Geometric structure and electronic properties of neutral and anionic Fe2C3 and Fe2C4 clusters, as obtained by density-functional calculations

We calculated the geometrical structures and electronic properties of neutral and anionic Fe2Cn clusters (n = 3,4) using a density-functional method that employs linear combinations of atomic orbitals as basis sets, standard nonlocal norm-conserving pseudopotentials, and the generalized gradient approximation to exchange and correlation. We show that the ground-state structures of Fe2C3 and Fe2C4 are essentially the same in the neutral and anionic states, namely, planar rings that feature nonadjacent Fe atoms. For the anionic clusters, these findings contrast with previously published results.     

Structure and mobility of metal clusters in MOFs: Au, Pd, and AuPd clusters in MOF-74

Understanding the adsorption and mobility of metal-organic framework (MOF)-supported metal nanoclusters is critical to the development of these catalytic materials. We present the first theoretical investigation of Au-, Pd-, and AuPd-supported clusters in a MOF, namely MOF-74. We combine density functional theory (DFT) calculations with a genetic algorithm (GA) to reliably predict the structure of the adsorbed clusters. This approach allows comparison of hundreds of adsorbed configurations for each cluster. From the investigation of Au(8), Pd(8), and Au(4)Pd(4) we find that the organic part of the MOF is just as important for nanocluster adsorption as open Zn or Mg metal sites. Using the large number of clusters generated by the GA, we developed a systematic method for predicting the mobility of adsorbed clusters. Through the investigation of diffusion paths a relationship between the cluster's adsorption energy and diffusion barrier is established, confirming that Au clusters are highly mobile in the MOF-74 framework and Pd clusters are less mobile.     

金团簇二十面体结构融合过程中其催化活性的演变

近年来,由有机配体保护的原子精确金属团簇在合成方面已取得了重要进展,其独特的原子结构对一些化学反应产生独特的催化效果.原子精确的团簇催化剂明显不同于纳米颗粒催化剂和单原子催化剂,是一种关联均相和多相的、原子数目确定、尺寸均一、结构精确的新型催化剂.从原子尺度上精确构筑团簇催化剂,探究亚纳米尺度的微观结构对催化性能的影响...     

Ionic liquids from Car-Parrinello simulations, part I: liquid AlCl3

The properties of isolated AlCl3 clusters and the bulk system are investigated by means of static and dynamic electronic structure methods. We find important structural motifs with the edge connectivity dominant in a dimer and the corner connectivity dominant in a trimer. Furthermore, the trimer cluster exhibits an interesting ring structure with large cooperative effects relative to the dimer. Comparing the found structural motifs in isolated molecule calculations with the structure of the liquid allows us to determine the dominance of edge connectivity in the liquid. The size of the clusters present in the liquid indicates indeed that the dimer is the most abundant species, but there are also trimers, tetramers, and pentamers present. From the local dipole analysis both for the isolated clusters as well as for the liquid, further proof for the edge connectivity is given. However, all results point to the fact that there is also some small percentage of corner connectivity present that might be attributed to the most stable corner-connected cluster, namely the trimer. Importantly, we find that energetic considerations of isolated (static) clusters only do not represent the findings in liquid phase. Instead, a quantum cluster equilibrium approach or simulations are needed.     

Analysis of nucleation ability of cluster configurations with Monte Carlo simulations of argon

We determine the nucleation ability of argon clusters from Monte Carlo simulations. The nucleation rate appears to be defined by a sole characteristic of the clusters, namely, the stability. The stability is calculated as the ratio of grand canonical growth and decay rates and can be assigned to individual cluster configurations. We study the connection between the stability of the cluster configurations and their volume and total potential energy. Neither the potential energy nor the volume of a cluster configuration has a clear relation to its stability, and thus to the nucleation ability. On the other hand, we show that it is possible to use a specific volume for each cluster size to calculate the work of the cluster formation. These clusters with a unique volume have the same average stability as the full set of clusters. Our simulation method allows us to study the effect of possible deviations from equilibrium in the cluster configuration distributions. We argue that the nucleation process itself can produce a source for such a deviation. We show that even a small deviation from equilibrium in the cluster configuration distribution can lead to a dramatic deceleration of the nucleation rate. Although our simulations may overestimate the magnitude of the effect, they give qualitative estimates for its importance.     

Anomalous behavior of atomic hydrogen interacting with gold clusters

The change in the electronic structure of Au(n)- clusters induced by the exchange of an Au atom by hydrogen is studied using photoelectron spectroscopy. Au anion clusters react with one hydrogen atom but not with molecular hydrogen. The spectra of Au(n)- and Au(n-1)H- clusters show almost identical features for n > 2 suggesting that hydrogen behaves as a protonated species by contributing one electron to the valence pool of the Au(n)- cluster. This behavior is in sharp contrast to that of the commonly understood electronic structure of hydrogen in metals; namely, it attracts an electron from the conduction band of the metal and remains in an "anionic" form or forms covalent bonding. We discuss the influence of the unique electronic structure of H on the unusual catalytic behavior of Au clusters.     

Search for global-minimum geometries of medium-sized germanium clusters. II. Motif-based low-lying clusters Ge21-Ge29

We performed a constrained search for the geometries of low-lying neutral germanium clusters Ge(N) in the size range of 21 < or = N < or = 29. The basin-hopping global optimization method is employed for the search. The potential-energy surface is computed based on the plane-wave pseudopotential density functional theory. A new series of low-lying clusters is found on the basis of several generic structural motifs identified previously for silicon clusters [S. Yoo and X. C. Zeng, J. Chem. Phys. 124, 054304 (2006)] as well as for smaller-sized germanium clusters [S. Bulusu et al., J. Chem. Phys. 122, 164305 (2005)]. Among the generic motifs examined, we found that two motifs stand out in producing most low-lying clusters, namely, the six/nine motif, a puckered-hexagonal-ring Ge6 unit attached to a tricapped trigonal prism Ge9, and the six/ten motif, a puckered-hexagonal-ring Ge6 unit attached to a bicapped antiprism Ge10. The low-lying clusters obtained are all prolate in shape and their energies are appreciably lower than the near-spherical low-energy clusters. This result is consistent with the ion-mobility measurement in that medium-sized germanium clusters detected are all prolate in shape until the size N approximately 65.     

Magnetic properties of rare earth clusters

We report results of Stern-Gerlach deflection experiments on terbium clusters, which resemble earlier results for gadolinium clusters. As in gadolinium, we observe two distinct behaviors: clusters that are superparamagnetic and clusters that are described by a locked-moment model. The magnetic behavior is highly size dependent. Certain clusters make a transition from locked-moment to superparamagnetic behavior with increasing temperature and, in this process, exhibit an intermediate behavior. Both superparamagnetic and locked-moment clusters have magnetic moments per atom well below the bulk value. We show that oxygen atoms attached to the clusters have little effect on the clusters' magnetic properties and are not responsible for the two distinct behaviors observed in rare earth clusters. We also present preliminary results from studies on dysprosium clusters.     

Structural,spectroscopic aspects,and electronic properties of (TiO2)n clusters: A study based on the use of natural algorithms in association with quantum chemical methods

In this article, we propose a stochastic search‐based method, namely genetic algorithm (GA) and simulated annealing (SA) in conjunction with density functional theory (DFT) to evaluate global and local minimum structures of (TiO₂)_n clusters with n = 1–12. Once the structures are established, we evaluate the infrared spectroscopic modes, cluster formation energy, vertical excitation energy, vertical ionization potential, vertical electron affinity, highest occupied molecular orbital (HOMO)‐lowest unoccupied molecular orbital (LUMO) gaps, and so forth. We show that an initial determination of structure using stochastic techniques (GA/SA), also popularly known as natural algorithms as their working principle mimics certain natural processes, and following it up with density functional calculations lead to high‐quality structures for these systems. We have shown that the clusters tend to form three‐dimensional networks. We compare our results with the available experimental and theoretical results. The results obtained from SA/GA‐DFT technique agree well with available theoretical and experimental data of literature. © 2013 Wiley Periodicals, Inc.     

Is the uniform electron gas limit important for small Ag clusters? Assessment of different density functionals for Ag(n) (n < or = 4)

Twenty-three density functional theory (DFT) methods, including the second- and the third-generation functionals, are tested in conjunction with two basis sets (LANL2DZ and SDD) for studying the properties of neutral and ionic silver clusters. We find that DFT methods incorporating the uniform electron gas limit in the correlation functional, namely, those with Perdew's correlation functionals (PW91, PBE, P86, and TPSS), Becke's B95, and the Van Voorhis-Scuseria functional VSXC, generally perform better than the other group of functionals, e.g., those incorporating the LYP correlation functional and variations of the B97 functional. Strikingly, these two groups of functionals can produce qualitatively different results for the Ag3 and Ag4 clusters. The energetic properties and vibrational frequencies of Ag(n) are also evaluated by the different functionals. The present study shows that the choice of DFT methods for heavy metals may be critical. It is found that the exact-exchange-incorporated PBE functional (PBE1PBE) is among the best for predicting the range of properties.     

NMR solvent shifts of acetonitrile from frozen density embedding calculations

We present a density functional theory (DFT) study of solvent effects on nuclear magnetic shielding parameters. As a test example we have focused on the sensitive nitrogen shift of acetonitrile immersed in a selected set of solvents, namely water, chloroform, and cyclohexane. To include the effect of the solvent environment in an accurate and efficient manner, we employed the frozen-density embedding (FDE) scheme. We have included up to 500 solvent molecules in the NMR computations and obtained the cluster geometries from a large set of conformations generated with molecular dynamics. For small solute-solvent clusters comparison of the FDE results with conventional supermolecular DFT calculations shows close agreement. For the large solute-solvent clusters the solvent shift values are compared with experimental data and with values obtained using continuum solvent models. For the water --> cyclohexane shift the obtained value is in very good agreement with experiments. For the water --> chloroform NMR solvent shift the classical force field used in the molecular dynamics simulations is found to introduce an error. This error can be largely avoided by using geometries taken from Car-Parrinello molecular dynamics simulations.     

Theoretical modeling of the benzoic acid adsorption on the GaAs (001)-β2(2 × 4) oxidized surface

We describe a computational model of benzoic acid adsorbed on the most abundant and technologically important GaAs surface. The performances of many electronic devices based on organic layers deposited on semiconductor surfaces, critically depend on the quality of the layer, and thus on the features of the organic/inorganic bonds. Since very few is known about the atomic structure of such interfaces, theoretical modeling plays a central role in understanding these systems at the microscopic scale. We have optimized the structures of several clusters mimicking the unoxidized and oxidized GaAs (001) surface, using them to study the preferred arrangements of adsorbed benzoic acid molecules. The largest clusters were also used to investigate the cooperative effects between two adsorbed molecules, obtaining the most likely structure for a perfectly packed layer. Finally, we show the correlation of a microscopic observable, namely the energy of the lowest lying empty orbital concentrated on the organic moiety, with the electron affinity measured for para-substituted benzoic acids adsorbed on GaAs.     

Disparate effects of Cu and V on structures of exohedral transition metal-doped silicon clusters: a combined far-infrared spectroscopic and computational study

The growth mechanisms of small cationic silicon clusters containing up to 11 Si atoms, exohedrally doped by V and Cu atoms, are described. We find that as dopants, V and Cu follow two different paths: while V prefers substitution of a silicon atom in a highly coordinated position of the cationic bare silicon clusters, Cu favors adsorption to the neutral or cationic bare clusters in a lower coordination site. The different behavior of the two transition metals becomes evident in the structures of Si(n)M(+) (n = 4-11 for M = V, and n = 6-11 for M = Cu), which are investigated by density functional theory and, for several sizes, confirmed by comparison with their experimental vibrational spectra. The spectra are measured on the corresponding Si(n)M(+)·Ar complexes, which can be formed for the exohedrally doped silicon clusters. The comparison between experimental and calculated spectra indicates that the BP86 functional is suitable to predict far-infrared spectra of these clusters. In most cases, the calculated infrared spectrum of the lowest-lying isomer fits well with the experiment, even when various isomers and different electronic states are close in energy. However, in a few cases, namely Si(9)Cu(+), Si(11)Cu(+), and Si(10)V(+), the experimentally verified isomers are not the lowest in energy according to the density functional theory calculations, but their structures still follow the described growth mechanism. The different growth patterns of the two series of doped Si clusters reflect the role of the transition metal's 3d orbitals in the binding of the dopant atoms.     

Interplay between bonding and magnetism in the binding of NO to Rh clusters

We have studied the binding of NO to small Rh clusters, containing one to five atoms, using density functional theory in both spin-polarized and non-spin-polarized forms. We find that NO bonds more strongly to Rh clusters than it does to Rh(100) or Rh(111), suggesting that Rh clusters may be good catalysts for NO reduction. However, binding to NO also quenches the magnetism of the clusters. This (local) effect results in reducing the magnitude of the NO binding energy, and also washes out the clear size-dependent trend observed in the nonmagnetic case. Our results illustrate the competition present between the tendencies to bond and to magnetize, in small clusters.     

Conversion of double layer charge-stabilized Ag@citrate colloids to thiol passivated luminescent quantum clusters

A red luminescent silver cluster was synthesized in milligram quantities by the direct core reduction of the most widely studied class of large silver nanoparticles, namely silver@citrate of tens of nanometres diameter. No byproducts such as thiolates were detected, unlike in the case of typical methods of making such clusters. The route provides nearly pure clusters. The possibility to make diverse clusters from large nanoparticles expands the scope of cluster research.     

Electronic shell structure in Cs-O clusters

Unusually high ionization energies have been observed for Cs-O clusters having certain sizes and composition, namely for Cs_2n+zO_n with z=8, 18, 34, 58 and 92. The anomalies are well-defined for clusters containing from 1 to 7 oxygen atoms. The indicated values of z are identical to the number of electrons in closed shells of angular momentum.     

Geometrical bounding of data space and nonlinear classification of chemical data using MPGA algorithm

This paper develops a multi-parturition genetic algorithm (MPGA) to be used in geometrical bounding of the overlapped clusters in a data set for the classification of chemical data. Two new operators have been introduced to modify the conventional genetic algorithm, namely, multi-parturition and decimation and orientated creation to improve the linear classification results and diminish the computational time. To circumvent the difficulty commonly encountered in the treatment of linearly inseparable chemical data sets, the optimized linear classifier is further modified to provide a complementary nonlinear classifier. For this reason the space regions of the overlapped clusters have been bounded by erection of half-hyperellipsoids over the linearly misclassified patterns. The proposed MPGA was applied to classify a number of chemical and other data sets with a dimension from 4 to 14. Experimental results have indicated that the proposed MPGA could classify seriously overlapped data sets with an acceptable error rate.     

A Poisson-based adaptive affinity propagation clustering for SAGE data

Serial analysis of gene expression (SAGE) is a powerful tool to obtain gene expression profiles. Clustering analysis is a valuable technique for analyzing SAGE data. In this paper, we propose an adaptive clustering method for SAGE data analysis, namely, PoissonAPS. The method incorporates a novel clustering algorithm, Affinity Propagation (AP). While AP algorithm has demonstrated good performance on many different data sets, it also faces several limitations. PoissonAPS overcomes the limitations of AP using the clustering validation measure as a cost function of merging and splitting, and as a result, it can automatically cluster SAGE data without user-specified parameters. We evaluated PoissonAPS and compared its performance with other methods on several real life SAGE datasets. The experimental results show that PoissonAPS can produce meaningful and interpretable clusters for SAGE data.     

Electrospray ionization mass spectrometry of pyrimidine base-rubidium complexes

Nucleobases and alkali metal cations, under electrospray ionisation conditions, tend to form the so-called magic number clusters (unusually stable clusters in comparison with the neighbouring ones). The effect of the ion source parameters, namely cone voltage and desolvation temperature and relative concentrations of thymine and RbCl on the [T5+Rb]+ ion abundance has been studied.     

Structure, bonding, and magnetism in manganese clusters

We investigate the structures and magnetic properties of small Mn(n) clusters in the size range of 2-13 atoms using first-principles density functional theory. We arrive at the lowest energy structures for clusters in this size range by simultaneously optimizing the cluster geometries, total spins, and relative orientations of individual atomic moments. The results for the net magnetic moments for the optimal clusters are in good agreement with experiment. The magnetic behavior of Mn(n) clusters in the size range studied in this work ranges from ferromagnetic ordering (large net cluster moment) for the smallest (n=2, 3, and 4) clusters to a near degeneracy between ferromagnetic and antiferromagnetic solutions in the vicinity of n=5 and 6 to a clear preference for antiferromagnetic (small net cluster moment) ordering at n=7 and beyond. We study the details of this evolution and present a picture in which bonding in these clusters predominantly occurs due to a transfer of electrons from antibonding 4s levels to minority 3d levels.