Cluster Geometry Research Articles

Effect of palladium doping on the stability and fragmentation patterns of cationic gold clusters

We analyze in detail how the interplay between electronic structure and cluster geometry determines the stability and the fragmentation channels of single Pd-doped cationic Au clusters, $\mathrm{PdA}{\mathrm{u}}_{N}{}_{\ensuremath{-}1}{}^{+}$ ($N=2\ensuremath{-}20$). For this purpose, a combination of photofragmentation experiments and density functional theory calculations was employed. A remarkable agreement between the experiment and the calculations is obtained. Pd doping is found to modify the structure of the Au clusters, in particular altering the two-dimensional to three-dimensional transition size, with direct consequences on the stability of the clusters. Analysis of the electronic density of states of the clusters shows that depending on cluster size, Pd delocalizes one $4d$ electron, giving an enhanced stability to $\mathrm{PdA}{{\mathrm{u}}_{6}}^{+}$, or remains with all $4{d}^{10}$ electrons localized, closing an electronic shell in $\mathrm{PdA}{{\mathrm{u}}_{9}}^{+}$. Furthermore, it is observed that for most clusters, Au evaporation is the lowest-energy decay channel, although for some sizes Pd evaporation competes. In particular, $\mathrm{PdA}{{\mathrm{u}}_{7}}^{+}$ and $\mathrm{PdA}{{\mathrm{u}}_{9}}^{+}$ decay by Pd evaporation due to the high stability of the $\mathrm{A}{{\mathrm{u}}_{7}}^{+}$ and $\mathrm{A}{{\mathrm{u}}_{9}}^{+}$ fragmentation products.

A density functional study of second-row dicarbides C2X (X = Na-Cl) with carbon monosulfide molecule: molecular structure and bonding mechanism

In present work, a systematic study regarding molecular structure, and bonding mechanism of carbon monosulfide (CS) on second-row dicarbides C2X with (X = Na-Cl) has been investigated within the framework of density functional theory (DFT). In presence of carbon monosulfide molecule, the structures of C2Na, C2Mg, C2Al, and C2Si are found be changed from cyclic to linear, whereas geometries of C2P, C2S, and C2Cl clusters are almost remain unchanged. Interestingly, the bare carbon monosulfide molecule is attached with carbon site of bare C2X clusters rather than the second-row elements (X = Na-Cl). Furthermore, the nature of bonding in C2XCS clusters has been studiedthrough Bader's topological analysis of the electron charge density distribution ρ(r), Laplacian ∇2ρ(r) and total energy density HBCP at the bond critical points (BCPs) of the clusters within the framework of the atoms in molecules theory (AIM). In C2XCS clusters, electron density at the bond critical point ρ(r) > 0.30 a.u. with negative values of Laplacian ∇2ρ(r) indicates shared-kind of interactions between both the carbon atoms of C2X and CS molecule. In addition, we also analyze IR spectra that could assist for the experimental detection.

Fuzzy clustering and fuzzy validity measures for knowledge discovery and decision making in agricultural engineering

This paper concerns the application of fuzzy clustering methods and fuzzy validity measures for decision support in agricultural environment. Data clustering methods, namely, K-Means, Fuzzy C-Means, Gustafson-Kessel, and Gath-Geva, are briefly reviewed and considered for analyses. The efficiency of the methods is determined by indices such as the Xie-Beni criterion, Partition Coefficient, and Partition and Dunn indices. In particular, fuzzy classifiers are developed to assist decision making regarding the control of variables such as bed moisture, temperature, and bed aeration in compost bedded pack barns. The idea is to identify interactive factors, promote cattle welfare, improve productivity indices, and increase property value. Data from 42 CBP barns in the state of Kentucky, US, were considered. Six classes related to the degree of efficiency of the composting process were identified. The GG method was the most accurate followed by the GK method. The main reason for the best results is the use of maximum-likelihood and Mahalanobis distance measures. A remark on the use of the Dunn validation index for different cluster geometries is given. Fuzzy models and linguistic information have shown to be useful to help decision making in cattle containment systems.

Uptake of methanol on mixed HNO3/H2O clusters: An absolute pickup cross section

The uptake of atmospheric oxidized organics on acid clusters is relevant for atmospheric new particle formation. We investigate the pickup of methanol (CH3OH) on mixed nitric acid-water clusters (HNO3)M(H2O)N by a combination of mass spectrometry and cluster velocity measurements in a molecular beam. The mass spectra of the mixed clusters exhibit (HNO3)m(H2O)nH+ series with m = 0-3 and n = 0-12. In addition, CH3OH·(HNO3)m(H2O)nH+ series with very similar patterns appear in the spectra after the methanol pickup. The velocity measurements prove that the undoped (HNO3)m(H2O)nH+ mass peaks in the pickup spectra originate from the neutral (HNO3)M(H2O)N clusters which have not picked up any CH3OH molecule, i.e., methanol has not evaporated upon the ionization. Thus the fraction of the doped clusters can be determined and the mean pickup cross section can be estimated, yielding σs¯≈ 20 Å2. This is compared to the lower estimate of the mean geometrical cross section σg¯≈ 60 Å2 obtained from the theoretical cluster geometries. Thus the "size" of the cluster corresponding to the methanol pickup is at least 3-times smaller than its geometrical size. We have introduced a method which can yield the absolute pickup cross sections relevant to the generation and growth of atmospheric aerosols, as illustrated in the example of methanol and nitric acid clusters.

Photoactivatable substrates for systematic study of the impact of an extracellular matrix ligand on appearance of leader cells in collective cell migration

Epithelial cells migrate as multicellular units. The directionality and speed of these units are determined by actively moving leader cells. It is important to understand how external cues affect the appearance of these leader cells in physiological and pathological processes. However, the impact of extracellular matrices (ECMs) is still controversial, because physically-adsorbed ECM proteins are amenable to protein remodeling, and uncontrolled cluster geometry can vary migration phenotypes. Here, we demonstrate a photoactivatable substrate, which we used to study the impact of a cyclic Arg-Gly-Asp (cRGD) ligand on leader cell formation in MDCK cells. This robust platform allowed us to investigate the effect of cRGD density on leader cell formation, in any given cluster geometry, with minimized ECM remodeling. Our results show a biphasic response of leader cell appearance upon reducing the surface cRGD density. The increase, in leader cell appearance, within the higher density range, is not only associated with the weakening of circumferential actomyosin belts, but also reduction of cellular mechanical tension and intercellular junctional E-cadherin. These results indicate that cRGD-mediated cell-ECM interactions positively regulate mechanical and biochemical coupling within cell clusters; both are critical for the coordination of cell collectives and eventual reduction in the appearance of leader cells.

Local Fluxionality of Surface-Deposited Cluster Catalysts: The Case of Pt7 on Al2O3.

Subnano surface-supported catalytic clusters can be generally characterized by many low-energy isomers accessible at elevated temperatures of catalysis. The most stable isomer may not be the most catalytically active. Additionally, isomers may interconvert across barriers, i.e., exhibit fluxionality, during catalysis. To study the big picture of the cluster fluxional behavior, we model such a process as isomerization graph using bipartite matching algorithm, harmonic transition state theory, and paralleled nudged elastic band method. All the minimal energy paths form a minimum spanning tree (MST) of the original graph. Detailed inspection shows that, at temperatures typical for catalysis, the cluster geometry changes frequently within several regions in the MST, while transition across regions is less likely. As a further confirmation, the structural similarity analysis was additionally performed based on molecular dynamics trajectories. This local fluxionality picture provides a new perspective on understanding finite-temperate catalytic processes.

The Global Optimization of Pt13 Cluster Using the First-Principle Molecular Dynamics with the Quenching Technique

The high-temperature first-principle molecular dynamics method used to obtain the low energy configurations of clusters [L. L. Wang and D. D. Johnson, PRB 75, 235405 (2007)] is extended to a considerably large temperature range by combination with the quenching technique. Our results show that there are strong correlations between the possibilities for obtaining the ground-state structure and the temperatures. Larger possibilities can be obtained at relatively low temperatures (as corresponds to the pre-melting temperature range). Details of the structural correlation with the temperature are investigated by taking the Pt13 cluster as an example, which suggests a quite efficient method to obtain the lowest-energy geometries of metal clusters.

The dichotomous nature of dose enhancement by gold nanoparticle aggregates in radiotherapy.

In nanoparticle-aided radiotherapy, the computational paradigm has been that inside the cell, nanoparticles are distributed sparsely and solitarily. However, experiments reveal significant cluster formation, which affects radiosensitization and must be considered in clinical treatment planning. We characterize the impact of gold nanoparticle agglomeration on the predicted radiation dose enhancement as function of size, geometry, morphology and incident beam energy. Next-generation coupled electron-photon deterministic computations were performed using subnanometric unstructured spatial mesh. Unlike single nanoparticles, agglomerates develop two types of dose enhancement, smooth peripheral distributions and isolated hotspots, which depend on the cluster size and geometry in opposite ways. The peripheral dose enhancement may have less importance than the hotspots, which can have greater contribution to cell kill via radical creation. Hence, aggregate formation may be beneficial in nanoparticle-aided radiotherapy.

Electronic Structure and Bonding Situation in M2O2 (M = Be, Mg, Ca) Rhombic Clusters.

Quantum chemical calculations using ab initio methods at the CCSD(T) level and density functional theory have been carried out for the title molecules. The electronic structures of the molecules were analyzed with a variety of charge and energy decomposition methods. The equilibrium geometries of the M2O2 rhombic clusters exhibit very short distances between the transannular metal atoms M = Be, Mg, Ca. The calculated distances are close to standard values between double and triple bonds, but there are no chemical M-M bonds. The metal atoms M carry large positive partial charges, which are even bigger than in diatomic MO. The valence electrons of M are essentially shifted toward oxygen in M2O2, which makes it possible that there is practically no electronic charge in the region between the metal atoms. The bond dissociation energies for fragmentation of M2O2 into two metal oxides MO are very large. The metal-oxide bonds in the rhombic clusters are shorter and stronger than in diatomic MO. A detailed analysis of the electronic structure suggests that there is no significant direct M-M interaction in the M2O2 rhombic clusters, albeit weak three-center M-O-M bonding.

Mapping Emission from Clusters of CdSe/ZnS Nanoparticles

We have carried out correlated super-resolution and SEM imaging studies of clusters of CdSe/ZnS nanoparticles containing up to ten particles to explore how the fluorescence behavior of these clusters depends on the number of particles, the specific cluster geometry, the shell thickness, and the technique used to produce the clusters. The total emission yield was less than proportional to the number of particles in the clusters for both thick and thin shells. With super-resolution imaging, the emission center of the cluster could be spatially resolved at distance scales on the order of the cluster size. The intrinsic fluorescence intermittency of the nanoparticles altered the emission distribution across the cluster, which enabled the identification of relative emission intensities of individual particles or small groups of particles within the cluster. For clusters undergoing interparticle energy transfer, donor/acceptor pairs and regions where energy was funneled could be identified.

Fractal Geometry of Seismic Clusters in the Rhodope Mountain (South Bulgaria-Northeast Greece)

The Rhodope Mountain (South Bulgaria-Northeast Greece) is the largest mountain system in the eastern part of the Balkan Peninsula. It occupies a median position within the peninsula and thus is close enough to the main tectonic processes in this part of the Eastern Mediterranean (transcontinental collision between the African continental macro plate and Eurasian continental macro plate). This is an important prerequisite for the development of endogenous geodynamic processes with risky nature (earthquakes).The paper presents the results of the study of fractal geometry of the seismic clusters in the Rhodope Mountain. A combined seismic catalog (USGS and IRIS), composed of 640 seismic events (all values) occurring within the mountain massif for the 1965-2016 statistical period, was used in the analysis. Based on the methodology adopted for the calculation of surface fractals, the areas of the individual earthquake clusters were measured and their fractal geometry has been checked. The obtained results confirm the self-organizing nature of the seismic processes operating in the Rhodope region.

Anisotropy crossover in the frustrated Hubbard model on four-chain cylinders

Motivated by dimensional crossover in layered organic ${\kappa}$ salts, we determine the phase diagram of a system of four periodically coupled Hubbard chains with frustration at half filling as a function of the interchain hopping ${t_{\perp}/t}$ and interaction strength ${U/t}$ at a fixed ratio of frustration and interchain hopping ${t'/t_{\perp}=-0.5}$. We cover the range from the one-dimensional limit of uncoupled chains (${t_{\perp}/t=0.0}$) to the isotropic model (${t_{\perp}/t=1.0}$). For strong ${U/t}$, we find an antiferromagnetic insulator; in the weak-to-moderate-interaction regime, the phase diagram features quasi-one-dimensional antiferromagnetic behavior, an incommensurate spin-density wave, and a metallic phase as ${t_{\perp}/t}$ is increased. We characterize the phases through their magnetic ordering, dielectric response, and dominant static correlations. Our analysis is based primarily on a variant of the density-matrix renormalization-group algorithm based on an efficient hybrid-real-momentum-space formulation, in which we can treat relatively large lattices albeit of a limited width. This is complemented by a variational cluster approximation study with a cluster geometry corresponding to the cylindrical lattice allowing us to directly compare the two methods for this geometry. As an outlook, we make contact with work studying dimensional crossover in the full two-dimensional system.

A density functional theory study of structural, electronic and magnetic properties of small PdnAg (n = 1–8) clusters

The geometries, stabilities, electronic and magnetic properties of small PdnAg (n = 1–8) clusters have been estimated within the frame work of density functional theory (DFT) at B3P86/LANL2DZ level of theory. Various possible geometries have been examined in order to identify the lowest energy structures of the PdnAg clusters. It has been found that the lowest energy geometries of the binary clusters are in three-dimensional (3D) configurations. The stability analysis of the most stable structures has indicated that PdAg, Pd2Ag and Pd3Ag clusters are more stable and less reactive than their neighbouring clusters. A universal charge transfer from Ag atom to Pd atoms within the ground-state PdnAg clusters has been found. It has also been revealed that the electrons transfer internally from 5s and 4d states to 5p state in Ag atom, and from 4d state to 5s and 5p states in Pd atoms. Additionally, the Ag atom tends to lose some of its electrons to Pd atoms in the PdnAg cluster. The total magnetic moments of all ground-state PdnAg clusters are found to be equal to 1 μB, except the Pd7Ag cluster which has a value of 3 μB. The total magnetic moments of the ground-state PdnAg clusters have been found to be nearly located on Pd atoms only, except the PdAg cluster where the total magnetic moment is distributed on both Pd and Ag atoms. Moreover, the structural and chemical stabilities of the clusters are further corroborated from second order difference energy, fragmentation energy and chemical hardness analysis.

Geometry and Stability of Molecular Clusters: Factor to Be Considered in Biomolecular Activity

Betulinic and melaleucic acids, lupan-skeleton triterpenes with very similar structure, present marked differences in anti-malarial activity. While betulinic acid and some of its analogs exhibit strong activity, melaleucic acid is inactive. In the present work, a theoretical approach was used to explain such differences, using Austin Model 1 (AM1) and density functional theory (DFT)/Becke, three-parameter, Lee-Yang-Parr (B3LYP) approaches, and AutoDock Vina calculations. The initial results showed no significant differences between structural and electronic properties. On the other hand, studies of the geometry of molecular clusters with both compounds revealed significant differences. Melaleucic acid clusters were shown to be stable enough to influence the substrate-protein interaction, unlike betulinic acid, which was unable to form clusters comparable to melaleucic acid ones. The present study suggests the molecular clusters as a new factor that has a great influence on the mechanism of biomolecular activity.

Self-assembly of amphiphilic truncated cones to form hollow nanovesicles.

To mimic the unique properties of capsid (protein shell of a virus), we performed Brownian dynamics simulations of the self-assembly of amphiphilic truncated cone particles with anisotropic interactions. The particle shape of a truncated cone in our simulations depended on the cone angle θ, truncated height hc and particle type (AxBy and BxAyBz). The hydrophobic A moieties and hydrophilic B moieties are responsible for attractive and repulsive interactions, respectively. By varying the particle shape, truncated cones can assemble into hollow and vesicle-like clusters with a specific cluster size N. To assemble into hollow vesicles, the truncated height hc must be below a critical value. When hc exceeds this critical value, malformation will occur. The dynamics shows that the vesicle formation occurs in three stages: initially the growth is slow, then rapid, and finally it slows down. The truncated height hc has a stronger impact on the growth kinetics than the cone angle θ or the particle type. We explored how the cluster packing depended on the cooling rate and particle number as well as discussing the relationship between the cluster geometry and the interparticle interactions. Further, we also discuss possible methods to experimentally prepare the truncated cones. The results of our work deepen our understanding of the self-assembly behavior of truncated cones and our results will aid the effective design of particle building blocks for novel nanostructures.

Solvation of 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol revealed by circular dichroism: a case of chromane helicity rule breaking.

The primary goal of this work is to clarify why 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol {(S)-TMChM} deviates from the chromane helicity rule under solvent change. The rule, applicable to determining the absolute configuration of molecules containing the chromane chromophore, binds the sign of the 1Lb Cotton effect (CE) with the helicity of the dihydropyran ring. In case of TMChM, however, this CE exhibits extreme solvent dependence: it is negative in non-coordinating solvents and positive in coordinating ones, irrespective of the helicity of the heterocyclic ring. TD-DFT calculations using PCM and hybrid solvation models were performed to explain origin of this phenomenon. It turned out that the 1Lb CE sign directly depends on the position of the phenolic OH group at carbon atom C6 (OHC6). In the absence of interactions with solvents (as in CCl4 or nC6H14) or when a solvent plays proton donor role (as in CHCl3), the OHC6 lies in the phenyl plane and the 1Lb CE sign follows the P/M helicity rule. In contrast, in proton acceptor solvents, like DMSO, CH3OH or CH3CN, the OHC6 group is deflected from the phenyl plane, and the 1Lb CE sign of individual (S)-TMChM conformers depends on the sector in which the OHC6 is located. Thus, in solution, the 1Lb CE sign is an average over different orientations of the OHC6 group and can be positive (as in DMSO and CH3OH) or negative (as in CH3CN) which means that it does not follow the chromane helicity rule. The impact of OHC6 on the 1Lb CE sign and thus the conclusions for the stereochemistry of chromans are demonstrated here for the first time. Additionally, a comparison of experimental and simulated ECD spectra, supported by VCD data, allowed to determine the geometry of intermolecular clusters formed in different solvents.

Spin-orbit coupling effect on structural and magnetic properties of ConRh13−n (n = 0–13) clusters

The effect of spin-orbit interaction on the structures and magnetism of ConRh13−n (n = 0–13) clusters have been systematically investigated by using the spin-orbit coupling (SOC) implementation of the density functional theory (DFT). The results calculated without SOC (NSOC) show that Rh13 prefers the double simple-cubic configuration, and icosahedron is the favorable structure for n = 1–9, while n ≥ 10, clusters favor the hexagonal bilayer structure. The inclusion of SOC in calculation does not change the geometries of clusters. Compared with that in NSOC calculation, although the binding energy per atom in clusters with same composition decreases in SOC calculation, the relative stability of clusters with different compositions does not change. An interesting result is that the spin moments of clusters for n = 1–9 are almost constant (21 μB). Spin-orbit interaction recovers orbital moment and its anisotropy by removing crystal-field effect in calculation. The destruction of bonding symmetry and relaxation of bonding account for high anisotropies of orbital moments in Co11Rh2 and CoRh12 clusters. With atomic composition (Co/Rh) around 4/9–5/8 and 9/4, the Co-Rh clusters exhibit high magnetic anisotropy energies.

Density functional theory study on the dihydrogen bond cooperativity in the growth behavior of dimethyl sulfoxide clusters

We have carried out a density functional theory study on the structures of DMSO clusters and analysed the structure and their stability using molecular electrostatic potential and quantum theory of atoms-in-molecules (QTAIM). The ground state geometry of the DMSO clusters, prefer to exist in ouroboros shape. Pair wise interaction energy calculation show the interaction between methyl groups of adjacent DMSO molecules and destabilization is created by the methyl groups which are away from each other. Molecular electrostatic potential analysis shows the existence of σ-hole on the odd numbered clusters, which helps in their highly directional growth. QTAIM analysis show the existence of two intermolecular hydrogen bonds, of type SO⋯HC hydrogen bonds and methyl CH⋯HC dihydrogen bonds. The computed ρ and Laplacian values were all positive for the intermolecular bonds, supporting the existence of noncovalent interactions. The computed ellipticity for the dihydrogen bonds have values>2, which confirms the delocalization of electron, are mainly due to the hydrogen-hydrogen interactions of methyl groups. A plot of total hydrogen bonding energy vs the observed total local electron density shows linearity with correlation coefficient of near unity, which indicates the cooperative effects of intermolecular dihydrogen H·H bonds.

Nanospectroscopy of thiacyanine dye molecules adsorbed on silver nanoparticle clusters

The adsorption of thiacyanine dye molecules on citrate-stabilized silver nanoparticle clusters drop-cast onto freshly cleaved mica or highly oriented pyrolytic graphite surfaces is examined using colocalized surface-enhanced Raman spectroscopy and atomic force microscopy. The incidence of dye Raman signatures in photoluminescence hotspots identified around nanoparticle clusters is considered for both citrate- and borate-capped silver nanoparticles and found to be substantially lower in the former case, suggesting that the citrate anions impede the efficient dye adsorption. Rigorous numerical simulations of light scattering on random nanoparticle clusters are used for estimating the electromagnetic enhancement and elucidating the hotspot formation mechanism. The majority of the enhanced Raman signal, estimated to be more than 90%, is found to originate from the nanogaps between adjacent nanoparticles in the cluster, regardless of the cluster size and geometry.

Single Crystal Casting with Fluidized Carbon Bed Cooling: A Process Innovation for Quality Improvement and Cost Reduction

Superalloy gas turbine blades are being produced by investment casting and directional solidification. A new process, Fluidized Carbon Bed Cooling (FCBC), has been developed and is now being optimized in a prototype casting unit with 10 kg pouring weight. In early test runs with still rather simple mold cluster geometries, a reduction of the primary dendrite arm spacing of around 40 pct compared to the standard radiation cooling process (HRS) could be demonstrated. The improvement is mainly attributed to higher temperature gradients driving solidification, made possible by a functioning Dynamic Baffle. Compared to earlier development efforts in the literature, contamination of the melt and damage to the equipment are avoided using carbon-based fluidized bed materials and the so-called “counter pressure concept.”