predict the sputtering from solid surfaces bombarded by energetic clusters, on the basis of shock wave generated at the impact of cluster. Under the shock compression the temperature increases causing the vaporization of material that requires an internal energy behind the shock, at least, of about twice the cohesive energy of target. The sputtering is treated as a gas of vaporized particles from a hemispherical volume behind the shock front. The sputter yield per cluster atoms is given as a universal function depending on the ratio of target to cluster atomic density and the ratio of cluster velocity to the velocity calculated on the basis of an internal energy equals about twice cohesive energy. The predictions of the model for self sputter yield of copper, gold, tungsten and of silver bombarded by C60 clusters agree well, with the corresponding data simulated by molecular dynamics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alexandrova, Anastassia N.; Nayhouse, Michael J.; Huynh, Mioy T.

CAl₄²-/- (D₄h, ¹A₁g) is is a cluster ion that has been established to be planar, aromatic, and contain a tetracoordinate planar C atom. Valence isoelectronic substitution of C with Si and Ge in this cluster leads to a radical change of structure toward distorted pentagonal species. We find that this structural change goes together with the cluster acquiring partial covalency of bonding between Si/Ge and Al₄, facilitated by hybridization of the atomic orbitals (AOs). Counter intuitively, for the AAl₄²-/- (A = C, Si, Ge) clusters, hybridization in the dopant atom is strengthened from C, to Si, and to Ge, evenmore » though typically AOs are more likely to hybridize if they are closer in energy (i.e. in earlier elements in the Periodic Table). The trend is explained by the better overlap of the hybrids of the heavier dopants with the orbitals of Al₄. From the thus understood trend, it is inferred that covalency in such clusters can be switched off, by varying the relative sizes of the AOs of the main element and the dopant. Using this mechanism, we then successfully killed covalency in Si, and predicted a new aromatic cluster ion containing a tetracoordinate square planar Si, SiIn₄²-/-.« less

Re-solution of xenon clusters in plutonium dioxide under the collision cascade impact: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Seitov, D. D.; Nekrasov, K. A.; Kupryazhkin, A. Ya.; Gupta, S. K.; Akilbekov, A. T.

2017-09-01

The interaction of xenon clusters with the collision cascades in the PuO2 crystals is investigated using the molecular dynamics simulation and the approximation of the pair interaction potentials. The potentials of interaction of Xe atoms with the surrounding particles in the crystal lattice are suggested, that are valid in the range of high collision energies. The cascades created by the recoil 235U ions formed as the plutonium α-decay product are considered, and the influence of such cascades on the structure of the xenon clusters is analyzed. It is shown, that the cascade-cluster interaction leads to release of the xenon atoms from the clusters and their subsequent re-solution in the crystal bulk.

Understanding the Cu-Zn brass alloys using a short-range-order cluster model: significance of specific compositions of industrial alloys

PubMed Central

Hong, H. L.; Wang, Q.; Dong, C.; Liaw, Peter K.

2014-01-01

Metallic alloys show complex chemistries that are not yet understood so far. It has been widely accepted that behind the composition selection lies a short-range-order mechanism for solid solutions. The present paper addresses this fundamental question by examining the face-centered-cubic Cu-Zn α-brasses. A new structural approach, the cluster-plus-glue-atom model, is introduced, which suits specifically for the description of short-range-order structures in disordered systems. Two types of formulas are pointed out, [Zn-Cu12]Zn1~6 and [Zn-Cu12](Zn,Cu)6, which explain the α-brasses listed in the American Society for Testing and Materials (ASTM) specifications. In these formulas, the bracketed parts represent the 1st-neighbor cluster, and each cluster is matched with one to six 2nd-neighbor Zn atoms or with six mixed (Zn,Cu) atoms. Such a cluster-based formulism describes the 1st- and 2nd-neighbor local atomic units where the solute and solvent interactions are ideally satisfied. The Cu-Ni industrial alloys are also explained, thus proving the universality of the cluster-formula approach in understanding the alloy selections. The revelation of the composition formulas for the Cu-(Zn,Ni) industrial alloys points to the common existence of simple composition rules behind seemingly complex chemistries of industrial alloys, thus offering a fundamental and practical method towards composition interpretations of all kinds of alloys. PMID:25399835

Understanding the Cu-Zn brass alloys using a short-range-order cluster model: Significance of specific compositions of industrial alloys

DOE PAGES

Hong, H. L.; Wang, Q.; Dong, C.; ...

2014-11-17

Metallic alloys show complex chemistries that are not yet understood so far. It has been widely accepted that behind the composition selection lies a short-range-order mechanism for solid solutions. The present paper addresses this fundamental question by examining the face-centered-cubic Cu-Zn α-brasses. A new structural approach, the cluster-plus-glue-atom model, is introduced, which suits specifically for the description of short-range-order structures in disordered systems. Two types of formulas are pointed out, [Zn-Cu 12]Zn 1~6 and [Zn-Cu 12](Zn,Cu) 6, which explain the α-brasses listed in the American Society for Testing and Materials (ASTM) specifications. In these formulas, the bracketed parts represent themore » 1 st-neighbor cluster, and each cluster is matched with one to six 2 nd-neighbor Zn atoms or with six mixed (Zn,Cu) atoms. Such a cluster-based formulism describes the 1 st- and 2 nd-neighbor local atomic units where the solute and solvent interactions are ideally satisfied. The Cu-Ni industrial alloys are also explained, thus proving the universality of the cluster-formula approach in understanding the alloy selections. As a result, the revelation of the composition formulas for the Cu-(Zn,Ni) industrial alloys points to the common existence of simple composition rules behind seemingly complex chemistries of industrial alloys, thus offering a fundamental and practical method towards composition interpretations of all kinds of alloys.« less

Mid-infrared signatures of hydroxyl containing water clusters: Infrared laser Stark spectroscopy of OH–H{sub 2}O and OH(D{sub 2}O){sub n} (n = 1-3)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez, Federico J.; INFIQC, Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón, X5000HUA Córdoba; Brice, Joseph T.

2015-10-28

Small water clusters containing a single hydroxyl radical are synthesized in liquid helium droplets. The OH–H{sub 2}O and OH(D{sub 2}O){sub n} clusters (n = 1-3) are probed with infrared laser spectroscopy in the vicinity of the hydroxyl radical OH stretch vibration. Experimental band origins are qualitatively consistent with ab initio calculations of the global minimum structures; however, frequency shifts from isolated OH are significantly over-predicted by both B3LYP and MP2 methods. An effective Hamiltonian that accounts for partial quenching of electronic angular momentum is used to analyze Stark spectra of the OH–H{sub 2}O and OH–D{sub 2}O binary complexes, revealing amore » 3.70(5) D permanent electric dipole moment. Computations of the dipole moment are in good agreement with experiment when large-amplitude vibrational averaging is taken into account. Polarization spectroscopy is employed to characterize two vibrational bands assigned to OH(D{sub 2}O){sub 2}, revealing two nearly isoenergetic cyclic isomers that differ in the orientation of the non-hydrogen-bonded deuterium atoms relative to the plane of the three oxygen atoms. The dipole moments for these clusters are determined to be approximately 2.5 and 1.8 D for “up-up” and “up-down” structures, respectively. Hydroxyl stretching bands of larger clusters containing three or more D{sub 2}O molecules are observed shifted approximately 300 cm{sup −1} to the red of the isolated OH radical. Pressure dependence studies and ab initio calculations imply the presence of multiple cyclic isomers of OH(D{sub 2}O){sub 3}.« less

Transfer-free synthesis of graphene-like atomically thin carbon films on SiC by ion beam mixing technique

NASA Astrophysics Data System (ADS)

Zhang, Rui; Chen, Fenghua; Wang, Jinbin; Fu, Dejun

2018-03-01

Here we demonstrate the synthesis of graphene directly on SiC substrates at 900 °C using ion beam mixing technique with energetic carbon cluster ions on Ni/SiC structures. The thickness of 7-8 nm Ni films was evaporated on the SiC substrates, followed by C cluster ion bombarding. Carbon cluster ions C4 were bombarded at 16 keV with the dosage of 4 × 1016 atoms/cm2. After thermal annealing process Ni silicides were formed, whereas C atoms either from the decomposition of the SiC substrates or the implanted contributes to the graphene synthesis by segregating and precipitating process. The limited solubility of carbon atoms in silicides, involving SiC, Ni2Si, Ni5Si2, Ni3Si, resulted in diffusion and precipitation of carbon atoms to form graphene on top of Ni and the interface of Ni/SiC. The ion beam mixing technique provides an attractive production method of a transfer-free graphene growth on SiC and be compatible with current device fabrication.

Preparation and Catalytic Activity for Aerobic Glucose Oxidation of Crown Jewel Structured Pt/Au Bimetallic Nanoclusters

NASA Astrophysics Data System (ADS)

Zhang, Haijun; Wang, Liqiong; Lu, Lilin; Toshima, Naoki

2016-08-01

Understanding of the “structure-activity” relations for catalysts at an atomic level has been regarded as one of the most important objectives in catalysis studies. Bimetallic nanoclusters (NCs) in its many types, such as core/shell, random alloy, cluster-in-cluster, bi-hemisphere, and crown jewel (one kind of atom locating at the top position of another kind of NC), attract significant attention owing to their excellent optical, electronic, and catalytic properties. PVP-protected crown jewel-structured Pt/Au (CJ-Pt/Au) bimetallic nanoclusters (BNCs) with Au atoms located at active top sites were synthesized via a replacement reaction using 1.4-nm Pt NCs as mother clusters even considering the fact that the replacement reaction between Pt and Au3+ ions is difficult to be occurred. The prepared CJ-Pt/Au colloidal catalysts characterized by UV-Vis, TEM, HR-TEM and HAADF-STEM-EELS showed a high catalytic activity for aerobic glucose oxidation, and the top Au atoms decorating the Pt NCs were about 15 times more active than the Au atoms of Au NCs with similar particle size.

Preparation and Catalytic Activity for Aerobic Glucose Oxidation of Crown Jewel Structured Pt/Au Bimetallic Nanoclusters

PubMed Central

Zhang, Haijun; Wang, Liqiong; Lu, Lilin; Toshima, Naoki

2016-01-01

Understanding of the “structure-activity” relations for catalysts at an atomic level has been regarded as one of the most important objectives in catalysis studies. Bimetallic nanoclusters (NCs) in its many types, such as core/shell, random alloy, cluster-in-cluster, bi-hemisphere, and crown jewel (one kind of atom locating at the top position of another kind of NC), attract significant attention owing to their excellent optical, electronic, and catalytic properties. PVP-protected crown jewel-structured Pt/Au (CJ-Pt/Au) bimetallic nanoclusters (BNCs) with Au atoms located at active top sites were synthesized via a replacement reaction using 1.4-nm Pt NCs as mother clusters even considering the fact that the replacement reaction between Pt and Au3+ ions is difficult to be occurred. The prepared CJ-Pt/Au colloidal catalysts characterized by UV-Vis, TEM, HR-TEM and HAADF-STEM-EELS showed a high catalytic activity for aerobic glucose oxidation, and the top Au atoms decorating the Pt NCs were about 15 times more active than the Au atoms of Au NCs with similar particle size. PMID:27476577

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Jun; Ma, Evan; Asta, Mark

Using molecular dynamics simulations, we have studied the atomic correlations characterizing the second peak in the radial distribution function (RDF) of metallic glasses and liquids. The analysis was conducted from the perspective of different connection schemes of atomic packing motifs, based on the number of shared atoms between two linked coordination polyhedra. The results demonstrate that the cluster connections by face-sharing, specifically with three common atoms, are most favored when transitioning from the liquid to glassy state, and exhibit the stiffest elastic response during shear deformation. These properties of the connections and the resultant atomic correlations are generally the samemore » for different types of packing motifs in different alloys. Splitting of the second RDF peak was observed for the inherent structure of the equilibrium liquid, originating solely from cluster connections; this trait can then be inherited in the metallic glass formed via subsequent quenching of the parent liquid through the glass transition, in the absence of any additional type of local structural order. In conclusion, increasing ordering and cluster connection during cooling, however, may tune the position and intensity of the split peaks.« less

Excited State Energetics and Dynamics of Large Molecules, Complexes and Clusters

DTIC Science & Technology

1988-07-01

tetracene. Ar (n=l-5) complexes, providing central information on microscopic solvent shifts. These studies were extended to M-metal atom com - plexes...corresponding to the bare molecule. At higher 2. Experimental stagnation pressures of Ar (p = 80-150 Toff) the contributions of van der Waals DPB. Ar, com - Our...gas aromatic-molecule complexes were docu- So - S1 transition of the trans-stilbene (TS)-Ar com - mented experimentally to lie in the rango - 30- plex

Triggering the formation of the supergiant H II region NGC 604 in M 33

NASA Astrophysics Data System (ADS)

Tachihara, Kengo; Gratier, Pierre; Sano, Hidetoshi; Tsuge, Kisetsu; Miura, Rie E.; Muraoka, Kazuyuki; Fukui, Yasuo

2018-05-01

Formation mechanism of a supergiant H II region NGC 604 is discussed in terms of collision of H I clouds in M 33. An analysis of the archival H I data obtained with the Very Large Array (VLA) reveals complex velocity distributions around NGC 604. The H I clouds are composed of two velocity components separated by ˜20 km s-1 for an extent of ˜700 pc, beyond the size of the the H II region. Although the H I clouds are not easily separated in velocity with some mixed component represented by merged line profiles, the atomic gas mass amounts to 6 × 106 M_{⊙} and 9 × 106 M_{⊙} for each component. These characteristics of H I gas and the distributions of dense molecular gas in the overlapping regions of the two velocity components suggest that the formation of giant molecular clouds and the following massive cluster formation have been induced by the collision of H I clouds with different velocities. Referring to the existence of a gas bridging feature connecting M 33 with M 31 reported by large-scale H I surveys, the disturbed atomic gas possibly represents the result of past tidal interaction between the two galaxies, which is analogous to the formation of the R 136 cluster in the LMC.

Effects of short-range order on electronic properties of Zr-Ni glasses as seen from low-temperature specific heat

NASA Astrophysics Data System (ADS)

Kroeger, D. M.; Koch, C. C.; Scarbrough, J. O.; McKamey, C. G.

1984-02-01

Measurements of the low-temperature specific heat Cp of liquid-quenched Zr-Ni glasses for a large number of compositions in the range from 55 to 74 at.% Zr revealed an unusual composition dependence of the density of states at the Fermi level, N(EF). Furthermore, for some compositions the variation of Cp near the superconducting transition temperature Tc indicated the presence of two superconducting phases, i.e., two superconducting transitions were detected. Comparison of the individual Tc's in phase-separated samples to the composition dependence of Tc for all of the samples suggests that amorphous phases with compositions near 60 and 66.7 at.% Zr occur. We discuss these results in terms of an "association model" for liquid alloys (due to Sommer), in which associations of unlike atoms with definite stoichiometries are assumed to exist in equilibrium with unassociated atoms. We conclude that in the composition range studied, associate clusters with the compositions Zr3Ni2 and Zr2Ni occur. In only a few cases are the clusters sufficiently large, compared with the superconducting coherence length, for separate superconducting transitions to be observed. The variation of N(EF) with composition is discussed, as well as the effects of this chemical short-range ordering on the crystallization behavior and glass-forming tendency.

Lowest-energy structures and electronic properties of Na-Si binary clusters from ab initio global search.

PubMed

Sai, Linwei; Tang, Lingli; Zhao, Jijun; Wang, Jun; Kumar, Vijay

2011-11-14

The ground state structures of neutral and anionic clusters of Na(n)Si(m) (1 ≤ n ≤ 3, 1 ≤ m ≤ 11) have been determined using genetic algorithm incorporated in first principles total energy code. The size dependence of the structural and electronic properties is discussed in detail. It is found that the lowest-energy structures of Na(n)Si(m) clusters resemble those of the pure Si clusters. Interestingly, Na atoms in neutral Na(n)Si(m) clusters are usually well separated by the Si(m) skeleton, whereas Na atoms can form Na-Na bonds in some anionic clusters. The ionization potentials, adiabatic electron affinities, and photoelectron spectra are also calculated and the results compare well with the experimental data. © 2011 American Institute of Physics

Predicting stability limits for pure and doped dicationic noble gas clusters undergoing coulomb explosion: A parallel tempering based study.

PubMed

Ghorai, Sankar; Chaudhury, Pinaki

2018-05-30

We have used a replica exchange Monte-Carlo procedure, popularly known as Parallel Tempering, to study the problem of Coulomb explosion in homogeneous Ar and Xe dicationic clusters as well as mixed Ar-Xe dicationic clusters of varying sizes with different degrees of relative composition. All the clusters studied have two units of positive charges. The simulations reveal that in all the cases there is a cutoff size below which the clusters fragment. It is seen that for the case of pure Ar, the value is around 95 while that for Xe it is 55. For the mixed clusters with increasing Xe content, the cutoff limit for suppression of Coulomb explosion gradually decreases from 95 for a pure Ar to 55 for a pure Xe cluster. The hallmark of this study is this smooth progression. All the clusters are simulated using the reliable potential energy surface developed by Gay and Berne (Gay and Berne, Phys. Rev. Lett. 1982, 49, 194). For the hetero clusters, we have also discussed two different ways of charge distribution, that is one in which both positive charges are on two Xe atoms and the other where the two charges are at a Xe atom and at an Ar atom. The fragmentation patterns observed by us are such that single ionic ejections are the favored dissociating pattern. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Interaction of boron cluster ions with water: Single collision dynamics and sequential etching

NASA Astrophysics Data System (ADS)

Hintz, Paul A.; Ruatta, Stephen A.; Anderson, Scott L.

1990-01-01

Reactions of mass-selected, cooled, boron cluster ions (B+n, n=1-14) with water have been studied for collision energies from 0.1 to 6.0 eV. Most work was done with D2O, however isotope effects were examined for selected reactant cluster ions. For all size clusters there are exoergic product channels, which in most cases have no activation barriers. Cross sections are generally large, however there are fluctuations with cluster size in total reactivity, collision energy dependences, and in product distributions. For small cluster ions, there is a multitude of product channels. For clusters larger than B+6, the product distributions are dominated by a single channel: Bn-1D++DBO. Under multiple collision conditions, the primary products undergo a remarkable sequence of secondary ``etching'' reactions. As these occur, boron atoms are continuously replaced by hydrogen, and the intermediate products retain the composition: Bn-mH+m. This highly efficient chemistry appears to continue unchanged as the composition changes from pure boron to mostly hydrogen. Comparison of these results is made with boron cluster ion reactions with O2 and D2, as well as reactions with water of aluminum and silicon cluster ions. Some discussion is given of the thermochemistry for these reactions, and a possible problem with the thermochemical data in the BOD/DBO system is discussed.

Rapid insights from remote sensing in the geosciences

NASA Astrophysics Data System (ADS)

Plaza, Antonio

2015-03-01

The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the communication cost remains modest. We discuss a variety of strategies for implementing SNAP in the LAMMPS molecular dynamics package. We present scaling results obtained running SNAP on three different classes of machine: a conventional Intel Xeon CPU cluster; the Titan GPU-based system; and the combined Sequoia and Vulcan BlueGene/Q. The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the communication cost remains modest. We discuss a variety of strategies for implementing SNAP in the LAMMPS molecular dynamics package. We present scaling results obtained running SNAP on three different classes of machine: a conventional Intel Xeon CPU cluster; the Titan GPU-based system; and the combined Sequoia and Vulcan BlueGene/Q. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corp., for the U.S. Dept. of Energy's National Nuclear Security Admin. under Contract DE-AC04-94AL85000.

Temperature-Dependent Evolution of the Oxidation States of Cobalt and Platinum in Co 1–xPt x Clusters under H 2 and CO + H 2 Atmospheres

DOE PAGES

Yang, Bing; Khadra, Ghassan; Tuaillon-Combes, Juliette; ...

2016-08-25

In this study, Co 1–xPt x clusters of 2.9-nm size with a range of atomically precise Pt/Co atomic ratios (x = 0, 0.25, 0.5, 0.75, 1) were synthesized using the mass-selected low-energy cluster beam deposition (LECBD) technique and soft-landed onto an amorphous alumina thin film prepared by atomic layer deposition (ALD). Utilizing ex situ X-ray photoemission spectroscopy (XPS), the oxidation state of the as-made clusters supported on Al 2O 3 was determined after both a 1-h-long exposure to air and aging for several weeks while exposed to air. Next, the aged cluster samples were characterized by grazing-incidence X-ray absorption spectroscopymore » (GIXAS) and then pretreated with diluted hydrogen and further exposed to the mixture of diluted CO and H 2 up to 225°C at atmospheric pressure, and the temperature-dependent evolutions of the particle size/shape and the oxidation states of the individual metal components within the clusters were monitored using in situ grazing-incidence small-angle X-ray scattering and X-ray absorption spectroscopy (GISAXS/GIXAS). The changes in the oxidation states of Co and Pt exhibited a nonlinear dependence on the Pt/Co atomic ratio of the clusters. For example, a low Pt/Co ratio (x ≤ 0.5) facilitates the formation of Co(OH) 2, whereas a high Pt/Co ratio (x = 0.75) stabilizes the Co 3O 4 composition instead through the formation of a Co–Pt core–shell structure where the platinum shell inhibits the reduction of cobalt in the core of the Co 1–xPt x alloy clusters. Finally, the obtained results indicate methods for optimizing the composition and structure of binary alloy clusters for catalysis.« less

Slider thickness promotes lubricity: from 2D islands to 3D clusters

NASA Astrophysics Data System (ADS)

Guerra, Roberto; Tosatti, Erio; Vanossi, Andrea

2016-05-01

The sliding of three-dimensional clusters and two-dimensional islands adsorbed on crystal surfaces represents an important test case to understand friction. Even for the same material, monoatomic islands and thick clusters will not as a rule exhibit the same friction, but specific differences have not been explored. Through realistic molecular dynamics simulations of the static friction of gold on graphite, an experimentally relevant system, we uncover as a function of gold thickness a progressive drop of static friction from monolayer islands, that are easily pinned, towards clusters, that slide more readily. The main ingredient contributing to this thickness-induced lubricity appears to be the increased effective rigidity of the atomic contact, acting to reduce the cluster interdigitation with the substrate. A second element which plays a role is the lateral contact size, which can accommodate the solitons typical of the incommensurate interface only above a critical contact diameter, which is larger for monolayer islands than for thick clusters. The two effects concur to make clusters more lubric than islands, and large sizes more lubric than smaller ones. These conclusions are expected to be of broader applicability in diverse nanotribological systems, where the role played by static, and dynamic, friction is generally quite important.

Slider thickness promotes lubricity: from 2D islands to 3D clusters.

PubMed

Guerra, Roberto; Tosatti, Erio; Vanossi, Andrea

2016-06-07

The sliding of three-dimensional clusters and two-dimensional islands adsorbed on crystal surfaces represents an important test case to understand friction. Even for the same material, monoatomic islands and thick clusters will not as a rule exhibit the same friction, but specific differences have not been explored. Through realistic molecular dynamics simulations of the static friction of gold on graphite, an experimentally relevant system, we uncover as a function of gold thickness a progressive drop of static friction from monolayer islands, that are easily pinned, towards clusters, that slide more readily. The main ingredient contributing to this thickness-induced lubricity appears to be the increased effective rigidity of the atomic contact, acting to reduce the cluster interdigitation with the substrate. A second element which plays a role is the lateral contact size, which can accommodate the solitons typical of the incommensurate interface only above a critical contact diameter, which is larger for monolayer islands than for thick clusters. The two effects concur to make clusters more lubric than islands, and large sizes more lubric than smaller ones. These conclusions are expected to be of broader applicability in diverse nanotribological systems, where the role played by static, and dynamic, friction is generally quite important.

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation

PubMed Central

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-01-01

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein–protein or protein–ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. PMID:27288028

Clustering/anticlustering effects on the GeSi Raman spectra at moderate (Ge,Si) contents: Percolation scheme vs. ab initio calculations

NASA Astrophysics Data System (ADS)

Torres, V. J. B.; Hajj Hussein, R.; Pagès, O.; Rayson, M. J.

2017-02-01

We test a presumed ability behind the phenomenological percolation scheme used for the basic description of the multi-mode Raman spectra of mixed crystals at one dimension along the linear chain approximation, to determine, via the Raman intensities, the nature of the atom substitution, as to whether this is random or due to local clustering/anticlustering. For doing so, we focus on the model percolation-type GeySi1-y system characterized by six oscillators { 1 × ( G e - G e ) , 3 × ( G e - S i ) , 2 × ( S i - S i ) } and place the study around the critical compositions y ˜ (0.16, 0.71, and 0.84) corresponding to nearly matching of intensities between the like Raman modes from a given multiplet ( G e - S i triplet or S i - S i doublet). The interplay between the GeySi1-y Raman intensities predicted by the percolation scheme depending on a suitable order parameter κ of local clustering/anticlustering is found to be consistent with ab initio calculations of the GeySi1-y Raman spectra done with the Ab Initio Modeling PROgram code using large (64-, 216-, and 512-atoms) disordered cubic supercells matching the required ( y , κ ) values. The actual "percolation vs. ab initio" comparative insight at moderate/dilute-(Ge,Si) limits, with an emphasis on the κ -induced intra-bond transfer of oscillator strength, extends a pioneering one earlier achieved at an intermediate composition ( y ˜ 0.50) by using small (32-atom) supercells [O. Pagès et al., J. Appl. Phys. 114, 033513 (2013)], mainly concerned with the inter-bond transfer of oscillator strength, providing altogether a complete picture.

Atomic and electronic structure of the silicon and silicon-metal Si{sub 20}, Si{sub 20}{sup -}, NaSi{sub 20}, KSi{sub 20} nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borshch, N. A., E-mail: ssd18@phys.vsu.ru; Pereslavtseva, N. S.; Kurganskii, S. I.

The results of atomic-structure optimization and calculation of the electronic structure of the Si{sub 20}, Si{sub 20}{sup -}, NaSi{sub 20}, and KSi{sub 20} clusters are reported. The PM3 and AM1 semiempirical methods were used in the calculations. It is shown that the Na and K atoms stabilize the fullerene-like silicon structure. The effect of configuration of the clusters on their electronic structure is analyzed.

Anomalous small-angle scattering as a way to solve the Babinet principle problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boiko, M. E., E-mail: m.e.boiko@mail.ioffe.ru; Sharkov, M. D.; Boiko, A. M.

2013-12-15

X-ray absorption spectra (XAS) have been used to determine the absorption edges of atoms present in a sample under study. A series of small-angle X-ray scattering (SAXS) measurements using different monochromatic X-ray beams at different wavelengths near the absorption edges is performed to solve the Babinet principle problem. The sizes of clusters containing atoms determined by the method of XAS were defined in SAXS experiments. In contrast to differential X-ray porosimetry, anomalous SAXS makes it possible to determine sizes of clusters of different atomic compositions.

Anomalous small-angle scattering as a way to solve the Babinet principle problem

NASA Astrophysics Data System (ADS)

Boiko, M. E.; Sharkov, M. D.; Boiko, A. M.; Bobyl, A. V.

2013-12-01

X-ray absorption spectra (XAS) have been used to determine the absorption edges of atoms present in a sample under study. A series of small-angle X-ray scattering (SAXS) measurements using different monochromatic X-ray beams at different wavelengths near the absorption edges is performed to solve the Babinet principle problem. The sizes of clusters containing atoms determined by the method of XAS were defined in SAXS experiments. In contrast to differential X-ray porosimetry, anomalous SAXS makes it possible to determine sizes of clusters of different atomic compositions.

Evolution of irradiation-induced strain in an equiatomic NiFe alloy

DOE PAGES

Ullah, Mohammad W.; Zhang, Yanwen; Sellami, Neila; ...

2017-07-10

Here, we investigate the formation and accumulation of irradiation-induced atomic strain in an equiatomic NiFe concentrated solid-solution alloy using both atomistic simulations and x-ray diffraction (XRD) analysis of irradiated samples. Experimentally, the irradiations are performed using 1.5 MeV Ni ions to fluences ranging from 1 × 10 13 to 1 × 10 14 cm -2. The irradiation simulations are carried out by overlapping 5 keV Ni recoils cascades up to a total of 300 recoils. An increase of volumetric strain is observed at low dose, which is associated with production of point defects and small clusters. A relaxation of strainmore » occurs at higher doses, when large defect clusters, like dislocation loops, dominate.« less

A Computational Study of Rare Gas Clusters: Stepping Stones to the Solid State

ERIC Educational Resources Information Center

Glendening, Eric D.; Halpern, Arthur M.

2012-01-01

An upper-level undergraduate or beginning graduate project is described in which students obtain the Lennard-Jones 6-12 potential parameters for Ne[subscript 2] and Ar[subscript 2] from ab initio calculations and use the results to express pairwise interactions between the atoms in clusters containing up to N = 60 atoms. The students use simulated…

Experimental methods of molecular matter-wave optics.

PubMed

Juffmann, Thomas; Ulbricht, Hendrik; Arndt, Markus

2013-08-01

We describe the state of the art in preparing, manipulating and detecting coherent molecular matter. We focus on experimental methods for handling the quantum motion of compound systems from diatomic molecules to clusters or biomolecules.Molecular quantum optics offers many challenges and innovative prospects: already the combination of two atoms into one molecule takes several well-established methods from atomic physics, such as for instance laser cooling, to their limits. The enormous internal complexity that arises when hundreds or thousands of atoms are bound in a single organic molecule, cluster or nanocrystal provides a richness that can only be tackled by combining methods from atomic physics, chemistry, cluster physics, nanotechnology and the life sciences.We review various molecular beam sources and their suitability for matter-wave experiments. We discuss numerous molecular detection schemes and give an overview over diffraction and interference experiments that have already been performed with molecules or clusters.Applications of de Broglie studies with composite systems range from fundamental tests of physics up to quantum-enhanced metrology in physical chemistry, biophysics and the surface sciences.Nanoparticle quantum optics is a growing field, which will intrigue researchers still for many years to come. This review can, therefore, only be a snapshot of a very dynamical process.

Systematization of actinides using cluster analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kopyrin, A.A.; Terent`eva, T.N.; Khramov, N.N.

1994-11-01

A representation of the actinides in multidimensional property space is proposed for systematization of these elements using cluster analysis. Literature data for their atomic properties are used. Owing to the wide variation of published ionization potentials, medians are used to estimate them. Vertical dendograms are used for classification on the basis of distances between the actinides in atomic-property space. The properties of actinium and lawrencium are furthest removed from the main group. Thorium and mendelevium exhibit individualized properties. A cluster based on the einsteinium-fermium pair is joined by californium.

Photoelectron spectroscopy and density functional theory study of TiAlO(y) (-) (y=1-3) and TiAl(2)O(y) (-) (y=2-3) clusters.

PubMed

Zhang, Zeng-Guang; Xu, Hong-Guang; Zhao, Yuchao; Zheng, Weijun

2010-10-21

Small titanium-aluminum oxide clusters, TiAlO(y) (-) (y=1-3) and TiAl(2)O(y) (-) (y=2-3), were studied by using anion photoelectron spectroscopy. The adiabatic detachment energies of TiAlO(y) (-) (y=1-3) were estimated to be 1.11±0.05, 1.70±0.08, and 2.47±0.08eV based on their photoelectron spectra; those of TiAl(2)O(2) (-) and TiAl(2)O(3) (-) were estimated to be 1.17±0.08 and 2.2±0.1eV, respectively. The structures of these clusters were determined by comparison of density functional calculations with the experimental results. The structure of TiAlO(-) is nearly linear with the O atom in the middle. That of TiAlO(2) (-) is a kite-shaped structure. TiAlO(3) (-) has a kite-shaped TiAlO(2) unit with the third O atom attaching to the Ti atom. TiAl(2)O(2) (-) has two nearly degenerate Al-O-Ti-O-Al chain structures that can be considered as cis and trans forms. TiAl(2)O(3) (-) has two low-lying isomers, kite structure and book structure. The structures of these clusters indicate that the Ti atom tends to bind to more O atoms.

Statistical study of defects caused by primary knock-on atoms in fcc Cu and bcc W using molecular dynamics

NASA Astrophysics Data System (ADS)

Warrier, M.; Bhardwaj, U.; Hemani, H.; Schneider, R.; Mutzke, A.; Valsakumar, M. C.

2015-12-01

We report on molecular Dynamics (MD) simulations carried out in fcc Cu and bcc W using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code to study (i) the statistical variations in the number of interstitials and vacancies produced by energetic primary knock-on atoms (PKA) (0.1-5 keV) directed in random directions and (ii) the in-cascade cluster size distributions. It is seen that around 60-80 random directions have to be explored for the average number of displaced atoms to become steady in the case of fcc Cu, whereas for bcc W around 50-60 random directions need to be explored. The number of Frenkel pairs produced in the MD simulations are compared with that from the Binary Collision Approximation Monte Carlo (BCA-MC) code SDTRIM-SP and the results from the NRT model. It is seen that a proper choice of the damage energy, i.e. the energy required to create a stable interstitial, is essential for the BCA-MC results to match the MD results. On the computational front it is seen that in-situ processing saves the need to input/output (I/O) atomic position data of several tera-bytes when exploring a large number of random directions and there is no difference in run-time because the extra run-time in processing data is offset by the time saved in I/O.

Nanopores creation in boron and nitrogen doped polycrystalline graphene: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Izadifar, Mohammadreza; Abadi, Rouzbeh; Nezhad Shirazi, Ali Hossein; Alajlan, Naif; Rabczuk, Timon

2018-05-01

In the present paper, molecular dynamic simulations have been conducted to investigate the nanopores creation on 10% of boron and nitrogen doped polycrystalline graphene by silicon and diamond nanoclusters. Two types of nanoclusters based on silicon and diamond are used to investigate their effect for the fabrication of nanopores. Therefore, three different diameter sizes of the clusters with five kinetic energies of 10, 50, 100, 300 and 500 eV/atom at four different locations in boron or nitrogen doped polycrystalline graphene nanosheets have been perused. We also study the effect of 3% and 6% of boron doped polycrystalline graphene with the best outcome from 10% of doping. Our results reveal that the diamond cluster with diameter of 2 and 2.5 nm fabricates the largest nanopore areas on boron and nitrogen doped polycrystalline graphene, respectively. Furthermore, the kinetic energies of 10 and 50 eV/atom can not fabricate nanopores in some cases for silicon and diamond clusters on boron doped polycrystalline graphene nanosheets. On the other hand, silicon and diamond clusters fabricate nanopores for all locations and all tested energies on nitrogen doped polycrystalline graphene. The area sizes of nanopores fabricated by silicon and diamond clusters with diameter of 2 and 2.5 nm are close to the actual area size of the related clusters for the kinetic energy of 300 eV/atom in all locations on boron doped polycrystalline graphene. The maximum area and the average maximum area of nanopores are fabricated by the kinetic energy of 500 eV/atom inside the grain boundary at the center of the nanosheet and in the corner of nanosheet with diameters of 2 and 3 nm for silicon and diamond clusters on boron and nitrogen doped polycrystalline graphene.

Shellwise Mackay transformation in iron nanoclusters.

PubMed

Rollmann, Georg; Gruner, Markus E; Hucht, Alfred; Meyer, Ralf; Entel, Peter; Tiago, Murilo L; Chelikowsky, James R

2007-08-24

Structure and magnetism of iron clusters with up to 641 atoms have been investigated by means of density functional theory calculations including full geometric optimizations. Body-centered cubic (bcc) isomers are found to be lowest in energy when the clusters contain more than about 100 atoms. In addition, another stable conformation has been identified for magic-number clusters, which lies well within the range of thermal energies as compared to the bcc isomers. Its structure is characterized by a close-packed particle core and an icosahedral surface, while intermediate shells are partially transformed along the Mackay path between icosahedral and cuboctahedral geometry. The gradual transformation results in a favorable bcc environment for the subsurface atoms. For Fe55, the shellwise Mackay-transformed morphology is a promising candidate for the ground state.

Structural evolution and atomic dynamics in Ni-Nb metallic glasses: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Xu, T. D.; Wang, X. D.; Zhang, H.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

2017-10-01

The composition and temperature dependence of static and dynamic structures in NixNb1-x (x = 50-70 at. %) were systematically studied using molecular dynamics with a new-released semi-empirical embedded atom method potential by Mendelev. The calculated pair correlation functions and the structure factor match well with the experimental data, demonstrating the reliability of the potential within relatively wide composition and temperature ranges. The local atomic structures were then characterized by bond angle distributions and Voronoi tessellation methods, demonstrating that the icosahedral ⟨0,0,12,0⟩ is only a small fraction in the liquid state but increases significantly during cooling and becomes dominant at 300 K. The most abundant clusters are identified as ⟨0,0,12,0⟩ and distorted icosahedron ⟨0,2,8,2⟩. The large fraction of these two clusters hints that the relatively good glass forming ability is near the eutectic point. Unlike Cu-Zr alloys, both the self-diffusion coefficient and shear viscosity are insensitive to compositions upon cooling in Ni-Nb alloys. The breakdown of the Stokes-Einstein relation happens at around 1.6Tg (Tg: glass transition temperature). In the amorphous state, the solid and liquid-like atoms can be distinguished based on the Debye-Waller factor ⟨u2⟩. The insensitivity of the dynamic properties of Ni-Nb alloys to compositions may result from the relatively simple solidification process in the phase diagram, in which only one eutectic point exists in the studied composition range.

The Influence of Atomic Diffusion on Stellar Ages and Chemical Tagging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dotter, Aaron; Conroy, Charlie; Cargile, Phillip

2017-05-10

In the era of large stellar spectroscopic surveys, there is an emphasis on deriving not only stellar abundances but also the ages for millions of stars. In the context of Galactic archeology, stellar ages provide a direct probe of the formation history of the Galaxy. We use the stellar evolution code MESA to compute models with atomic diffusion—with and without radiative acceleration—and extra mixing in the surface layers. The extra mixing consists of both density-dependent turbulent mixing and envelope overshoot mixing. Based on these models we argue that it is important to distinguish between initial, bulk abundances (parameters) and current,more » surface abundances (variables) in the analysis of individual stellar ages. In stars that maintain radiative regions on evolutionary timescales, atomic diffusion modifies the surface abundances. We show that when initial, bulk metallicity is equated with current, surface metallicity in isochrone age analysis, the resulting stellar ages can be systematically overestimated by up to 20%. The change of surface abundances with evolutionary phase also complicates chemical tagging, which is the concept that dispersed star clusters can be identified through unique, high-dimensional chemical signatures. Stars from the same cluster, but in different evolutionary phases, will show different surface abundances. We speculate that calibration of stellar models may allow us to estimate not only stellar ages but also initial abundances for individual stars. In the meantime, analyzing the chemical properties of stars in similar evolutionary phases is essential to minimize the effects of atomic diffusion in the context of chemical tagging.« less

Water Oxidation Catalysis via Size-Selected Iridium Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halder, Avik; Liu, Cong; LIU, ZHUN

The detailed mechanism and efficacy of four electron electrochemical water oxidation depend critically upon the detailed atomic structure of each catalytic site, which are numerous and diverse in most metal oxides anodes. In order to limit the diversity of sites, arrays of discrete iridium clusters with identical metal atom number (Ir-2, Ir-4, or Ir-8) were deposited in submonolayer coverage on conductive oxide supports, and the electrochemical properties and activity of each was evaluated. Exceptional electroactivity for the oxygen evolving reaction (OER) was observed for all cluster samples in acidic electrolyte. Reproducible cluster-size-dependent trends in redox behavior were also resolved. First-principlesmore » computational models of the individual discrete-size clusters allow correlation of catalytic-site structure and multiplicity with redox behavior.« less

Atomistic modeling of dropwise condensation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sikarwar, B. S., E-mail: bssikarwar@amity.edu; Singh, P. L.; Muralidhar, K.

The basic aim of the atomistic modeling of condensation of water is to determine the size of the stable cluster and connect phenomena occurring at atomic scale to the macroscale. In this paper, a population balance model is described in terms of the rate equations to obtain the number density distribution of the resulting clusters. The residence time is taken to be large enough so that sufficient time is available for all the adatoms existing in vapor-phase to loose their latent heat and get condensed. The simulation assumes clusters of a given size to be formed from clusters of smallermore » sizes, but not by the disintegration of the larger clusters. The largest stable cluster size in the number density distribution is taken to be representative of the minimum drop radius formed in a dropwise condensation process. A numerical confirmation of this result against predictions based on a thermodynamic model has been obtained. Results show that the number density distribution is sensitive to the surface diffusion coefficient and the rate of vapor flux impinging on the substrate. The minimum drop radius increases with the diffusion coefficient and the impinging vapor flux; however, the dependence is weak. The minimum drop radius predicted from thermodynamic considerations matches the prediction of the cluster model, though the former does not take into account the effect of the surface properties on the nucleation phenomena. For a chemically passive surface, the diffusion coefficient and the residence time are dependent on the surface texture via the coefficient of friction. Thus, physical texturing provides a means of changing, within limits, the minimum drop radius. The study reveals that surface texturing at the scale of the minimum drop radius does not provide controllability of the macro-scale dropwise condensation at large timescales when a dynamic steady-state is reached.« less

Theoretical analysis of hydrogen spillover mechanism on carbon nanotubes

PubMed Central

Juarez-Mosqueda, Rosalba; Mavrandonakis, Andreas; Kuc, Agnieszka B.; Pettersson, Lars G. M.; Heine, Thomas

2015-01-01

The spillover mechanism of molecular hydrogen on carbon nanotubes in the presence of catalytically active platinum clusters was critically and systematically investigated by using density-functional theory. Our simulation model includes a Pt4 cluster for the catalyst nanoparticle and curved and planar circumcoronene for two exemplary single-walled carbon nanotubes (CNT), the (10,10) CNT and one of large diameter, respectively. Our results show that the H2 molecule dissociates spontaneously on the Pt4 cluster. However, the dissociated H atoms have to overcome a barrier of more than 2 eV to migrate from the catalyst to the CNT, even if the Pt4 cluster is at full saturation with six adsorbed and dissociated hydrogen molecules. Previous investigations have shown that the mobility of hydrogen atoms on the CNT surface is hindered by a barrier. We find that instead the Pt4 catalyst may move along the outer surface of the CNT with activation energy of only 0.16 eV, and that this effect offers the possibility of full hydrogenation of the CNT. Thus, although we have not found a low-energy pathway to spillover onto the CNT, we suggest, based on our calculations and calculated data reported in the literature, that in the hydrogen-spillover process the observed saturation of the CNT at hydrogen background pressure occurs through mobile Pt nanoclusters, which move on the substrate more easily than the substrate-chemisorbed hydrogens, and deposit or reattach hydrogens in the process. Initial hydrogenation of the carbon substrate, however, is thermodynamically unfavoured, suggesting that defects should play a significant role. PMID:25699250

Electronic structure and properties of magnetic defects in Co(1+x)Al(1-x) and Fe(1+x)Al(1-x) alloys. Ph.D. Thesis - Paris Univ.

NASA Technical Reports Server (NTRS)

Abbe, D.

1984-01-01

CoAl and FeAl compounds are developed along two directions. Magnetic susceptibility and specific heat at low temperature on (NiCo)Al and (CoFe)Al ternary alloys are in good agreement with band calculations. Results on magnetization and specific heat under field at low temperature on nonstoichiometric compounds show clearly the importance of the nearest neighbor effects. In the case of CoAl, the isolated cobalt atoms substituting aluminum are characterized by a Kondo behavior, and, for FeAl, the isolated extra iron atoms are magnetic and polarize the matrix. Moreover, for the two compounds, clusters of higher order play a considerable part in the magnetic properties for CoAl, these clusters also seem to be characterized by a Kondo behavior, for FeAl, these clusters whose moment is higher than in the case of isolated atoms, could be constituted of excess parts of iron atoms.

Composition-dependent metallic glass alloys correlate atomic mobility with collective glass surface dynamics.

PubMed

Nguyen, Duc; Zhu, Zhi-Guang; Pringle, Brian; Lyding, Joseph; Wang, Wei-Hua; Gruebele, Martin

2016-06-22

Glassy metallic alloys are richly tunable model systems for surface glassy dynamics. Here we study the correlation between atomic mobility, and the hopping rate of surface regions (clusters) that rearrange collectively on a minute to hour time scale. Increasing the proportion of low-mobility copper atoms in La-Ni-Al-Cu alloys reduces the cluster hopping rate, thus establishing a microscopic connection between atomic mobility and dynamics of collective rearrangements at a glass surface made from freshly exposed bulk glass. One composition, La60Ni15Al15Cu10, has a surface resistant to re-crystallization after three heating cycles. When thermally cycled, surface clusters grow in size from about 5 glass-forming units to about 8 glass-forming units, evidence of surface aging without crystal formation, although its bulk clearly forms larger crystalline domains. Such kinetically stable glass surfaces may be of use in applications where glassy coatings stable against heating are needed.

Nonempirical calculations of the structure and stability of ALi/sub 2k/ lithium clusters of group-two elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klimenko, N.M.; Musaev, D.G.; Gorbik, A.A.

Nonempirical Hartree-Fock calculations of the geometric and relative energetic characteristics of linear ALi/sub 2/ molecules and square ALi/sub 4/ molecules, where A = Be, Mg, Ca, and Zn, have been performed. The results for BeLi/sup +/, BeLi/sup 2/, BeLi/sub 4/, and MgLi/sub 2/ have been refined with consideration of the electron correlation in the framework of the theory of self-consistent electron pairs (SCEP). It has been shown that the stability of ALi/sub 2k/ increases with increasing size of the cluster and that the energy of the singlet-triplet transitions does not exceed 0.5-1.5 eV in all cases. The interactions between themore » atoms in the clusters have a cooperative character: the overlapping Q(Li-Li) between the Li atoms is no less significant than the overlapping Q(A-Li) between the Li atoms and the central atom A.« less

Properties of Vacancy Complexes with Hydrogen and Helium Atoms in Tungsten from First Principles

DOE PAGES

Samolyuk, German D.; Osetsky, Yury N.; Stoller, Roger E.

2016-12-03

Tungsten and its alloys are the primary candidate materials for plasma-facing components in fusion reactors. The material is exposed to high-energy neutrons and the high flux of helium and hydrogen atoms. In this paper, we have studied the properties of vacancy clusters and their interaction with H and He in W using density functional theory. Convergence of calculations with respect to modeling cell size was investigated. It is demonstrated that vacancy cluster formation energy converges with small cells with a size of 6 × 6 × 6 (432 lattice sites) enough to consider a microvoid of up to six vacanciesmore » with high accuracy. Most of the vacancy clusters containing fewer than six vacancies are unstable. Introducing He or H atoms increases their binding energy potentially making gas-filled bubbles stable. Finally, according to the results of the calculations, the H 2 molecule is unstable in clusters containing six or fewer vacancies.« less

The adsorption of helium atoms on small cationic gold clusters.

PubMed

Goulart, Marcelo; Gatchell, Michael; Kranabetter, Lorenz; Kuhn, Martin; Martini, Paul; Gitzl, Norbert; Rainer, Manuel; Postler, Johannes; Scheier, Paul; Ellis, Andrew M

2018-04-04

Adducts formed between small gold cluster cations and helium atoms are reported for the first time. These binary ions, Aun+Hem, were produced by electron ionization of helium nanodroplets doped with neutral gold clusters and were detected using mass spectrometry. For a given value of n, the distribution of ions as a function of the number of added helium atoms, m, has been recorded. Peaks with anomalously high intensities, corresponding to so-called magic number ions, are identified and interpreted in terms of the geometric structures of the underlying Aun+ ions. These features can be accounted for by planar structures for Aun+ ions with n ≤ 7, with the addition of helium having no significant effect on the structures of the underlying gold cluster ions. According to ion mobility studies and some theoretical predictions, a 3-D structure is expected for Au8+. However, the findings for Au8+ in this work are more consistent with a planar structure.

Ultracold few fermionic atoms in needle-shaped double wells: spin chains and resonating spin clusters from microscopic Hamiltonians emulated via antiferromagnetic Heisenberg and t-J models

NASA Astrophysics Data System (ADS)

Yannouleas, Constantine; Brandt, Benedikt B.; Landman, Uzi

2016-07-01

Advances with trapped ultracold atoms intensified interest in simulating complex physical phenomena, including quantum magnetism and transitions from itinerant to non-itinerant behavior. Here we show formation of antiferromagnetic ground states of few ultracold fermionic atoms in single and double well (DW) traps, through microscopic Hamiltonian exact diagonalization for two DW arrangements: (i) two linearly oriented one-dimensional, 1D, wells, and (ii) two coupled parallel wells, forming a trap of two-dimensional, 2D, nature. The spectra and spin-resolved conditional probabilities reveal for both cases, under strong repulsion, atomic spatial localization at extemporaneously created sites, forming quantum molecular magnetic structures with non-itinerant character. These findings usher future theoretical and experimental explorations into the highly correlated behavior of ultracold strongly repelling fermionic atoms in higher dimensions, beyond the fermionization physics that is strictly applicable only in the 1D case. The results for four atoms are well described with finite Heisenberg spin-chain and cluster models. The numerical simulations of three fermionic atoms in symmetric DWs reveal the emergent appearance of coupled resonating 2D Heisenberg clusters, whose emulation requires the use of a t-J-like model, akin to that used in investigations of high T c superconductivity. The highly entangled states discovered in the microscopic and model calculations of controllably detuned, asymmetric, DWs suggest three-cold-atom DW quantum computing qubits.

Prediction of the Iron-Based Polynuclear Magnetic Superhalogens with Pseudohalogen CN as Ligands.

PubMed

Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Liu, Yun; Mu, Qiang

2017-07-17

To explore stable polynuclear magnetic superhalogens, we perform an unbiased structure search for polynuclear iron-based systems based on pseudohalogen ligand CN using the CALYPSO method in conjunction with density functional theory. The superhalogen properties, magnetic properties, and thermodynamic stabilities of neutral and anionic Fe 2 (CN) 5 and Fe 3 (CN) 7 clusters are investigated. The results show that both of the clusters have superhalogen properties due to their electron affinities (EAs) and that vertical detachment energies (VDEs) are significantly larger than those of the chlorine element and their ligand CN. The distribution of the extra electron analysis indicates that the extra electron is aggregated mainly into pseudohalogen ligand CN units in Fe 2 (CN) 5 ¯ and Fe 3 (CN) 7 ¯ cluster. These features contribute significantly to their high EA and VDE. Besides superhalogen properties, these two anionic clusters carry a large magnetic moment just like the Fe 2 F 5 ¯ cluster. Additionally, the thermodynamic stabilities are also discussed by calculating the energy required to fragment the cluster into various smaller stable clusters. It is found that Fe(CN) 2 is the most favorable fragmentation product for anionic Fe 2 (CN) 5 ¯ and Fe 3 (CN) 7 ¯ clusters, and both of the anions are less stable against ejection of Fe atoms than Fe(CN) n-x .

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Rong; Wu, Yongquan, E-mail: yqwu@shu.edu.cn; Xiao, Junjiang

We observed homogeneous nucleation process of supercooled liquid Fe by molecular dynamics simulations. Using bond-orientational order parameters together with Voronoi polyhedron method, we characterized local structure, calculated the volume of Voronoi polyhedra of atoms and identified the structure and density fluctuations. We monitored the formation of nucleus and analyzed its inner structure. The birth and growth of the pre-nucleus and nucleus are accompanied with aggregating and disaggregating processes in the time scale of femtosecond. Only the initial solid-like clusters (ISLC), ranging from 1 to 7 atoms, pop up directly from liquid. The relation between the logarithm of number of clustersmore » and the cluster size was found to be linear for ISLCs and was observed to be parabolic for all solid-like clusters (SLC) due to aggregating and disaggregating effects. The nucleus and pre-nuclei mainly consist of body centered cubic (BCC) and hexagonal close packed atoms, while the BCC atoms tend to be located at the surface. Medium-range structure fluctuations induce the birth of ISLCs, benefit the aggregation of embryos and remarkably promote the nucleation. But density fluctuations contribute little to nucleation. The lifetime of most icosahedral-like atoms (ICO) is shorter than 0.7 ps. No obvious relationship was found between structure/density fluctuations and the appearance of ICO atoms.« less

Magnetic behavior of Si-Ge bond in SixGe4-x nano-clusters

NASA Astrophysics Data System (ADS)

Nahali, Masoud; Mehri, Ali

2018-06-01

The structure of SixGe4-x nano-clusters were optimized by MPW1B95 level of theory using MG3S and SDB-aug-cc-PVTZ basis set. The agreement of the calculated ionization and dissociation energies with experimental values validates the reported structures of nano-clusters and justifies the use of hybrid meta density functional method. Since the Si-Si bond is stronger than Si-Ge and Ge-Ge bonds, the Si-Si, Si-Ge, and Ge-Ge diagonal bonds determine the precedence of the stability in these nano-clusters. The hybrid meta density functional calculations were carried out to investigate the adsorption of CO on all possible SixGe4-x nano-clusters. It was found that the silicon atom generally makes a stronger bond with CO than germanium and thereby preferentially affects the shape of structures having higher multiplicity. In Si-Ge structures with higher spin more than 95% of spins accumulate on positions with less bonds to other atoms of the cluster. Through CO adsorption on these clusters bridge structures are made that behave as spin bridge which conduct the spin from the nano-cluster surface to the adsorbate atoms. A better understanding of bridged structures was achieved upon introducing the 'spin bridge' concept. Based on exhaustive spin density analysis, it was found that the reason for the extra negative charge on oxygen in the bridged structures is the relocation of spin from the surface through the bridge.

Mechanistic Details and Reactivity Descriptors in Oxidation and Acid Catalysis of Methanol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deshlahra, Prashant; Carr, Robert T.; Chai, Song-Hai

2015-02-06

Acid and redox reaction rates of CH₃OH-O₂ mixtures on polyoxometalate (POM) clusters, together with isotopic, spectroscopic, and theoretical assessments of catalyst properties and reaction pathways, were used to define rigorous descriptors of reactivity and to probe the compositional effects for oxidative dehydrogenation (ODH) and dehydration reactions. ³¹P-MAS NMR, transmission electron microscopy and titrations of protons with di-tert-butylpyridine during catalysis showed that POM clusters retained their Keggin structure upon dispersion on SiO₂ and after use in CH₃OH reactions. The effects of CH₃OH and O₂ pressures and of D-substitution on ODH rates show that C-H activation in molecularly adsorbed CH₃OH is themore » sole kinetically relevant step and leads to reduced centers as intermediates present at low coverages; their concentrations, measured from UV-vis spectra obtained during catalysis, are consistent with the effects of CH₃OH/O₂ ratios predicted from the elementary steps proposed. First-order ODH rate constants depend strongly on the addenda atoms (Mo vs W) but weakly on the central atom (P vs Si) in POM clusters, because C-H activation steps inject electrons into the lowest unoccupied molecular orbitals (LUMO) of the clusters, which are the d-orbitals at Mo⁶⁺ and W⁶⁺ centers. H-atom addition energies (HAE) at O-atoms in POM clusters represent the relevant theoretical probe of the LUMO energies and of ODH reactivity. The calculated energies of ODH transition states at each O-atom depend linearly on their HAE values with slopes near unity, as predicted for late transition states in which electron transfer and C-H cleavage are essentially complete. HAE values averaged over all accessible O-atoms in POM clusters provide the appropriate reactivity descriptor for oxides whose known structures allow accurate HAE calculations. CH₃OH dehydration proceeds via parallel pathways mediated by late carbenium-ion transition states; effects of composition on dehydration reactivity reflect changes in charge reorganizations and electrostatic forces that stabilize protons at Brønsted acid sites.« less

Interactions of small platinum clusters with the TiC(001) surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Jianjun; Li, Shasha; Chu, Xingli

2015-11-14

Density functional theory calculations are used to elucidate the interactions of small platinum clusters (Pt{sub n}, n = 1–5) with the TiC(001) surface. The results are analyzed in terms of geometric, energetic, and electronic properties. It is found that a single Pt atom prefers to be adsorbed at the C-top site, while a Pt{sub 2} cluster prefers dimerization and a Pt{sub 3} cluster forms a linear structure on the TiC(001). As for the Pt{sub 4} cluster, the three-dimensional distorted tetrahedral structure and the two-dimensional square structure almost have equal stability. In contrast with the two-dimensional isolated Pt{sub 5} cluster, the adsorbed Pt{submore » 5} cluster prefers a three-dimensional structure on TiC(001). Substantial charge transfer takes place from TiC(001) surface to the adsorbed Pt{sub n} clusters, resulting in the negatively charged Pt{sub n} clusters. At last, the d-band centers of the absorbed Pt atoms and their implications in the catalytic activity are discussed.« less

Proceedings of the NATO Advances Research Workshop on Diamond Based Composites, Saint Petersburg, Russia, June 21-22, 1997, Volume 38

DTIC Science & Technology

1997-06-01

composites. The topics ranged from molecular clusters, nanophase materials, growth, processing, and synthesis. Commercial composite materials have been on...example, an analysis of the emission from a GaAs target shows mainly (99.4%) neutral Ga and As atoms. [63] However, the fraction of molecular species...sputtered from ionic crystals can be considerably higher. [64] There is evidence that a large fraction of the molecular species originate from

Theory of Positron Annihilation in Helium-Filled Bubbles in Plutonium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sterne, P A; Pask, J E

2003-02-13

Positron annihilation lifetime spectroscopy is a sensitive probe of vacancies and voids in materials. This non-destructive measurement technique can identify the presence of specific defects in materials at the part-per-million level. Recent experiments by Asoka-Kumar et al. have identified two lifetime components in aged plutonium samples--a dominant lifetime component of around 182 ps and a longer lifetime component of around 350-400ps. This second component appears to increase with the age of the sample, and accounts for only about 5 percent of the total intensity in 35 year-old plutonium samples. First-principles calculations of positron lifetimes are now used extensively to guidemore » the interpretation of positron lifetime data. At Livermore, we have developed a first-principles finite-element-based method for calculating positron lifetimes for defects in metals. This method is capable of treating system cell sizes of several thousand atoms, allowing us to model defects in plutonium ranging in size from a mono-vacancy to helium-filled bubbles of over 1 nm in diameter. In order to identify the defects that account for the observed lifetime values, we have performed positron lifetime calculations for a set of vacancies, vacancy clusters, and helium-filled vacancy clusters in delta-plutonium. The calculations produced values of 143ps for defect-free delta-Pu and 255ps for a mono-vacancy in Pu, both of which are inconsistent with the dominant experimental lifetime component of 182ps. Larger vacancy clusters have even longer lifetimes. The observed positron lifetime is significantly shorter than the calculated lifetimes for mono-vacancies and larger vacancy clusters, indicating that open vacancy clusters are not the dominant defect in the aged plutonium samples. When helium atoms are introduced into the vacancy cluster, the positron lifetime is reduced due to the increased density of electrons available for annihilation. For a mono-vacancy in Pu containing one helium atom, the calculated lifetime is 190 ps, while a di-vacancy containing two helium atoms has a positron lifetime of 205 ps. In general, increasing the helium density in a vacancy cluster or He-filled bubble reduces the positron lifetime, so that the same lifetime value can arise fi-om a range of vacancy cluster sizes with different helium densities. In order to understand the variation of positron lifetime with vacancy cluster size and helium density in the defect, we have performed over 60 positron lifetime calculations with vacancy cluster sizes ranging from 1 to 55 vacancies and helium densities ranging fi-om zero to five helium atoms per vacancy. The results indicate that the experimental lifetime of 182 ps is consistent with the theoretical value of 190 ps for a mono-vacancy with a single helium atom, but that slightly better agreement is obtained for larger clusters of 6 or more vacancies containing 2-3 helium atoms per vacancy. For larger vacancy clusters with diameters of about 3-5 nm or more, the annihilation with helium electrons dominates the positron annihilation rate; the observed lifetime of 180ps is then consistent with a helium concentration in the range of 3 to 3.5 Hehacancy, setting an upper bound on the helium concentration in the vacancy clusters. In practice, the single lifetime component is most probably associated with a family of helium-filled bubbles rather than with a specific unique defect size. The longer 350-400ps lifetime component is consistent with a relatively narrow range of defect sizes and He concentration. At zero He concentration, the lifetime values are matched by small vacancy clusters containing 6-12 vacancies. With increasing vacancy cluster size, a small amount of He is required to keep the lifetime in the 350-400 ps range, until the value saturates for larger helium bubbles of more than 50 vacancies (bubble diameter > 1.3 nm) at a helium concentration close to 1 He/vacancy. These results, taken together with the experimental data, indicate that the features observed in TEM data by Schwartz et al are not voids, but are in fact helium-filled bubbles with a helium pressure of around 2-3 helium atoms per vacancy, depending on the bubble size. This is consistent with the conclusions of recently developed models of He-bubble growth in aged plutonium.« less

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

NASA Astrophysics Data System (ADS)

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-11-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance.

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

PubMed Central

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-01-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance. PMID:27901129

Improvements in Ionized Cluster-Beam Deposition

NASA Technical Reports Server (NTRS)

Fitzgerald, D. J.; Compton, L. E.; Pawlik, E. V.

1986-01-01

Lower temperatures result in higher purity and fewer equipment problems. In cluster-beam deposition, clusters of atoms formed by adiabatic expansion nozzle and with proper nozzle design, expanding vapor cools sufficiently to become supersaturated and form clusters of material deposited. Clusters are ionized and accelerated in electric field and then impacted on substrate where films form. Improved cluster-beam technique useful for deposition of refractory metals.

Evidence for a Catalytically and Kinetically Competent Enzyme–Substrate Cross-Linked Intermediate in Catalysis by Lipoyl Synthase

PubMed Central

2015-01-01

Lipoyl synthase (LS) catalyzes the final step in lipoyl cofactor biosynthesis: the insertion of two sulfur atoms at C6 and C8 of an (N6-octanoyl)-lysyl residue on a lipoyl carrier protein (LCP). LS is a member of the radical SAM superfamily, enzymes that use a [4Fe–4S] cluster to effect the reductive cleavage of S-adenosyl-l-methionine (SAM) to l-methionine and a 5′-deoxyadenosyl 5′-radical (5′-dA•). In the LS reaction, two equivalents of 5′-dA• are generated sequentially to abstract hydrogen atoms from C6 and C8 of the appended octanoyl group, initiating sulfur insertion at these positions. The second [4Fe–4S] cluster on LS, termed the auxiliary cluster, is proposed to be the source of the inserted sulfur atoms. Herein, we provide evidence for the formation of a covalent cross-link between LS and an LCP or synthetic peptide substrate in reactions in which insertion of the second sulfur atom is slowed significantly by deuterium substitution at C8 or by inclusion of limiting concentrations of SAM. The observation that the proteins elute simultaneously by anion-exchange chromatography but are separated by aerobic SDS-PAGE is consistent with their linkage through the auxiliary cluster that is sacrificed during turnover. Generation of the cross-linked species with a small, unlabeled (N6-octanoyl)-lysyl-containing peptide substrate allowed demonstration of both its chemical and kinetic competence, providing strong evidence that it is an intermediate in the LS reaction. Mössbauer spectroscopy of the cross-linked intermediate reveals that one of the [4Fe–4S] clusters, presumably the auxiliary cluster, is partially disassembled to a 3Fe-cluster with spectroscopic properties similar to those of reduced [3Fe–4S]0 clusters. PMID:24901788

Molecular Mechanisms in the shock induced decomposition of FOX-7

NASA Astrophysics Data System (ADS)

Mishra, Ankit; Tiwari, Subodh C.; Nakano, Aiichiro; Vashishta, Priya; Kalia, Rajiv; CACS Team

Experimental and first principle computational studies on FOX 7 have either involved a very small system consisting of a few atoms or they did not take into account the decomposition mechanisms under extreme conditions of temperature and pressure. We have performed a large-scale reactive MD simulation using ReaxFF-lg force field to study the shock decomposition of FOX 7. The chemical composition of the principal decomposition products correlates well with experimental observations. Furthermore, we observed that the production of N2 and H2O was inter molecular in nature and was through different chemical pathways. Moreover, the production of CO and CO2 was delayed due to production of large stable C,O atoms cluster. These critical insights into the initial processes involved in the shock induced decomposition of FOX-7 will greatly help in understanding the factors playing an important role in the insensitiveness of this high energy material. This research is supported by AFOSR Award No. FA9550-16-1-0042.

Methanol Oxidative Dehydrogenation on Oxide Catalysts: Molecular and Dissociative Routes and Hydrogen Addition Energies as Descriptors of Reactivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deshlahra, Prashant; Iglesia, Enrique

The oxidative dehydrogenation (ODH) of alkanols on oxide catalysts is generally described as involving H-abstraction from alkoxy species formed via O–H dissociation. Kinetic and isotopic data cannot discern between such routes and those involving kinetically-relevant H-abstraction from undissociated alkanols. Here, we combine such experiments with theoretical estimates of activation energies and entropies to show that the latter molecular routes prevail over dissociative routes for methanol reactions on polyoxometalate (POM) clusters at all practical reaction temperatures. The stability of the late transition states that mediate H-abstraction depend predominantly on the stability of the O–H bond formed, making H-addition energies (HAE) accuratemore » and single-valued descriptors of reactivity. Density functional theory-derived activation energies depend linearly on HAE values at each O-atom location on clusters with a range of composition (H3PMo12, H4SiMo12, H3PW12, H4PV1Mo11, and H4PV1W11); both barriers and HAE values reflect the lowest unoccupied molecular orbital energy of metal centers that accept the electron and the protonation energy of O-atoms that accept the proton involved in the H-atom transfer. Bridging O-atoms form O–H bonds that are stronger than those of terminal atoms and therefore exhibit more negative HAE values and higher ODH reactivity on all POM clusters. For each cluster composition, ODH turnover rates reflect the reactivity-averaged HAE of all accessible O-atoms, which can be evaluated for each cluster composition to provide a rigorous and accurate predictor of ODH reactivity for catalysts with known structure. These relations together with oxidation reactivity measurements can then be used to estimate HAE values and to infer plausible structures for catalysts with uncertain active site structures.« less

Carbon atom and cluster sputtering under low-energy noble gas plasma bombardment

NASA Astrophysics Data System (ADS)

Oyarzabal, E.; Doerner, R. P.; Shimada, M.; Tynan, G. R.

2008-08-01

Exit-angle resolved carbon atom and cluster (C2 and C3) sputtering yields are measured during different noble gas (Xe, Kr, Ar, Ne, and He) ion bombardments from a plasma, for low incident energies (75-225 eV). A quadrupole mass spectrometer (QMS) is used to detect the fraction of sputtered neutrals that is ionized in the plasma and to obtain the angular distribution by changing the angle between the target normal and the QMS aperture. A one-dimensional Monte Carlo code is used to simulate the interaction of the plasma and the sputtered particles in the region between the sample and the QMS. The effective elastic scattering cross sections of C, C2, and C3 with the different bombarding gas neutrals are obtained by varying the distance between the sample and the QMS and by performing a best fit of the simulation results to the experimental results. The total sputtering yield (C+C2+C3) for each bombarding gas is obtained from weight-loss measurements and the sputtering yield for C, C2, and C3 is then calculated from the integration of the measured angular distribution, taking into account the scattering and ionization of the sputtered particles between the sample and the QMS. We observe undercosine angular distributions of the sputtered atoms and clusters for all the studied bombarding gases and a clear decrease of the atom to cluster (C2 and C3) sputtering ratio as the incident ion mass increases, changing from a carbon atom preferential erosion for the lower incident ion masses (He, Ne, and Ar) to a cluster preferential erosion for the higher incident ion masses (Kr and Xe).

Antibody-gold cluster conjugates

DOEpatents

Hainfeld, J.F.

1988-06-28

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be about 5.0 nm. Methods and reagents are disclosed in which antibodies or Fab' fragments thereof are covalently bound to a stable cluster of gold atoms. 2 figs.

Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis.

PubMed

Demerdash, Omar N A; Mitchell, Julie C

2012-07-01

Normal mode analysis has emerged as a useful technique for investigating protein motions on long time scales. This is largely due to the advent of coarse-graining techniques, particularly Hooke's Law-based potentials and the rotational-translational blocking (RTB) method for reducing the size of the force-constant matrix, the Hessian. Here we present a new method for domain decomposition for use in RTB that is based on hierarchical clustering of atomic density gradients, which we call Density-Cluster RTB (DCRTB). The method reduces the number of degrees of freedom by 85-90% compared with the standard blocking approaches. We compared the normal modes from DCRTB against standard RTB using 1-4 residues in sequence in a single block, with good agreement between the two methods. We also show that Density-Cluster RTB and standard RTB perform well in capturing the experimentally determined direction of conformational change. Significantly, we report superior correlation of DCRTB with B-factors compared with 1-4 residue per block RTB. Finally, we show significant reduction in computational cost for Density-Cluster RTB that is nearly 100-fold for many examples. Copyright © 2012 Wiley Periodicals, Inc.

The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

NASA Astrophysics Data System (ADS)

Förner, Wolfgang

1992-03-01

Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

Understanding the detection of carbon in austenitic high-Mn steel using atom probe tomography.

PubMed

Marceau, R K W; Choi, P; Raabe, D

2013-09-01

A high-Mn TWIP steel having composition Fe-22Mn-0.6C (wt%) is considered in this study, where the need for accurate and quantitative analysis of clustering and short-range ordering by atom probe analysis requires a better understanding of the detection of carbon in this system. Experimental measurements reveal that a high percentage of carbon atoms are detected as molecular ion species and on multiple hit events, which is discussed with respect to issues such as optimal experimental parameters, correlated field evaporation and directional walk/migration of carbon atoms at the surface of the specimen tip during analysis. These phenomena impact the compositional and spatial accuracy of the atom probe measurement and thus require careful consideration for further cluster-finding analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

The First Non-Dispersive High-Resolution Spectroscopy of an X-ray-bright Galaxy Cluster

NASA Astrophysics Data System (ADS)

Yamaguchi, Hiroya; Hitomi Collaboration

2018-06-01

The Hitomi X-ray Observatory was equipped with the Soft X-ray Spectrometer (SXS), an X-ray microcalorimeter that achieved an energy resolution of 5 eV (@0.5-10 keV) for extended objects. This offered an unprecedented benchmark of atomic modeling and database for hot collisional plasmas, revealing both successes and challenges in the current atomic codes that are widely used by the X-ray astronomy community. I will review the Hitomi observations of the brightest part of the Perseus Cluster, whose X-ray spectrum is dominated by thermal emission from the intra-cluster medium (ICM). The SXS successfully measured the turbulent velocities and metal abundances of the ICM, which radically altered our understanding of the dynamics and chemical enrichment in this object. At the same time, the high-resolution X-ray data led to significant improvement in the atomic models, such as AtomDB and SPEX -- I will briefly overview how this improvement was made. Nevertheless, there are still significant discrepancies among the public atomic models, causing systematic uncertainties in measurements of the temperature, abundance, and degree of the resonance scattering. Requirements for future improvements will be summarized in this context.

Effect of local structures on crystallization in deeply undercooled metallic glass-forming liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, S. Q.; Li, M. Z., E-mail: maozhili@ruc.edu.cn; Wu, Z. W.

2016-04-21

The crystallization mechanism in deeply undercooled ZrCu metallic glass-forming liquids was investigated via molecular dynamics simulations. It was found that the crystallization process is mainly controlled by the growth of crystal nuclei formed by the BCC-like atomic clusters, consistent with experimental speculations. The crystallization rate is found to relate to the number of growing crystal nuclei in the crystallization process. The crystallization rate in systems with more crystal nuclei is significantly hindered by the larger surface fractions of crystal nuclei and their different crystalline orientations. It is further revealed that in the crystallization in deeply undercooled regions, the BCC-like crystalmore » nuclei are formed from the inside of the precursors formed by the FCC-like atomic clusters, and growing at the expense of the precursors. Meanwhile, the precursors are expanding at the expense of the outside atomic clusters. This process is consistent with the so-called Ostwald step rule. The atomic structures of metallic glasses are found to have significant impact on the subsequent crystallization process. In the Zr{sub 85}Cu{sub 15} system, the stronger spatial correlation of Cu atoms could hinder the crystallization processes in deeply undercooled regions.« less

Candicidin Biosynthesis Gene Cluster Is Widely Distributed among Streptomyces spp. Isolated from the Sediments and the Neuston Layer of the Trondheim Fjord, Norway▿ †

PubMed Central

Jørgensen, Hanne; Fjærvik, Espen; Hakvåg, Sigrid; Bruheim, Per; Bredholt, Harald; Klinkenberg, Geir; Ellingsen, Trond E.; Zotchev, Sergey B.

2009-01-01

A large number of Streptomyces bacteria with antifungal activity isolated from samples collected in the Trondheim fjord (Norway) were found to produce polyene compounds. Investigation of polyene-containing extracts revealed that most of the isolates produced the same compound, which had an atomic mass and UV spectrum corresponding to those of candicidin D. The morphological diversity of these isolates prompted us to speculate about the involvement of a mobile genetic element in dissemination of the candicidin biosynthesis gene cluster (can). Eight candicidin-producing isolates were analyzed by performing a 16S rRNA gene-based taxonomic analysis, pulsed-field gel electrophoresis, PCR, and Southern blot hybridization with can-specific probes. These analyses revealed that most of the isolates were related, although they were morphologically diverse, and that all of them contained can genes. The majority of the isolates studied contained large plasmids, and two can-specific probes hybridized to a 250-kb plasmid in one isolate. Incubation of the latter isolate at a high temperature resulted in loss of the can genes and candicidin production, while mating of the “cured” strain with a plasmid-containing donor restored candicidin production. The latter result suggested that the 250-kb plasmid contains the complete can gene cluster and could be responsible for conjugative transfer of this cluster to other streptomycetes. PMID:19286787

DFT STUDY OF CO AND NO ADSORPTION ON BORON NITRIDE (BN)n = 3 - 5 NANOCLUSTERS

NASA Astrophysics Data System (ADS)

Zahedi, Ehsan; Pangh, Abdolhakim; Ghorbanpour, Hamed

2015-11-01

Interaction of CO and NO molecules by different orientations on (BN)n=3-5 clusters have been studied at the B3LYP/6-311+G* level of theory. Total electronic energies have been corrected for geometrical counterpoise (gCP) and dispersion (D3) energies at the B3LYP/6-31G* level. Formation of a new sigma bond between the gas and (BN)3 cluster, atom in molecules (AIM) results, density of states spectrums (DOS), molecular electrostatic potential (MEP) surfaces, and visualization of wave function of molecular orbitals in the nearest bonding regions to the Fermi level have confirmed that adsorption of CO by carbon end atom, and NO by nitrogen end atom is covalent in nature, so that the charge transfer is occurred from gas molecule to the cluster.

Study on the structural transition of CoNi nanoclusters using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Xia, J. H.; Gao, Xue-Mei

2018-04-01

In this work, the segregation and structural transitions of CoNi clusters, between 1500 and 300 K, have been investigated using molecular dynamics simulations with the embedded atom method potential. The radial distribution function was used to analyze the segregation during the cooling processes. It is found that Co atoms segregate to the inside and Ni atoms preferably to the surface during the cooling processes, the Co147Ni414 cluster becomes a core-shell structure. We discuss the structural transition according to the pair-correction function and pair-analysis technique, and finally the liquid Co147Ni414 crystallizes into the coexistence of hcp and fcc structure at 300 K. At the same time, it is found that the frozen structure of CoNi cluster is strongly related to the Co concentration.

First principles calculations for interaction of tyrosine with (ZnO)3 cluster

NASA Astrophysics Data System (ADS)

Singh, Satvinder; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

2018-04-01

First Principles Calculations have been performed to study interactions of Phenol ring of Tyrosine (C6H5OH) with (ZnO)3 atomic cluster. All the calculations have been performed under the Density Functional Theory (DFT) framework. Structural and electronic properties of (ZnO)3/C6H5OH have been studied. Gaussian basis set approach has been adopted for the calculations. A ring type most stable (ZnO)3 atomic cluster has been modeled, analyzed and used for the calculations. The compatibility of the results with previous studies has been presented here.

Synthesis of Two-Electron Bimetallic Cu-Ag and Cu-Au Clusters by using [Cu13 (S2 CNn Bu2 )6 (C≡CPh)4 ]+ as a Template.

PubMed

Silalahi, Rhone P Brocha; Chakrahari, Kiran Kumarvarma; Liao, Jian-Hong; Kahlal, Samia; Liu, Yu-Chiao; Chiang, Ming-Hsi; Saillard, Jean-Yves; Liu, C W

2018-03-02

Atomically precise Cu-rich bimetallic superatom clusters have been synthesized by adopting a galvanic exchange strategy. [Cu@Cu 12 (S 2 CN n Bu 2 ) 6 (C≡CPh) 4 ][CuCl 2 ] (1) was used as a template to generate compositionally uniform clusters [M@Cu 12 (S 2 CN n Bu 2 ) 6 (C≡CPh) 4 ][CuCl 2 ], where M=Ag (2), Au (3). Structures of 1, 2 and 3 were determined by single crystal X-ray diffraction and the results were supported by ESI-MS. The anatomies of clusters 1-3 are very similar, with a centred cuboctahedral cationic core that is surrounded by six di-butyldithiocarbamate (dtc) and four phenylacetylide ligands. The doped Ag and Au atoms were found to preferentially occupy the centre of the 13-atom cuboctahedral core. Experimental and theoretical analyses of the synthesized clusters revealed that both Ag and Au doping result in significant changes in cluster stability, optical characteristics and enhancement in luminescence properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photofragment slice imaging studies of pyrrole and the Xe{center_dot}{center_dot}{center_dot}pyrrole cluster

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rubio-Lago, L.; Zaouris, D.; Sakellariou, Y.

The photolysis of pyrrole has been studied in a molecular beam at wavelengths of 250, 240, and 193.3 nm, using two different carrier gases, He and Xe. A broad bimodal distribution of H-atom fragment velocities has been observed at all wavelengths. Near threshold at both 240 and 250 nm, sharp features have been observed in the fast part of the H-atom distribution. Under appropriate molecular beam conditions, the entire H-atom loss signal from the photolysis of pyrrole at both 240 and 250 nm (including the sharp features) disappear when using Xe as opposed to He as the carrier gas. Wemore » attribute this phenomenon to cluster formation between Xe and pyrrole, and this assumption is supported by the observation of resonance enhanced multiphoton ionization spectra for the (Xe{center_dot}{center_dot}{center_dot}pyrrole) cluster followed by photofragmentation of the nascent cation cluster. Ab initio calculations are presented for the ground states of the neutral and cationic (Xe{center_dot}{center_dot}{center_dot}pyrrole) clusters as a means of understanding their structural and energetic properties.« less

Study of clusters using negative ion photodetachment spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Yuexing

1995-12-01

The weak van der Waals interaction between an open-shell halogen atom and a closed-shell atom or molecule has been investigated using zero electron kinetic energy (ZEKE) spectroscopy. This technique is also applied to study the low-lying electronic states in GaAs and GaAs -. In addition, the spectroscopy and electron detachment dynamics of several small carbon cluster anions are studied using resonant multiphoton detachment spectroscopy.

Infrared Multiple Photon Dissociation Spectroscopy Of Metal Cluster-Adducts

NASA Astrophysics Data System (ADS)

Cox, D. M.; Kaldor, A.; Zakin, M. R.

1987-01-01

Recent development of the laser vaporization technique combined with mass-selective detection has made possible new studies of the fundamental chemical and physical properties of unsupported transition metal clusters as a function of the number of constituent atoms. A variety of experimental techniques have been developed in our laboratory to measure ionization threshold energies, magnetic moments, and gas phase reactivity of clusters. However, studies have so far been unable to determine the cluster structure or the chemical state of chemisorbed species on gas phase clusters. The application of infrared multiple photon dissociation IRMPD to obtain the IR absorption properties of metal cluster-adsorbate species in a molecular beam is described here. Specifically using a high power, pulsed CO2 laser as the infrared source, the IRMPD spectrum for methanol chemisorbed on small iron clusters is measured as a function of the number of both iron atoms and methanols in the complex for different methanol isotopes. Both the feasibility and potential utility of IRMPD for characterizing metal cluster-adsorbate interactions are demonstrated. The method is generally applicable to any cluster or cluster-adsorbate system dependent only upon the availability of appropriate high power infrared sources.

Application of a parallel genetic algorithm to the global optimization of medium-sized Au-Pd sub-nanometre clusters

NASA Astrophysics Data System (ADS)

Hussein, Heider A.; Demiroglu, Ilker; Johnston, Roy L.

2018-02-01

To contribute to the discussion of the high activity and reactivity of Au-Pd system, we have adopted the BPGA-DFT approach to study the structural and energetic properties of medium-sized Au-Pd sub-nanometre clusters with 11-18 atoms. We have examined the structural behaviour and stability as a function of cluster size and composition. The study suggests 2D-3D crossover points for pure Au clusters at 14 and 16 atoms, whereas pure Pd clusters are all found to be 3D. For Au-Pd nanoalloys, the role of cluster size and the influence of doping were found to be extensive and non-monotonic in altering cluster structures. Various stability criteria (e.g. binding energies, second differences in energy, and mixing energies) are used to evaluate the energetics, structures, and tendency of segregation in sub-nanometre Au-Pd clusters. HOMO-LUMO gaps were calculated to give additional information on cluster stability and a systematic homotop search was used to evaluate the energies of the generated global minima of mono-substituted clusters and the preferred doping sites, as well as confirming the validity of the BPGA-DFT approach.

Evaluation of effervescent atomizer internal design on the spray unsteadiness using a phase/Doppler particle analyzer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Meng; Duan, YuFeng; Zhang, TieNan

2010-09-15

The purpose of this research was to investigate the dependence of effervescent spray unsteadiness on operational conditions and atomizer internal design by the ideal spray theory of Edwards and Marx. The convergent-divergent effervescent atomizer spraying water with air as atomizing medium in the ''outside-in'' gas injection was used in this study. Results demonstrated that droplet formation process at various air to liquid ratio (ALR) led to the spray unsteadiness and all droplet size classes exhibited unsteadiness behavior in spray. The spray unsteadiness reduced quickly at ALR of 3% and decreased moderately at ALR of other values as the axial distancemore » increased. When the axial distance was 200 mm, the spray unsteadiness reduced dramatically with the increase in radial distance, but lower spray unsteadiness at the center of spray and higher spray unsteadiness at the edge of spray were shown as the axial distance increased. The spray unsteadiness at the center region of spray increased with the injection pressure. Low spray unsteadiness and good atomization performance can be obtained when the diameter of incline aeration holes increased at ALR of 10%. Although short mixing chamber with large discharge orifice diameter for convergent-divergent effervescent atomizer produced good atomization, the center region of spay showed high spray unsteadiness and maybe formed the droplet clustering. (author)« less

A cluster expansion model for predicting activation barrier of atomic processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rehman, Tafizur; Jaipal, M.; Chatterjee, Abhijit, E-mail: achatter@iitk.ac.in

2013-06-15

We introduce a procedure based on cluster expansion models for predicting the activation barrier of atomic processes encountered while studying the dynamics of a material system using the kinetic Monte Carlo (KMC) method. Starting with an interatomic potential description, a mathematical derivation is presented to show that the local environment dependence of the activation barrier can be captured using cluster interaction models. Next, we develop a systematic procedure for training the cluster interaction model on-the-fly, which involves: (i) obtaining activation barriers for handful local environments using nudged elastic band (NEB) calculations, (ii) identifying the local environment by analyzing the NEBmore » results, and (iii) estimating the cluster interaction model parameters from the activation barrier data. Once a cluster expansion model has been trained, it is used to predict activation barriers without requiring any additional NEB calculations. Numerical studies are performed to validate the cluster expansion model by studying hop processes in Ag/Ag(100). We show that the use of cluster expansion model with KMC enables efficient generation of an accurate process rate catalog.« less

Molybdenum and carbon atom and carbon cluster sputtering under low-energy noble gas plasma bombardment

NASA Astrophysics Data System (ADS)

Oyarzabal, Eider

Exit-angle resolved Mo atom sputtering yield under Xe ion bombardment and carbon atom and cluster (C2 and C3) sputtering yields under Xe, Kr, Ar, Ne and He ion bombardment from a plasma are measured for low incident energies (75--225 eV). An energy-resolved quadrupole mass spectrometer (QMS) is used to detect the fraction of un-scattered sputtered neutrals that become ionized in the plasma; the angular distribution is obtained by changing the angle between the target and the QMS aperture. A one-dimensional Monte Carlo code is used to simulate the interaction of the plasma and the sputtered particles between the sample and the QMS. The elastic scattering cross-sections of C, C2 and C3 with the different bombarding gas neutrals is obtained by varying the distance between the sample and the QMS and by performing a best fit of the simulation results to the experimental results. Because the results obtained with the QMS are relative, the Mo atom sputtering results are normalized to the existing data in the literature and the total sputtering yield for carbon (C+C 2+C3) for each bombarding gas is obtained from weight loss measurements. The absolute sputtering yield for C, C2 and C 3 is then calculated from the integration of the measured angular distribution, taking into account the scattering and ionization of the sputtered particles between the sample and the QMS. The angular sputtering distribution for Mo has a maximum at theta=60°, and this maximum becomes less pronounced as the incident ion energy increases. The results of the Monte Carlo TRIDYN code simulation for the angular distribution of Mo atoms sputtered by Xe bombardment are in agreement with the experiments. For carbon sputtering under-cosine angular distributions of the sputtered atoms and clusters for all the studied bombarding gases are also observed. The C, C2 and C3 sputtering yield data shows a clear decrease of the atom to cluster (C/C2 and C/C3) sputtering ratio as the incident ion mass increases, changing from a carbon atom preferential erosion for the lower incident ion masses (He, Ne and Ar) to a cluster preferential erosion for the higher incident ion masses (Kr and Xe).

The role of silicon, vacancies, and strain in carbon distribution for low temperature bainite

DOE PAGES

Sampath, S.; Rementeria, R.; Huang, X.; ...

2016-02-19

Here, we investigated the phenomenon of carbon supersaturation and carbon clustering in bainitic ferrite with atom probe tomography (APT) and ab-initio density functional theory (DFT) calculations. The experimental results show a homogeneous distribution of silicon in the microstructure, which contains both ferrite and retained austenite. This distribution is mimicked well by the computational approach. In addition, an accumulation of C in certain regions of the bainitic ferrite with C concentrations up to 13 at % is observed. Based on the DFT results, these clusters are explained as strained, tetragonal regions in the ferritic bainite, in which the solution enthalpy ofmore » C can reach large, negative values. It seems that Si itself only has a minor influence on this phenomenon.« less

In Situ Scanning Tunneling Microscopy Topography Changes of Gold (111) in Aqueous Sulfuric Acid Produced by Electrochemical Surface Oxidation and Reduction and Relaxation Phenomena

NASA Astrophysics Data System (ADS)

Pasquale, M. A.; Nieto, F. J. Rodríguez; Arvia, A. J.

The electrochemical formation and reduction of O-layers on gold (111) films in 1 m sulfuric acid under different potentiodynamic routines are investigated utilizing in situ scanning tunneling microscopy. The surface dynamics is interpreted considering the anodic and cathodic reaction pathways recently proposed complemented with concurrent relaxation phenomena occurring after gold (111) lattice mild disruption (one gold atom deep) and moderate disruption (several atoms deep). The dynamics of both oxidized and reduced gold topographies depends on the potentiodynamic routine utilized to form OH/O surface species. The topography resulting from a mild oxidative disruption is dominated by quasi-2D holes and hillocks of the order of 5 nm, involving about 500-600 gold atoms each, and their coalescence. A cooperative turnover process at the O-layer, in which the anion ad-layer and interfacial water play a key role, determines the oxidized surface topography. The reduction of these O-layers results in gold clusters, their features depending on the applied potential routine. A moderate oxidative disruption produces a surface topography of hillocks and holes several gold atoms high and deep, respectively. The subsequent reduction leads to a spinodal gold pattern. Concurrent coalescence appears to be the result of an Ostwald ripening that involves the surface diffusion of both gold atoms and clusters. These processes produce an increase in surface roughness and an incipient gold faceting. The dynamics of different topographies can be qualitatively explained employing the arguments from colloidal science theory. For 1.1 V ≤ E ≅ Epzc weak electrostatic repulsions favor gold atom/cluster coalescence, whereas for E < Epzc the attenuated electrostatic repulsions among gold surfaces stabilize small clusters over the substrate producing string-like patterns.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chezhina, N.V., E-mail: chezhina@nc2490.spb.edu; Korolev, D.A.; Zhuk, N.A.

On the basis of the results of magnetic susceptibility and ESR studies of the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions iron atoms in the solid solutions of cubic modification of bismuth niobate were found to exist as Fe(III) monomers and exchange bound Fe(III)-O-Fe(III) dimers with antiferro- and ferromagnetic type of superexchange. The exchange parameters and the distribution of monomers and dimers in the solid solutions were calculated as a function of paramagnetic atom content. - Graphical abstract: The study of the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions showed that the introduction of iron atoms into the structure ofmore » Bi{sub 3}NbO{sub 7} stabilizes the cubic structure of bismuth niobate making the phase transition tetragonal ↔ cubic structure irreversible. In the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions we observe the formation of dimers with antiferro- and ferromagnetic exchange. Such clusters are partially retained even at the infinite dilution of the solid solution, which testifies for their rigidity. A sufficiently high parameter of ferromagnetic exchange in a dimer (+53 cm{sup −1}) seems to result from iron atoms being located in the vicinity of oxygen vacancy. - Highlights: • The reversible transition cubic – tetragonal modifications in Bi{sub 3}NbO{sub 7} becomes irreversible. • Only cubic modification of Bi{sub 3}Nb{sub 1-x}Fe{sub x}O{sub 7-δ} is stable due to clusters of Fe atoms. • These clusters are sufficiently strong and retained even at the infinite dilution. • The calculations of magnetic susceptibility give the distribution of the clusters and single atoms.« less

Investigation on structure, electronic and magnetic properties of Cr doped (ZnO)12 clusters: First-principles calculations

NASA Astrophysics Data System (ADS)

Liu, Huan; Zhang, Jian-Min

2018-05-01

The structural, electronic, and magnetic properties of (ZnO)12 clusters doped with Cr atoms have been investigated by using spin-polarized first-principles calculations. The exohedral a3 isomer is favorable than endohedral a2 isomer. The isomer a1 and a5 respectively have the narrowest and biggest gap between highest unoccupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO) of 0.473 and 1.291 eV among these five monodoped isomers. The magnetic moment may be related to the local environment around the Cr atom that the a2 isomer whose total magnetic moment is 6 μB while the other monodoped isomers which all isomers have nearly total magnetic moments 4 μB . For Cr-doped (ZnO)12 on a1 or a3 isomer, the DOS of spin-up channel cross the Fermi level EF showing a finite magnitude near the Fermi level which might be useful for half metallic character. For the bidoped cases, the exohedral isomers are found to be most favorable. Including all bipoed isomers of substitutional, exohedral and endohedral bidoped clusters, the total magnetic moment of the ferromagnetic (antiferromagnetic) state is 8 (0) μB and the HOMO-LUMO gap of antiferromagnetic state is slightly larger than that of ferromagnetic state. The magnetic coupling between the Cr atoms in bidoped configurations is mainly governed by the competition between direct Cr and Cr atoms antiferromagnetic interaction and the ferromagnetic interaction between two Cr atoms via O atom due to strong p-d hybridization. Most importantly, we show that the exohedral bidoped (ZnO)12 clusters favor the ferromagnetic state, which may have the future applications in spin-dependent magneto-optical and magneto-electrical devices.

Star-like superalkali cations featuring planar pentacoordinate carbon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Jin-Chang; Tian, Wen-Juan; Zhao, Xue-Feng

Superalkali cations, known to possess low vertical electron affinities (VEAs), high vertical detachment energies, and large highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, are intriguing chemical species. Thermodynamically, such species need to be the global minima in order to serve as the promising targets for experimental realization. In this work, we propose the strategies of polyhalogenation and polyalkalination for designing the superalkali cations. By applying these strategies, the local-minimum planar pentacoordinate carbon (ppC) cluster CBe{sub 5} can be modified to form a series of star-like superalkali ppC or quasi-ppC CBe{sub 5}X{sub 5}{sup +} (X = F,more » Cl, Br, Li, Na, K) cations containing a CBe{sub 5} moiety. Polyhalogenation and polyalkalination on the CBe{sub 5} unit may help eliminate the high reactivity of bare CBe{sub 5} molecule by covering the reactive Be atoms with noble halogen anions and alkali cations. Computational exploration of the potential energy surfaces reveals that the star-like ppC or quasi-ppC CBe{sub 5}X{sub 5}{sup +} (X = F, Cl, Br, Li, Na, K) clusters are the true global minima of the systems. The predicted VEAs for CBe{sub 5}X{sub 5}{sup +} range from 3.01 to 3.71 eV for X = F, Cl, Br and 2.12–2.51 eV for X = Li, Na, K, being below the lower bound of the atomic ionization potential of 3.89 eV in the periodic table. Large HOMO-LUMO energy gaps are also revealed for the species: 10.76–11.07 eV for X = F, Cl, Br and 4.99–6.91 eV for X = Li, Na, K. These designer clusters represent the first series of superalkali cations with a ppC center. Bonding analyses show five Be–X–Be three-center two-electron (3c-2e) σ bonds for the peripheral bonding, whereas the central C atom is associated with one 6c-2e π bond and three 6c-2e σ bonds, rendering (π and σ) double aromaticity. Born-Oppenheimer molecular dynamics simulations indicate that the CBe{sub 5} motif is robust in the clusters. As planar hypercoordination carbon species are often thermodynamically unstable and highly reactive, the superalkali cation characters of these ppC species should be highlighted, which may be suitable for experimental realization.« less

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oka, Yurie, E-mail: ok-yu@fuji.waseda.jp; Yanao, Tomohiro, E-mail: yanao@waseda.jp; Koon, Wang Sang, E-mail: koon@cds.caltech.edu

2015-04-07

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internalmore » centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.« less

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

NASA Astrophysics Data System (ADS)

Oka, Yurie; Yanao, Tomohiro; Koon, Wang Sang

2015-04-01

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internal centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

PubMed

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-06-15

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).

Aggregation Number in Water/n-Hexanol Molecular Clusters Formed in Cyclohexane at Different Water/n-Hexanol/Cyclohexane Compositions Calculated by Titration 1H NMR.

PubMed

Flores, Mario E; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

2017-11-09

Upon titration of n-hexanol/cyclohexane mixtures of different molar compositions with water, water/n-hexanol clusters are formed in cyclohexane. Here, we develop a new method to estimate the water and n-hexanol aggregation numbers in the clusters that combines integration analysis in one-dimensional 1 H NMR spectra, diffusion coefficients calculated by diffusion-ordered NMR spectroscopy, and further application of the Stokes-Einstein equation to calculate the hydrodynamic volume of the clusters. Aggregation numbers of 5-15 molecules of n-hexanol per cluster in the absence of water were observed in the whole range of n-hexanol/cyclohexane molar fractions studied. After saturation with water, aggregation numbers of 6-13 n-hexanol and 0.5-5 water molecules per cluster were found. O-H and O-O atom distances related to hydrogen bonds between donor/acceptor molecules were theoretically calculated using density functional theory. The results show that at low n-hexanol molar fractions, where a robust hydrogen-bond network is held between n-hexanol molecules, addition of water makes the intermolecular O-O atom distance shorter, reinforcing molecular association in the clusters, whereas at high n-hexanol molar fractions, where dipole-dipole interactions dominate, addition of water makes the intermolecular O-O atom distance longer, weakening the cluster structure. This correlates with experimental NMR results, which show an increase in the size and aggregation number in the clusters upon addition of water at low n-hexanol molar fractions, and a decrease of these magnitudes at high n-hexanol molar fractions. In addition, water produces an increase in the proton exchange rate between donor/acceptor molecules at all n-hexanol molar fractions.

Atomistic Interrogation of B–N Co-dopant Structures and Their Electronic Effects in Graphene

DOE PAGES

Schiros, Theanne; Nordlund, Dennis; Palova, Lucia; ...

2016-06-21

Chemical doping has been demonstrated to be an effective method for producing high-quality, large-area graphene with controlled carrier concentrations and an atomically tailored work function. Furthermore, the emergent optoelectronic properties and surface reactivity of carbon nanostructures are dictated by the microstructure of atomic dopants. Co-doping of graphene with boron and nitrogen offers the possibility to further tune the electronic properties of graphene at the atomic level, potentially creating p- and n-type domains in a single carbon sheet, opening a gap between valence and conduction bands in the 2-D semimetal. When using a suite of high-resolution synchrotron-based X-ray techniques, scanning tunnelingmore » microscopy, and density functional theory based computation we visualize and characterize B–N dopant bond structures and their electronic effects at the atomic level in single-layer graphene grown on a copper substrate. We find there is a thermodynamic driving force for B and N atoms to cluster into BNC structures in graphene, rather than randomly distribute into isolated B and N graphitic dopants, although under the present growth conditions, kinetics limit segregation of large B–N domains. We also observe that the doping effect of these BNC structures, which open a small band gap in graphene, follows the B:N ratio (B > N, p-type; B < N, n-type; B=N, neutral). We attribute this to the comparable electron-withdrawing and -donating effects, respectively, of individual graphitic B and N dopants, although local electrostatics also play a role in the work function change.« less

Theoretical and experimental insights into the origin of the catalytic activity of subnanometric gold clusters: attempts to predict reactivity with clusters and nanoparticles of gold.

PubMed

Boronat, Mercedes; Leyva-Pérez, Antonio; Corma, Avelino

2014-03-18

Particle size is one of the key parameters determining the unexpected catalytic activity of gold, with reactivity improving as the particle gets smaller. While this is valid in the 1-5 nm range, chemists are now investigating the influence of particle size in the subnanometer regime. This is due to recent advances in both characterization techniques and synthetic routes capable of stabilizing these size-controlled gold clusters. Researchers reported in early studies that small clusters or aggregates of a few atoms can be extremely active in some reactions, while 1-2 nm nanoparticles are catalytically more efficient for other reactions. Furthermore, the possibility that small gold clusters generated in situ from gold salts or complexes could be the real active species in homogeneous gold-catalyzed organic reactions should be considered. In this Account, we address two questions. First, what is the origin of the enhanced reactivity of gold clusters on the subnanometer scale? And second, how can we predict the reactions where small clusters should work better than larger nanoparticles? Both geometric factors and electronic or quantum size effects become important in the subnanometer regime. Geometric reasons play a key role in hydrogenation reactions, where only accessible low coordinated neutral Au atoms are needed to dissociate H2. The quantum size effects of gold clusters are important as well, as clusters formed by only a few atoms have discrete molecule-like electronic states and their chemical reactivity is related to interactions between the cluster's frontier molecular orbitals and those of the reactant molecules. From first principles calculations, we predict an enhanced reactivity of small planar clusters for reactions involving activation of CC multiple bonds in alkenes and alkynes through Lewis acid-base interactions, and a better catalytic performance of 3D gold nanoparticles in redox reactions involving bond dissociation by oxidative addition and new bond formation by reductive elimination. In oxidation reactions with molecular O2, initial dissociation of O2 into basic oxygen atoms would be more effectively catalyzed by gold nanoparticles of ∼1 nm diameter. In contrast, small planar clusters should be more active for reactions following a radical pathway involving peroxo or hydroperoxo intermediates. We have experimentally confirmed these predictions for a series of Lewis acid and oxidation reactions catalyzed by gold clusters and nanoparticles either in solution or supported on solid carriers.

Theoretical studies on the electronic structures and photoelectron spectra of tri-rhenium oxide clusters: Re3O(n)(-) and Re3O(n) (n=1-6).

PubMed

Zhou, Qi; Gong, Wei-Chao; Xie, Lu; Zheng, Cun-Gong; Zhang, Wei; Wang, Bin; Zhang, Yong-Fan; Huang, Xin

2014-01-03

Density functional theory (DFT) calculations are performed to study the structural and electronic properties of tri-rhenium oxide clusters Re3On(-/0) (n=1-6). Generalized Koopmans' theorem is applied to predict the vertical detachment energies (VDEs) and simulate the photoelectron spectra (PES). Theoretical calculations at the B3LYP level are carried out to search for the global minima for both the anions and the neutrals. For the anions, the first two O atoms prefer the same corner position of a Re3 triangle. Whereas, Re3O3(-) possesses a C2v symmetry with one bridging and two terminal O atoms. The next three O atoms (n=4-6) are adding sequentially on the basis of Re3O3(-) motif, i.e., adding one terminal O atom for Re3O4(-), one terminal and one bridging O atoms for Re3O5(-), and one terminal and two bridging O atoms for Re3O6(-), respectively. Their corresponding neutral species are similar to the anions in geometry except Re3O4 and Re3O5. Molecular orbital analyses are employed to investigate the chemical bonding and structural evolution in these tri-rhenium oxide clusters. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular-dynamics analysis of mobile helium cluster reactions near surfaces of plasma-exposed tungsten

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu; Hammond, Karl D.

We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (He{sub n}, 4 ≤ n ≤ 7) near low-Miller-index tungsten (W) surfaces, aiming at a fundamental understanding of the near-surface dynamics of helium-carrying species in plasma-exposed tungsten. These small mobile helium clusters are attracted to the surface and migrate to the surface by Fickian diffusion and drift due to the thermodynamic driving force for surface segregation. As the clusters migrate toward the surface, trap mutation (TM) and cluster dissociation reactions are activated at rates higher than in the bulk. TM produces W adatoms and immobile complexes ofmore » helium clusters surrounding W vacancies located within the lattice planes at a short distance from the surface. These reactions are identified and characterized in detail based on the analysis of a large number of molecular-dynamics trajectories for each such mobile cluster near W(100), W(110), and W(111) surfaces. TM is found to be the dominant cluster reaction for all cluster and surface combinations, except for the He{sub 4} and He{sub 5} clusters near W(100) where cluster partial dissociation following TM dominates. We find that there exists a critical cluster size, n = 4 near W(100) and W(111) and n = 5 near W(110), beyond which the formation of multiple W adatoms and vacancies in the TM reactions is observed. The identified cluster reactions are responsible for important structural, morphological, and compositional features in the plasma-exposed tungsten, including surface adatom populations, near-surface immobile helium-vacancy complexes, and retained helium content, which are expected to influence the amount of hydrogen re-cycling and tritium retention in fusion tokamaks.« less

Formation of bimetallic clusters in superfluid helium nanodroplets analysed by atomic resolution electron tomography

PubMed Central

Haberfehlner, Georg; Thaler, Philipp; Knez, Daniel; Volk, Alexander; Hofer, Ferdinand; Ernst, Wolfgang E.; Kothleitner, Gerald

2015-01-01

Structure, shape and composition are the basic parameters responsible for properties of nanoscale materials, distinguishing them from their bulk counterparts. To reveal these in three dimensions at the nanoscale, electron tomography is a powerful tool. Advancing electron tomography to atomic resolution in an aberration-corrected transmission electron microscope remains challenging and has been demonstrated only a few times using strong constraints or extensive filtering. Here we demonstrate atomic resolution electron tomography on silver/gold core/shell nanoclusters grown in superfluid helium nanodroplets. We reveal morphology and composition of a cluster identifying gold- and silver-rich regions in three dimensions and we estimate atomic positions without using any prior information and with minimal filtering. The ability to get full three-dimensional information down to the atomic scale allows understanding the growth and deposition process of the nanoclusters and demonstrates an approach that may be generally applicable to all types of nanoscale materials. PMID:26508471

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Chang W.; Iddir, Hakim; Uzun, Alper

To address the challenge of fast, direct atomic-scale visualization of the diffusion of atoms and clusters on surfaces, we used aberration-corrected scanning transmission electron microscopy (STEM) with high scan speeds (as little as ~0.1 s per frame) to visualize the diffusion of (1) a heavy atom (Ir) on the surface of a support consisting of light atoms, MgO(100), and (2) an Ir 3 cluster on MgO(110). Sequential Z-contrast images elucidate the diffusion mechanisms, including the hopping of Ir1 and the rotational migration of Ir 3 as two Ir atoms remain anchored to the surface. Density functional theory (DFT) calculations providedmore » estimates of the diffusion energy barriers and binding energies of the iridium species to the surfaces. The results show how the combination of fast-scan STEM and DFT calculations allow real-time visualization and fundamental understanding of surface diffusion phenomena pertaining to supported catalysts and other materials.« less

The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility

PubMed Central

Bashan, Anat; Yonath, Ada

2009-01-01

Crystallography of ribosomes, the universal cell nucleoprotein assemblies facilitating the translation of the genetic-code into proteins, met with severe problems owing to their large size, complex structure, inherent flexibility and high conformational variability. For the case of the small ribosomal subunit, which caused extreme difficulties, post crystallization treatment by minute amounts of a heteropolytungstate cluster allowed structure determination at atomic resolution. This cluster played a dual role in ribosomal crystallography: providing anomalous phasing power and dramatically increased the resolution, by stabilization of a selected functional conformation. Thus, four out of the fourteen clusters that bind to each of the crystallized small subunits are attached to a specific ribosomal protein in a fashion that may control a significant component of the subunit internal flexibility, by “gluing” symmetrical related subunits. Here we highlight basic issues in the relationship between metal ions and macromolecules and present common traits controlling in the interactions between polymetalates and various macromolecules, which may be extended towards the exploitation of polymetalates for therapeutical treatment. PMID:19915655

Alloy formation and metal oxide segregation in Pt-Re/. gamma. -Al/sub 2/O/sub 3/ catalysts as investigated by temperature-programmed reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagstaff, N.; Prins, R.

1979-10-15

Temperature-programmed reduction has been used to characterize the finely dispersed metal compounds in a series of Pt-Re/..gamma..-Al/sub 2/O/sub 3/ catalysts. Strong evidence has been obtained that zerovalent Pt and Re atoms are in intimate contact with each other after catalyst reduction. The formation of bimetallic clusters supports the alloy explanation for the improved performance of this type of bimetallic reforming catalyst. Treatment of the reduced catalysts with oxygen above about 200/sup 0/C causes segregation of platinum and rhenium oxides. Adsorption of oxygen at temperatures up to 100/sup 0/C leaves the bimetallic clusters largely intact, but subsequent high-temperature treatment in themore » absence of extra oxygen leads to segregation of Pt and Re species. This suggests that in the presence of adsorbed oxygen the Pt-Re clusters are thermodynamically unstable, but that under mild conditions the rate of segregation is slow. 10 figures, 4 tables.« less

Tidal origin of NGC 1427A in the Fornax cluster

NASA Astrophysics Data System (ADS)

Lee-Waddell, K.; Serra, P.; Koribalski, B.; Venhola, A.; Iodice, E.; Catinella, B.; Cortese, L.; Peletier, R.; Popping, A.; Keenan, O.; Capaccioli, M.

2018-02-01

We present new HI observations from the Australia Telescope Compact Array and deep optical imaging from OmegaCam on the VLT Survey Telescope of NGC 1427A, an arrow-shaped dwarf irregular galaxy located in the Fornax cluster. The data reveal a star-less HI tail that contains ˜10 per cent of the atomic gas of NGC 1427A as well as extended stellar emission that shed new light on the recent history of this galaxy. Rather than being the result of ram pressure induced star formation, as previously suggested in the literature, the disturbed optical appearance of NGC 1427A has tidal origins. The galaxy itself likely consists of two individual objects in an advanced stage of merging. The HI tail may be made of gas expelled to large radii during the same tidal interaction. It is possible that some of this gas is subject to ram pressure, which would be considered a secondary effect and implies a north-west trajectory of NGC 1427A within the Fornax cluster.

Magnetism and exchange interaction of small rare-earth clusters; Tb as a representative

PubMed Central

Peters, Lars; Ghosh, Saurabh; Sanyal, Biplab; van Dijk, Chris; Bowlan, John; de Heer, Walt; Delin, Anna; Di Marco, Igor; Eriksson, Olle; Katsnelson, Mikhail I.; Johansson, Börje; Kirilyuk, Andrei

2016-01-01

Here we follow, both experimentally and theoretically, the development of magnetism in Tb clusters from the atomic limit, adding one atom at a time. The exchange interaction is, surprisingly, observed to drastically increase compared to that of bulk, and to exhibit irregular oscillations as a function of the interatomic distance. From electronic structure theory we find that the theoretical magnetic moments oscillate with cluster size in exact agreement with experimental data. Unlike the bulk, the oscillation is not caused by the RKKY mechanism. Instead, the inter-atomic exchange is shown to be driven by a competition between wave-function overlap of the 5d shell and the on-site exchange interaction, which leads to a competition between ferromagnetic double-exchange and antiferromagnetic super-exchange. This understanding opens up new ways to tune the magnetic properties of rare-earth based magnets with nano-sized building blocks. PMID:26795239

Blue emitting undecaplatinum clusters

NASA Astrophysics Data System (ADS)

Chakraborty, Indranath; Bhuin, Radha Gobinda; Bhat, Shridevi; Pradeep, T.

2014-07-01

A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents.A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents. Electronic supplementary information (ESI) available: Details of experimental procedures, instrumentation, chromatogram of the crude cluster; SEM/EDAX, DLS, PXRD, TEM, FT-IR, and XPS of the isolated Pt11 cluster; UV/Vis, MALDI MS and SEM/EDAX of isolated 2 and 3; and 195Pt NMR of the K2PtCl6 standard. See DOI: 10.1039/c4nr02778g